CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims benefits under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 62/290,891, entitled: USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS, filed February 3, 2016, and U.S. Patent Application No. 15/382,508, entitled: USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS, filed 16 December 2016, which are herein incorporated by reference in their entireties for all purposes.

BACKGROUND

[0001] One of the critical endeavors in human medical research is the discovery of genetic abnormalities that produce adverse health consequences. In many cases, specific genes and/or critical diagnostic markers have been identified in portions of the genome that are present at abnormal copy numbers. For example, in prenatal diagnosis, extra or missing copies of whole chromosomes are frequently occurring genetic lesions. In cancer, deletion or multiplication of copies of whole chromosomes or chromosomal segments, and higher level amplifications of specific regions of the genome, are common occurrences. [0002] Most information about copy number variation (CNV) has been provided by cytogenetic resolution that has permitted recognition of structural abnormalities. Conventional procedures for genetic screening and biological dosimetry have utilized invasive procedures, e.g., amniocentesis, cordocentesis, or chorionic villus sampling (CVS), to obtain cells for the analysis of karyotypes. Recognizing the need for more rapid testing methods that do not require cell culture, fluorescence in situ hybridization (FISH), quantitative fluorescence PCR (QF-PCR) and array- Comparative Genomic Hybridization (array-CGH) have been developed as molecular-cytogenetic methods for the analysis of copy number variations.

[0003] One of the critical endeavors in human medical research is the discovery of genetic abnormalities that produce adverse health consequences. In many cases, specific genes and/or critical diagnostic markers have been identified in portions of the genome that are present at abnormal copy numbers. For example, in prenatal diagnosis, extra or missing copies of whole chromosomes are frequently occurring genetic lesions. In cancer, deletion or multiplication of copies of whole chromosomes or chromosomal segments, and higher level amplifications of specific regions of the genome, are common occurrences.

[0004] Most information about copy number variation (CNV) has been provided by cytogenetic resolution that has permitted recognition of structural abnormalities. Conventional procedures for genetic screening and biological dosimetry have utilized invasive procedures, e.g., amniocentesis, cordocentesis, or chorionic villus sampling (CVS), to obtain cells for the analysis of karyotypes. Recognizing the need for more rapid testing methods that do not require cell culture, fluorescence in situ hybridization (FISH), quantitative fluorescence PCR (QF-PCR) and array- Comparative Genomic Hybridization (array-CGH) have been developed as molecular-cytogenetic methods for the analysis of copy number variations.

[0005] The advent of technologies that allow for sequencing entire genomes in relatively short time, and the discovery of circulating cell-free DNA (cfDNA) have provided the opportunity to compare genetic material originating from one chromosome to be compared to that of another without the risks associated with invasive sampling methods, which provides a tool to diagnose various kinds of copy number variations of genetic sequences of interest.

[0006] Limitations of existing methods in noninvasive prenatal diagnostics, which include insufficient sensitivity stemming from the limited levels of cfDNA, and the sequencing bias of the technology stemming from the inherent nature of genomic information, underlie the continuing need for noninvasive methods that would provide any or all of the specificity, sensitivity, and applicability, to reliably diagnose copy number changes in a variety of clinical settings. It has been shown that the average lengths of the fetal cfDNA fragments are shorter than the maternal cfDNA fragments in the plasma of pregnant women. This difference between maternal and fetal cfDNA is exploited in the implementation herein to determine CNV and/or fetal fraction. Embodiments disclosed herein fulfill some of the above needs. Some embodiments may be implemented with a PCR free library preparation coupled with paired end DNA sequencing. Some embodiments provide high analytical sensitivity and specificity for noninvasive prenatal diagnostics and diagnoses of a variety of diseases.

SUMMARY

[0007] In some embodiments, methods are provided for determining copy number variation (CNV) of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNVs that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes. In some embodiments, the methods involve identifying CNVs of a nucleic acid sequence of interest, e.g., a clinically relevant sequence, in a test sample. The method assesses copy number variation of the specific sequence of interest.

[0008] In some embodiments, the method is implemented at a computer system that includes one or more processors and system memory to evaluate copy number of a nucleic acid sequence of interest in a test sample comprising nucleic acids of one or more genomes.

[0009] One aspect of the disclosure relates to a method for determining a copy number variation (CNV) of a nucleic acid sequence of interest in a test sample including cell-free nucleic acid fragments originating from two or more genomes. The method includes: (a) receiving sequence reads obtained by sequencing the cell- free nucleic acid fragments in the test sample; (b) aligning the sequence reads of the cell-free nucleic acid fragments or aligning fragments containing the sequence reads to bins of a reference genome including the sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins; (c) determining fragment sizes of at least some of the cell-free nucleic acid fragments present in the test sample; (d) calculating coverages of the sequence tags for the bins of the reference genome by, for each bin: (i) determining a number of sequence tags aligning to the bin, and (ii) normalizing the number of sequence tags aligning to the bin by accounting for bin-to-bin variations due to factors other than copy number variation; (e) determining a t-statistic for the sequence of interest using coverages of bins in the sequence of interest and coverages of bins in a reference region for the sequence of interest; and (f) determining a copy number variation in the sequence of interest using a likelihood ratio calculated from the t-statistic and information about the sizes of the cell-free nucleic acid fragments.

[0010] In some implementations, the method includes performing (d) and (e) twice, once for fragments in a first size domain and again for fragments in a second size domain. In some implementations, the first size domain includes cell-free nucleic acid fragments of substantially all sizes in the sample, and the second size domain includes only cell-free nucleic acid fragments smaller than a defined size. In some implementations, the second size domain includes only the cell-free nucleic acid fragments smaller than about 150 bp. In some implementations, the likelihood ratio is calculated from a first t-statistic for the sequence of interest using sequence tags for fragments in a first size range, and a second t-statistic for the sequence of interest using sequence tags for fragments in a second size range.

[0011] In some implementations, the likelihood ratio is calculated as a first likelihood that the test sample is an aneuploid sample over a second likelihood that the test sample is a euploid sample.

[0012] In some implementations, the likelihood ratio is calculated from one or more values of fetal fraction in addition to the t-statistic and information about the sizes of the cell-free nucleic acid fragments.

[0013] In some implementations, the one or more values of fetal fraction include a value of fetal fraction calculated using the information about the sizes of the cell-free nucleic acid fragments. In some implementations, the value of fetal fraction is calculated by: obtaining a frequency distribution of the fragment sizes; and applying the frequency distribution to a model relating fetal fraction to frequency of fragment size to obtain the fetal fraction value. In some implementations, the model relating fetal fraction to frequency of fragment size includes a general linear model having a plurality of terms and coefficients for a plurality of fragment sizes.

[0014] In some implementations, the one or more values of fetal fraction include a value of fetal fraction calculated using coverage information for the bins of the reference genome. In some implementations, the value of fetal fraction is calculated by applying coverage values of a plurality of bins to a model relating fetal fraction to coverage of bin to obtain the fetal fraction value. In some implementations, the model relating fetal fraction to the coverage of bin includes a general linear model having a plurality of terms and coefficients for a plurality of bins. In some implementations, the plurality of bins have high correlation between fetal fraction and coverage in training samples.

[0015] In some implementations, the one or more values of fetal fraction include a value of fetal fraction calculated using frequencies of a plurality of 8-mers found in the reads. In some implementations, the value of fetal fraction is calculated by: applying frequencies of a plurality of 8-mers to a model relating fetal fraction to 8-mer frequency to obtain the fetal fraction value. In some implementations, the model relating fetal fraction to 8-mer frequency includes a general linear model having a plurality of terms and coefficients for a plurality of 8-mers. In some implementations, the plurality of 8-mers have high correlation between fetal fraction and 8-mer frequency.

[0016] In some implementations, the one or more values of fetal fraction include a value of fetal fraction calculated using coverage information for the bins of a sex chromosome.

[0017] In some implementations, the likelihood ratio is calculated from a fetal fraction, a t-statistic of short fragments, and a t statistics of all fragments, wherein the short fragments are cell-free nucleic acid fragments in a first size range smaller than a criterion size, and the all fragments are cell-free nucleic acid fragments including the short fragments and fragments longer than the criterion size. In some implementations, the likelihood ratio is calculated:

Po (T shortfall)

[0019] where pi represents the likelihood that data come from a multivariate normal distribution representing a 3-copy or 1-copy model, po represents the likelihood that data come from a multivariate normal distribution representing a 2- copy model, T _S hort, T _all are T scores calculated from chromosomal coverage generated from short fragments and all fragments, and q(fftotai) is ^a density distribution of the fetal fraction.

[0020] In some implementations, the likelihood ratio is calculated from one or more values of fetal fraction in addition to the t-statistic and information about the sizes of the cell-free nucleic acid fragments. [0021] In some implementations, the likelihood ratio is calculated for monosomy X, trisomy X, trisomy 13, trisomy 18, or trisomy 21.

[0022] In some implementations, normalizing the number of sequence tags includes: normalizing for GC content of the sample, normalizing for a global wave profile of variation of a training set, and/or normalizing for one or more components obtained from a principal component analysis.

[0023] In some implementations, the sequence of interest is a human chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. [0024] In some implementations, the reference region is all robust chromosomes, robust chromosomes not including the sequence of interest, at least a chromosome outside of the sequence of interest, and/or a subset of chromosomes selected from the robust chromosomes. In some implementations, the reference region includes robust chromosomes that have been determined to provide the best signal detection ability for a set of training samples.

[0025] In some implementations, the method further includes calculating values of a size parameter for the bins by, for each bin: (i) determining a value of the size parameter from sizes of cell-free nucleic acid fragments in the bin, and (ii) normalizing the value of the size parameter by accounting for bin-to-bin variations due to factors other than copy number variation. The method also includes determining a size-based t-statistic for the sequence of interest using values of the size parameter of bins in the sequence of interest and values of the size parameter of bins in the reference region for the sequence of interest. In some implementations, the likelihood ratio of (f) is calculated from the t-statistic and the size-based t-statistic. In some implementations, the likelihood ratio of (f) is calculated from the size-based t- statistic and a fetal fraction.

[0026] In some implementations, the method further includes comparing the likelihood ratio to a call criterion to determine a copy number variation in the sequence of interest. In some implementations, the likelihood ratio is converted to a log likelihood ratio before being compared to the call criterion. In some implementations, the call criterion is obtained by applying different criteria to a training set of training samples, and selecting a criterion that provides a defined sensitivity and a defined selectivity.

[0027] In some implementations, the method further includes obtaining a plurality of likelihood ratios and applying the plurality of likelihood ratios to a decision tree to determine a ploidy case for the sample.

[0028] In some implementations, the method further includes obtaining a plurality of likelihood ratios and one or more coverage values of the sequence of interest, and applying the plurality of likelihood ratios and one or more coverage values of the sequence of interest to a decision tree to determine a ploidy case for the sample.

[0029] Another aspect of the disclosure relates to a method for determining a copy number variation (CNV) of a nucleic acid sequence of interest in a test sample including cell-free nucleic acid fragments originating from two or more genomes. The method includes: (a) receiving sequence reads obtained by sequencing the cell- free nucleic acid fragments in the test sample; (b) aligning the sequence reads of the cell-free nucleic acid fragments or aligning fragments containing the sequence reads to bins of a reference genome including the sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins; (c) calculating coverages of the sequence tags for the bins of the reference genome by, for each bin: (i) determining a number of sequence tags aligning to the bin, and (ii) normalizing the number of sequence tags aligning to the bin by accounting for bin-to- bin variations due to factors other than copy number variation. The method also includes: (d) determining a t-statistic for the sequence of interest using coverages of bins in the sequence of interest and coverages of bins in a reference region for the sequence of interest; (e) estimating one or more fetal fraction values of the cell-free nucleic acid fragments in the test sample; and (f) determining a copy number variation in the sequence of interest using the t-statistic and the one or more fetal fraction values.

[0030] In some implementations, (f) includes calculating a likelihood ratio from the t-statistic and the one or more fetal fraction values. In some implementations, the likelihood ratio is calculated for monosomy X, trisomy X, trisomy 13, trisomy 18, or trisomy 21. [0031] In some implementations, normalizing the number of sequence tags includes: normalizing for GC content of the sample, normalizing for a global wave profile of variation of a training set, and/or normalizing for one or more components obtained from a principal component analysis. [0032] In some implementations, the sequence of interest is a human chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

[0033] A further aspect of the disclosure relates to a method for determining a copy number variation (CNV) of a nucleic acid sequence of interest in a test sample including cell-free nucleic acid fragments originating from two or more genomes. The method includes: (a) receiving sequence reads obtained by sequencing the cell- free nucleic acid fragments in the test sample; (b) aligning the sequence reads of the cell-free nucleic acid fragments or aligning fragments containing the sequence reads to bins of a reference genome including the sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins; (c) determining fragment sizes of the cell-free nucleic acid fragments existing in the test sample; (d) calculating coverages of the sequence tags for the bins of the reference genome using sequence tags for the cell-free nucleic acid fragments having sizes in a first size domain; (e) calculating coverages of the sequence tags for the bins of the reference genome using sequence tags for the cell-free nucleic acid fragments having sizes in a second size domain, wherein the second size domain is different from the first size domain; (f) calculating size characteristics for the bins of the reference genome using the fragment sizes determined in (c); and (g) determining a copy number variation in the sequence of interest using the coverages calculated in (d) and (e) and the size characteristics calculated in (f).

[0034] In some implementations, the first size domain includes cell-free nucleic acid fragments of substantially all sizes in the sample, and the second size domain includes only cell-free nucleic acid fragments smaller than a defined size. In some implementations, the second size domain includes only the cell-free nucleic acid fragments smaller than about 150 bp. [0035] In some implementations, the sequence of interest is a human chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

[0036] In some implementations, (g) includes calculating a t-statistic for the sequence of interest using the coverages of bins in the sequence of interest calculated in (d) and/or (e). In some implementations, wherein calculating the t-statistic for the sequence of interest includes using the coverages of bins in the sequence of interest and coverages of bins in a reference region for the sequence of interest.

[0037] In some implementations, (g) includes calculating a t-statistic for the sequence of interest using the size characteristics of bins in the sequence of interest calculated in (f). In some implementations, calculating the t-statistic for the sequence of interest includes using the size characteristics of bins in the sequence of interest and size characteristics of bins in a reference region for the sequence of interest.

[0038] In some implementations, the size characteristic for a bin includes a ratio of fragments of size smaller than a defined value to total fragments in the bin.

[0039] In some implementations, (g) includes calculating a likelihood ratio from the t-statistic.

[0040] In some implementations, (g) includes calculating a likelihood ratio from a first t-statistic for the sequence of interest using the coverages calculated in (d), and a second t-statistic for the sequence of interest using the coverages calculated in (e).

[0041] In some implementations, (g) includes calculating a likelihood ratio from a first t-statistic for the sequence of interest using the coverages calculated in (d), a second t-statistic for the sequence of interest using the coverages calculated in (e), and third t-statistic for the sequence of interest using the size characteristics calculated in (f).

[0042] In some implementations, the likelihood ratio is calculated from one or more values of fetal fraction in addition to at least the first and second t-statistic. In some implementations, the method further includes calculating the one or more values of fetal fraction using the information about the sizes of the cell-free nucleic acid fragments. [0043] In some implementations, the method further includes calculating the one or more values of fetal fraction using coverage information for the bins of the reference genome. In some implementations, the one or more values of fetal fraction include a value of fetal fraction calculated using coverage information for the bins of a sex chromosome. In some implementations, the likelihood ratio is calculated for monosomy X, trisomy X, trisomy 13, trisomy 18, or trisomy 21.

[0044] In some implementations, (d) and/or (e) includes: (i) determining a number of sequence tags aligning to the bin, and (ii) normalizing the number of sequence tags aligning to the bin by accounting for bin-to-bin variations due to factors other than copy number variation. In some implementations, normalizing the number of sequence tags includes: normalizing for GC content of the sample, normalizing for a global wave profile of variation of a training set, and/or normalizing for one or more components obtained from a principal component analysis.

[0045] In some implementations, (f) includes calculating values of a size parameter for the bins by, for each bin: (i) determining a value of the size parameter from sizes of cell-free nucleic acid fragments in the bin, and (ii) normalizing the value of the size parameter by accounting for bin-to-bin variations due to factors other than copy number variation.

[0046] Another aspect of the disclosure relates to a system for evaluation of copy number of a nucleic acid sequence of interest in a test sample, the system includes: a sequencer for receiving nucleic acid fragments from the test sample and providing nucleic acid sequence information of the test sample; a processor; and one or more computer-readable storage media having stored thereon instructions for execution on said processor. The instructions includes instruction to: (a) receive sequence reads obtained by sequencing the cell-free nucleic acid fragments in the test sample; (b) align the sequence reads of the cell-free nucleic acid fragments or aligning fragments containing the sequence reads to bins of a reference genome including the sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins; (c) determine fragment sizes of at least some of the cell-free nucleic acid fragments present in the test sample; and (d) calculate coverages of the sequence tags for the bins of the reference genome by, for each bin: (i) determining a number of sequence tags aligning to the bin, and (ii) normalizing the number of sequence tags aligning to the bin by accounting for bin-to- bin variations due to factors other than copy number variation. The method also includes: (e) determine a t-statistic for the sequence of interest using coverages of bins in the sequence of interest and coverages of bins in a reference region for the sequence of interest; and (f) determine a copy number variation in the sequence of interest using a likelihood ratio calculated from the t-statistic and information about the sizes of the cell-free nucleic acid fragments.

[0047] In some implementations, the system is configured to perform any of the methods described above.

[0048] An additional aspect of the disclosure relates a computer program product including one or more computer-readable non-transitory storage media having stored thereon computer-executable instructions that, when executed by one or more processors of a computer system, cause the computer system to implement any of the methods above.

[0049] Although the examples herein concern humans and the language is primarily directed to human concerns, the concepts described herein are applicable to genomes from any plant or animal. These and other objects and features of the present disclosure will become more fully apparent from the following description and appended claims, or may be learned by the practice of the disclosure as set forth hereinafter. INCORPORATION BY REFERENCE

[0050] All patents, patent applications, and other publications, including all sequences disclosed within these references, referred to herein are expressly incorporated herein by reference, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. All documents cited are, in relevant part, incorporated herein by reference in their entireties for the purposes indicated by the context of their citation herein. However, the citation of any document is not to be construed as an admission that it is prior art with respect to the present disclosure. BRIEF DESCRIPTION OF THE DRAWINGS

[0051] Figure 1 is a flowchart of a method 100 for determining the presence or absence of a copy number variation in a test sample comprising a mixture of nucleic acids. [0052] Figure 2A thematically illustrates how paired end sequencing may be used to determine both fragment size and sequence coverage.

[0053] Figure 2B shows a flowchart of a process for using size-based coverage to determine a copy number variation of a nucleic acid sequence of interest in a test sample. [0054] Figure 2C depicts a flowchart of a process for determining fragment size parameter for a nucleic acid sequence of interest used for evaluation of the copy number.

[0055] Figure 2D shows a flow chart of two overlapping passes of workflow.

[0056] Figure 2E shows a flow chart of a three-pass process for evaluating copy number.

[0057] Figure 2F shows implementations that apply a t-statistic to copy number analysis to improve the accuracy of the analysis.

[0058] Figure 2G shows an example process for determining fetal fraction from coverage information according to some implementations of the disclosure. [0059] Figure 2H shows a process for determining fetal fraction from size distribution information according to some implementations.

[0060] Figure 21 shows an example process for determining fetal fraction from

8-mer frequency information according to some implementations of the disclosure.

[0061] Figure 2J shows a workflow for processing sequence reads information of which can be used to obtain fetal fraction estimates.

[0062] Figure 3A shows a flowchart of an example of a process for reducing the noise in sequence data from a test sample.

[0063] Figures 3B-3K present analyses of data obtained at various stages of the process depicted in Figure 3 A. [0064] Figure 4A shows a flow chart of a process for creating a sequence mask for reducing noise in sequence data.

[0065] Figure 4B shows that MapQ score has a strong monotonous correlation with CV of normalized coverage quantities. [0066] Figure 5 is a block diagram of a dispersed system for processing a test sample and ultimately making a diagnosis.

[0067] Figure 6 schematically illustrates how different operations in processing test samples may be grouped to be handled by different elements of a system. [0068] Figures 7 A and 7B shows electropherograms of a cfDNA sequencing library prepared according to the abbreviated protocol described in Example la (Fig. 7A), and the protocol described in Example lb (Fig. 7B).

[0069] Figure 8 shows the overall workflow and timeline for a new version of

NIPT compared to the standard laboratory workflow. [0070] Figure 9 shows sequencing library yield as a function of input extracted cfDNA, indicating a strong linear correlation with library concentration to input concentration with a high conversion efficiency.

[0071] Figure 10 shows the cfDNA fragment size distribution as measured from 324 samples from pregnancies with a male fetus. [0072] Figure 11 shows the relative fetal fraction from the total counts of mapped paired end reads compared to the counts from paired end reads that are less than 150 bp.

[0073] Figure 12 shows combined t-statistic aneuploidy score for detection of trisomy 21 samples for (A) counts of all fragments; (B) counts of short fragments (<150bp) only; (C) fraction of short fragments (counts between 80 and 150 bp/counts <250bp); (D) combined t-statistic from (B) and (C); and (E) results for same samples obtained using the Illumina Redwood City CLIA laboratory process with an average of 16 M counts/sample.

[0074] Figure 13 shows fetal fractions estimated from selected bins versus those measured with normalized chromosome values (REF) for the X-chromosome. Set 1 was used to calibrate the fetal fraction value and an independent set 2 to test the correlation.

DETAILED DESCRIPTION

Definitions [0075] Unless otherwise indicated, the practice of the method and system disclosed herein involves conventional techniques and apparatus commonly used in molecular biology, microbiology, protein purification, protein engineering, protein and DNA sequencing, and recombinant DNA fields, which are within the skill of the art. Such techniques and apparatus are known to those of skill in the art and are described in numerous texts and reference works (See e.g., Sambrook et al., "Molecular Cloning: A Laboratory Manual," Third Edition (Cold Spring Harbor), [2001]); and Ausubel et al., "Current Protocols in Molecular Biology" [1987]).

[0076] Numeric ranges are inclusive of the numbers defining the range. It is intended that every maximum numerical limitation given throughout this specification includes every lower numerical limitation, as if such lower numerical limitations were expressly written herein. Every minimum numerical limitation given throughout this specification will include every higher numerical limitation, as if such higher numerical limitations were expressly written herein. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.

[0077] The headings provided herein are not intended to limit the disclosure.

[0078] Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. Various scientific dictionaries that include the terms included herein are well known and available to those in the art. Although any methods and materials similar or equivalent to those described herein find use in the practice or testing of the embodiments disclosed herein, some methods and materials are described.

[0079] The terms defined immediately below are more fully described by reference to the Specification as a whole. It is to be understood that this disclosure is not limited to the particular methodology, protocols, and reagents described, as these may vary, depending upon the context they are used by those of skill in the art. As used herein, the singular terms "a," "an," and "the" include the plural reference unless the context clearly indicates otherwise.

[0080] Unless otherwise indicated, nucleic acids are written left to right in 5' to 3' orientation and amino acid sequences are written left to right in amino to carboxy orientation, respectively.

[0081] The term "parameter" is used herein represents a physical feature whose value or other characteristic has an impact a relevant condition such as copy number variation. In some cases, the term parameter is used with reference to a variable that affects the output of a mathematical relation or model, which variable may be an independent variable (i.e., an input to the model) or an intermediate variable based on one or more independent variables. Depending on the scope of a model, an output of one model may become an input of another model, thereby becoming a parameter to the other model. [0082] The term "fragment size parameter" refers to a parameter that relates to the size or length of a fragment or a collection of fragments such nucleic acid fragments; e.g., a cfDNA fragments obtained from a bodily fluid. As used herein, a parameter is "biased toward a fragment size or size range" when: 1) the parameter is favorably weighted for the fragment size or size range, e.g., a count weighted more heavily when associated with fragments of the size or size range than for other sizes or ranges; or 2) the parameter is obtained from a value that is favorably weighted for the fragment size or size range, e.g., a ratio obtained from a count weighted more heavily when associated with fragments of the size or size range. A fragment size or size range may be a characteristic of a genome or a portion thereof when the genome produces nucleic acid fragments enriched in or having a higher concentration of the size or size range relative to nucleic acid fragments from another genome or another portion of the same genome.

[0083] The term "weighting" refers to modifying a quantity such as a parameter or variable using one or more values or functions, which are considered the "weight." In certain embodiments, the parameter or variable is multiplied by the weight. In other embodiments, the parameter or variable is modified exponentially. In some embodiments, the function may be a linear or non-linear function. Examples of applicable non-linear functions include, but are not limited to Heaviside step functions, box-car functions, stair-case functions, or sigmoidal functions. Weighting an original parameter or variable may systematically increase or decrease the value of the weighted variable. In various embodiments, weighting may result in positive, non- negative, or negative values.

[0084] The term "copy number variation" herein refers to variation in the number of copies of a nucleic acid sequence present in a test sample in comparison with the copy number of the nucleic acid sequence present in a reference sample. In certain embodiments, the nucleic acid sequence is 1 kb or larger. In some cases, the nucleic acid sequence is a whole chromosome or significant portion thereof. A "copy number variant" refers to the sequence of nucleic acid in which copy-number differences are found by comparison of a nucleic acid sequence of interest in test sample with an expected level of the nucleic acid sequence of interest. For example, the level of the nucleic acid sequence of interest in the test sample is compared to that present in a qualified sample. Copy number variants/variations include deletions, including microdeletions, insertions, including microinsertions, duplications, multiplications, and translocations. CNVs encompass chromosomal aneuploidies and partial aneuploidies.

[0085] The term "aneuploidy" herein refers to an imbalance of genetic material caused by a loss or gain of a whole chromosome, or part of a chromosome.

[0086] The terms "chromosomal aneuploidy" and "complete chromosomal aneuploidy" herein refer to an imbalance of genetic material caused by a loss or gain of a whole chromosome, and includes germline aneuploidy and mosaic aneuploidy.

[0087] The terms "partial aneuploidy" and "partial chromosomal aneuploidy" herein refer to an imbalance of genetic material caused by a loss or gain of part of a chromosome, e.g., partial monosomy and partial trisomy, and encompasses imbalances resulting from translocations, deletions and insertions.

[0088] The term "plurality" refers to more than one element. For example, the term is used herein in reference to a number of nucleic acid molecules or sequence tags that are sufficient to identify significant differences in copy number variations in test samples and qualified samples using the methods disclosed herein. In some embodiments, at least about 3 x 10 ⁶ sequence tags of between about 20 and 40bp are obtained for each test sample. In some embodiments, each test sample provides data for at least about 5 x 10 ⁶ , 8 x 10 ⁶ , 10 x 10 ⁶ , 15 x 10 ⁶ , 20 x 10 ⁶ , 30 x 10 ⁶ , 40 x 10 ⁶ , or 50 x 10 ⁶ sequence tags, each sequence tag comprising between about 20 and 40bp.

[0089] The term "paired end reads" refers to reads from paired end sequencing that obtains one read from each end of a nucleic acid fragment. Paired end sequencing may involve fragmenting strands of polynucleotides into short sequences called inserts. Fragmentation is optional or unnecessary for relatively short polynucleotides such as cell free DNA molecules.

[0090] The terms "polynucleotide," "nucleic acid" and "nucleic acid molecules" are used interchangeably and refer to a covalently linked sequence of nucleotides (i.e., ribonucleotides for RNA and deoxyribonucleotides for DNA) in which the 3' position of the pentose of one nucleotide is joined by a phosphodiester group to the 5' position of the pentose of the next. The nucleotides include sequences of any form of nucleic acid, including, but not limited to RNA and DNA molecules such as cfDNA molecules. The term "polynucleotide" includes, without limitation, single- and double-stranded polynucleotide.

[0091] The term "test sample" herein refers to a sample, typically derived from a biological fluid, cell, tissue, organ, or organism, comprising a nucleic acid or a mixture of nucleic acids comprising at least one nucleic acid sequence that is to be screened for copy number variation. In certain embodiments the sample comprises at least one nucleic acid sequence whose copy number is suspected of having undergone variation. Such samples include, but are not limited to sputum/oral fluid, amniotic fluid, blood, a blood fraction, or fine needle biopsy samples (e.g., surgical biopsy, fine needle biopsy, etc.), urine, peritoneal fluid, pleural fluid, and the like. Although the sample is often taken from a human subject (e.g., patient), the assays can be used to copy number variations (CNVs) in samples from any mammal, including, but not limited to dogs, cats, horses, goats, sheep, cattle, pigs, etc. The sample may be used directly as obtained from the biological source or following a pretreatment to modify the character of the sample. For example, such pretreatment may include preparing plasma from blood, diluting viscous fluids and so forth. Methods of pretreatment may also involve, but are not limited to, filtration, precipitation, dilution, distillation, mixing, centrifugation, freezing, lyophilization, concentration, amplification, nucleic acid fragmentation, inactivation of interfering components, the addition of reagents, lysing, etc. If such methods of pretreatment are employed with respect to the sample, such pretreatment methods are typically such that the nucleic acid(s) of interest remain in the test sample, sometimes at a concentration proportional to that in an untreated test sample (e.g., namely, a sample that is not subjected to any such pretreatment method(s)). Such "treated" or "processed" samples are still considered to be biological "test" samples with respect to the methods described herein.

[0092] The term "qualified sample" or "unaffected sample" herein refers to a sample comprising a mixture of nucleic acids that are present in a known copy number to which the nucleic acids in a test sample are to be compared, and it is a sample that is normal, i.e., not aneuploid, for the nucleic acid sequence of interest. In some embodiments, qualified samples are used as unaffected training samples of a training set to derive sequence masks or sequence profiles. In certain embodiments, qualified samples are used for identifying one or more normalizing chromosomes or segments for a chromosome under consideration. For example, qualified samples may be used for identifying a normalizing chromosome for chromosome 21. In such case, the qualified sample is a sample that is not a trisomy 21 sample. Another example involves using only females as qualifying samples for chromosome X. Qualified samples may also be employed for other purposes such as determining thresholds for calling affected samples, identifying thresholds for defining mask regions on a reference sequence, determining expected coverage quantities for different regions of a genome, and the like.

[0093] The term "training set" herein refers to a set of training samples that can comprise affected and/or unaffected samples and are used to develop a model for analyzing test samples. In some embodiments, the training set includes unaffected samples. In these embodiments, thresholds for determining CNV are established using training sets of samples that are unaffected for the copy number variation of interest. The unaffected samples in a training set may be used as the qualified samples to identify normalizing sequences, e.g., normalizing chromosomes, and the chromosome doses of unaffected samples are used to set the thresholds for each of the sequences, e.g., chromosomes, of interest. In some embodiments, the training set includes affected samples. The affected samples in a training set can be used to verify that affected test samples can be easily differentiated from unaffected samples. [0094] A training set is also a statistical sample in a population of interest, which statistical sample is not to be confused with a biological sample. A statistical sample often comprises multiple individuals, data of which individuals are used to determine one or more quantitative values of interest generalizable to the population. The statistical sample is a subset of individuals in the population of interest. The individuals may be persons, animals, tissues, cells, other biological samples (i.e., a statistical sample may include multiple biological samples), and other individual entities providing data points for statistical analysis.

[0095] Usually, a training set is used in conjunction with a validation set. The term "validation set" is used to refer to a set of individuals in a statistical sample, data of which individuals are used to validate or evaluate the quantitative values of interest determined using a training set. In some embodiments, for instance, a training set provides data for calculating a mask for a reference sequence, while a validation set provides data to evaluate the validity or effectiveness of the mask. [0096] "Evaluation of copy number" is used herein in reference to the statistical evaluation of the status of a genetic sequence related to the copy number of the sequence. For example, in some embodiments, the evaluation comprises the determination of the presence or absence of a genetic sequence. In some embodiments the evaluation comprises the determination of the partial or complete aneuploidy of a genetic sequence. In other embodiments the evaluation comprises discrimination between two or more samples based on the copy number of a genetic sequence. In some embodiments, the evaluation comprises statistical analyses, e.g., normalization and comparison, based on the copy number of the genetic sequence.

[0097] The term "qualified nucleic acid" is used interchangeably with "qualified sequence," which is a sequence against which the amount of a sequence or nucleic acid of interest is compared. A qualified sequence is one present in a biological sample preferably at a known representation, i.e., the amount of a qualified sequence is known. Generally, a qualified sequence is the sequence present in a "qualified sample." A "qualified sequence of interest" is a qualified sequence for which the amount is known in a qualified sample, and is a sequence that is associated with a difference of a sequence of interest between a control subject and an individual with a medical condition. [0098] The term "sequence of interest" or "nucleic acid sequence of interest" herein refers to a nucleic acid sequence that is associated with a difference in sequence representation between healthy and diseased individuals. A sequence of interest can be a sequence on a chromosome that is misrepresented, i.e., over- or under-represented, in a disease or genetic condition. A sequence of interest may be a portion of a chromosome, i.e., chromosome segment, or a whole chromosome. For example, a sequence of interest can be a chromosome that is over-represented in an aneuploidy condition, or a gene encoding a tumor-suppressor that is under- represented in a cancer. Sequences of interest include sequences that are over- or under- represented in the total population, or a subpopulation of cells of a subject. A "qualified sequence of interest" is a sequence of interest in a qualified sample. A "test sequence of interest" is a sequence of interest in a test sample.

[0099] The term "normalizing sequence" herein refers to a sequence that is used to normalize the number of sequence tags mapped to a sequence of interest associated with the normalizing sequence. In some embodiments, a normalizing sequence comprises a robust chromosome. A "robust chromosome" is one that is unlikely to be aneuploid. In some cases involving the human chromosome, a robust chromosome is any chromosome other than the X chromosome, Y chromosome, chromosome 13, chromosome 18, and chromosome 21. In some embodiments, the normalizing sequence displays a variability in the number of sequence tags that are mapped to it among samples and sequencing runs that approximates the variability of the sequence of interest for which it is used as a normalizing parameter. The normalizing sequence can differentiate an affected sample from one or more unaffected samples. In some implementations, the normalizing sequence best or effectively differentiates, when compared to other potential normalizing sequences such as other chromosomes, an affected sample from one or more unaffected samples. In some embodiments, the variability of the normalizing sequence is calculated as the variability in the chromosome dose for the sequence of interest across samples and sequencing runs. In some embodiments, normalizing sequences are identified in a set of unaffected samples.

[00100] A "normalizing chromosome," "normalizing denominator chromosome," or "normalizing chromosome sequence" is an example of a "normalizing sequence." A "normalizing chromosome sequence" can be composed of a single chromosome or of a group of chromosomes. In some embodiments, a normalizing sequence comprises two or more robust chromosomes. In certain embodiments, the robust chromosomes are all autosomal chromosomes other than chromosomes, X, Y, 13, 18, and 21. A "normalizing segment" is another example of a "normalizing sequence." A "normalizing segment sequence" can be composed of a single segment of a chromosome or it can be composed of two or more segments of the same or of different chromosomes. In certain embodiments, a normalizing sequence is intended to normalize for variability such as process-related, interchromosomal (intra-run), and inter-sequencing (inter-run) variability. [00101] The term "differentiability" herein refers to a characteristic of a normalizing chromosome that enables one to distinguish one or more unaffected, i.e., normal, samples from one or more affected, i.e., aneuploid, samples. A normalizing chromosome displaying the greatest "differentiability" is a chromosome or group of chromosomes that provides the greatest statistical difference between the distribution of chromosome doses for a chromosome of interest in a set of qualified samples and the chromosome dose for the same chromosome of interest in the corresponding chromosome in the one or more affected samples.

[00102] The term "variability" herein refers to another characteristic of a normalizing chromosome that enables one to distinguish one or more unaffected, i.e., normal, samples from one or more affected, i.e., aneuploid, samples. The variability of a normalizing chromosome, which is measured in a set of qualified samples, refers to the variability in the number of sequence tags that are mapped to it that approximates the variability in the number of sequence tags that are mapped to a chromosome of interest for which it serves as a normalizing parameter. [00103] The term "sequence tag density" herein refers to the number of sequence reads that are mapped to a reference genome sequence, e.g., the sequence tag density for chromosome 21 is the number of sequence reads generated by the sequencing method that are mapped to chromosome 21 of the reference genome.

[00104] The term "sequence tag density ratio" herein refers to the ratio of the number of sequence tags that are mapped to a chromosome of the reference genome, e.g., chromosome 21, to the length of the reference genome chromosome. [00105] The term "sequence dose" herein refers to a parameter that relates the number of sequence tags or another parameter identified for a sequence of interest and the number of sequence tags or the other parameter identified for the normalizing sequence. In some cases, the sequence dose is the ratio of the sequence tag coverage or the other parameter for a sequence of interest to the sequence tag coverage or the other parameter for a normalizing sequence. In some cases, the sequence dose refers to a parameter that relates the sequence tag density of a sequence of interest to the sequence tag density of a normalizing sequence. A "test sequence dose" is a parameter that relates the sequence tag density or the other parameter of a sequence of interest, e.g., chromosome 21, to that of a normalizing sequence, e.g., chromosome 9, determined in a test sample. Similarly, a "qualified sequence dose" is a parameter that relates the sequence tag density or the other parameter of a sequence of interest to that of a normalizing sequence determined in a qualified sample.

[00106] The term "coverage" refers to the abundance of sequence tags mapped to a defined sequence. Coverage can be quantitatively indicated by sequence tag density (or count of sequence tags), sequence tag density ratio, normalized coverage amount, adjusted coverage values, etc.

[00107] The term "coverage quantity" refers to a modification of raw coverage and often represents the relative quantity of sequence tags (sometimes called counts) in a region of a genome such as a bin. A coverage quantity may be obtained by normalizing, adjusting and/or correcting the raw coverage or count for a region of the genome. For example, a normalized coverage quantity for a region may be obtained by dividing the sequence tag count mapped to the region by the total number sequence tags mapped to the entire genome. Normalized coverage quantity allows comparison of coverage of a bin across different samples, which may have different depths of sequencing. It differs from sequence dose in that the latter is typically obtained by dividing by the tag count mapped to a subset of the entire genome. The subset is one or more normalizing segments or chromosomes. Coverage quantities, whether or not normalized, may be corrected for global profile variation from region to region on the genome, G-C fraction variations, outliers in robust chromosomes, etc.

[00108] The term "Next Generation Sequencing (NGS)" herein refers to sequencing methods that allow for massively parallel sequencing of clonally amplified molecules and of single nucleic acid molecules. Non-limiting examples of NGS include sequencing-by-synthesis using reversible dye terminators, and sequencing-by-ligation.

[00109] The term "parameter" herein refers to a numerical value that characterizes a property of a system. Frequently, a parameter numerically characterizes a quantitative data set and/or a numerical relationship between quantitative data sets. For example, a ratio (or function of a ratio) between the number of sequence tags mapped to a chromosome and the length of the chromosome to which the tags are mapped, is a parameter.

[00110] The terms "threshold value" and "qualified threshold value" herein refer to any number that is used as a cutoff to characterize a sample such as a test sample containing a nucleic acid from an organism suspected of having a medical condition. The threshold may be compared to a parameter value to determine whether a sample giving rise to such parameter value suggests that the organism has the medical condition. In certain embodiments, a qualified threshold value is calculated using a qualifying data set and serves as a limit of diagnosis of a copy number variation, e.g., an aneuploidy, in an organism. If a threshold is exceeded by results obtained from methods disclosed herein, a subject can be diagnosed with a copy number variation, e.g., trisomy 21. Appropriate threshold values for the methods described herein can be identified by analyzing normalized values (e.g. chromosome doses, NCVs or NSVs) calculated for a training set of samples. Threshold values can be identified using qualified (i.e., unaffected) samples in a training set which comprises both qualified (i.e., unaffected) samples and affected samples. The samples in the training set known to have chromosomal aneuploidies (i.e., the affected samples) can be used to confirm that the chosen thresholds are useful in differentiating affected from unaffected samples in a test set (see the Examples herein). The choice of a threshold is dependent on the level of confidence that the user wishes to have to make the classification. In some embodiments, the training set used to identify appropriate threshold values comprises at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 2000 , at least 3000 , at least 4000, or more qualified samples. It may be advantageous to use larger sets of qualified samples to improve the diagnostic utility of the threshold values. [00111] The term "bin" refers to a segment of a sequence or a segment of a genome. In some embodiments, bins are contiguous with one another within the genome or chromosome. Each bin may define a sequence of nucleotides in a reference genome. Sizes of the bin may be 1 kb, 100 kb, 1Mb, etc., depending on the analysis required by particular applications and sequence tag density. In addition to their positions within a reference sequence, bins may have other characteristics such as sample coverage and sequence structure characteristics such as G-C fraction.

[00112] The term "masking threshold" is used herein to refer to a quantity against which a value based on the number of sequence tags in a sequence bin is compared, wherein a bin having a value exceeding the masking threshold is masked. In some embodiments, the masking threshold can be a percentile rank, an absolute count, a mapping quality score, or other suitable values. In some embodiments, a masking threshold may be defined as the percentile rank of a coefficient of variation across multiple unaffected samples. In other embodiments, a masking threshold may be defined as a mapping quality score, e.g., a MapQ score, which relates to the reliability of aligning sequence reads to a reference genome. Note that a masking threshold value is different from a copy number variation (CNV) threshold value, the latter being a cutoff to characterize a sample containing a nucleic acid from an organism suspected of having a medical condition related to CNV. In some embodiment, a CNV threshold value is defined relative to a normalized chromosome value (NCV) or a normalized segment value (NSV) described elsewhere herein.

[00113] The term "normalized value" herein refers to a numerical value that relates the number of sequence tags identified for the sequence (e.g. chromosome or chromosome segment) of interest to the number of sequence tags identified for a normalizing sequence (e.g. normalizing chromosome or normalizing chromosome segment). For example, a "normalized value" can be a chromosome dose as described elsewhere herein, or it can be an NCV, or it can be an NSV as described elsewhere herein.

[00114] The term "read" refers to a sequence obtained from a portion of a nucleic acid sample. Typically, though not necessarily, a read represents a short sequence of contiguous base pairs in the sample. The read may be represented symbolically by the base pair sequence (in A, T, C, or G) of the sample portion. It may be stored in a memory device and processed as appropriate to determine whether it matches a reference sequence or meets other criteria. A read may be obtained directly from a sequencing apparatus or indirectly from stored sequence information concerning the sample. In some cases, a read is a DNA sequence of sufficient length (e.g., at least about 25 bp) that can be used to identify a larger sequence or region, e.g., that can be aligned and specifically assigned to a chromosome or genomic region or gene.

[00115] The term "genomic read" is used in reference to a read of any segments in the entire genome of an individual.

[00116] The term "sequence tag" is herein used interchangeably with the term "mapped sequence tag" to refer to a sequence read that has been specifically assigned, i.e., mapped, to a larger sequence, e.g., a reference genome, by alignment. Mapped sequence tags are uniquely mapped to a reference genome, i.e., they are assigned to a single location to the reference genome. Unless otherwise specified, tags that map to the same sequence on a reference sequence are counted once. Tags may be provided as data structures or other assemblages of data. In certain embodiments, a tag contains a read sequence and associated information for that read such as the location of the sequence in the genome, e.g., the position on a chromosome. In certain embodiments, the location is specified for a positive strand orientation. A tag may be defined to allow a limited amount of mismatch in aligning to a reference genome. In some embodiments, tags that can be mapped to more than one location on a reference genome, i.e., tags that do not map uniquely, may not be included in the analysis.

[00117] The term "non-redundant sequence tag" refers to sequence tags that do not map to the same site, which is counted for the purpose of determining normalized chromosome values (NCVs) in some embodiments. Sometimes multiple sequence reads are aligned to the same locations on a reference genome, yielding redundant or duplicated sequence tags. In some embodiments, duplicate sequence tags that map to the same position are omitted or counted as one "non-redundant sequence tag" for the purpose of determining NCVs. In some embodiments, non-redundant sequence tags aligned to non-excluded sites are counted to yield "non-excluded-site counts" (NES counts) for determining NCVs.

[00118] The term "site" refers to a unique position (i.e. chromosome ID, chromosome position and orientation) on a reference genome. In some embodiments, a site may provide a position for a residue, a sequence tag, or a segment on a sequence.

[00119] "Excluded sites" are sites found in regions of a reference genome that have been excluded for the purpose of counting sequence tags. In some embodiments, excluded sites are found in regions of chromosomes that contain repetitive sequences, e.g., centromeres and telomeres, and regions of chromosomes that are common to more than one chromosome, e.g., regions present on the Y- chromosome that are also present on the X chromosome.

[00120] "Non-excluded sites" (NESs) are sites that are not excluded in a reference genome for the purpose of counting sequence tags.

[00121] "Non-excluded-site counts" (NES counts) are the numbers of sequence tags that are mapped to NESs on a reference genome. In some embodiments, NES counts are the numbers of non-redundant sequence tags mapped to NESs. In some embodiments, coverage and related parameters such normalized coverage quantities, global profile removed coverage quantities, and chromosome dose are based on NES counts. In one example, a chromosome dose is calculated as the ratio of the NES count for a chromosome of interest to the count for a normalizing chromosome.

[00122] Normalized chromosome value (NCV) relates coverage of a test sample to coverages of a set of training/qualified samples. In some embodiments, NCV is based on chromosome dose. In some embodiments, NCV relates to the difference between the chromosome dose of a chromosome of interest in a test sample and the mean of the corresponding chromosome dose in a set of qualified samples as, and can be calculated as:

_NCV = i £i where . _j and ci _j are the estimated mean and standard deviation, respectively, for the j- th chromosome dose in a set of qualified samples, and Xjj is the observed j-th chromosome ratio (dose) for test sample i.

[00123] In some embodiments, NCV can be calculated "on the fly" by relating the chromosome dose of a chromosome of interest in a test sample to the median of the corresponding chromosome dose in multiplexed samples sequenced on the same flow cells as: where M _j is the estimated median for the j-th chromosome dose in a set of multiplexed samples sequenced on the same flow cell; <Tj is the standard deviation for the j-th chromosome dose in one or more sets of multiplexed samples sequenced on one or more flow cells, and Xjj is the observed j-th chromosome dose for test sample i. In this embodiment, test sample i is one of the multiplexed samples sequenced on the same flow cell from which M _j is determined.

[00124] For example, for chromosome of interest 21 in test sample A, which is sequenced as one of 64 multiplexed samples on one flow cell, the NCV for chromosome 21 in test sample A is calculated as the dose of chromosome 21 in sample A minus the median of the dose for chromosome 21 determined in the 64 multiplexed samples, divided by the standard deviation of the dose for chromosome 21 determined for the 64 multiplexed samples on flow cell 1, or of additional flow cells.

[00125] As used herein, the terms "aligned," "alignment," or "aligning" refer to the process of comparing a read or tag to a reference sequence and thereby determining whether the reference sequence contains the read sequence. If the reference sequence contains the read, the read may be mapped to the reference sequence or, in certain embodiments, to a particular location in the reference sequence. In some cases, alignment simply tells whether or not a read is a member of a particular reference sequence (i.e., whether the read is present or absent in the reference sequence). For example, the alignment of a read to the reference sequence for human chromosome 13 will tell whether the read is present in the reference sequence for chromosome 13. A tool that provides this information may be called a set membership tester. In some cases, an alignment additionally indicates a location in the reference sequence where the read or tag maps to. For example, if the reference sequence is the whole human genome sequence, an alignment may indicate that a read is present on chromosome 13, and may further indicate that the read is on a particular strand and/or site of chromosome 13.

[00126] Aligned reads or tags are one or more sequences that are identified as a match in terms of the order of their nucleic acid molecules to a known sequence from a reference genome. Alignment can be done manually, although it is typically implemented by a computer algorithm, as it would be impossible to align reads in a reasonable time period for implementing the methods disclosed herein. One example of an algorithm from aligning sequences is the Efficient Local Alignment of Nucleotide Data (ELAND) computer program distributed as part of the Illumina Genomics Analysis pipeline. Alternatively, a Bloom filter or similar set membership tester may be employed to align reads to reference genomes. See US Patent Application No. 61/552,374 filed October 27, 2011 which is incorporated herein by reference in its entirety. The matching of a sequence read in aligning can be a 100% sequence match or less than 100% (non-perfect match). [00127] The term "mapping" used herein refers to specifically assigning a sequence read to a larger sequence, e.g., a reference genome, by alignment.

[00128] As used herein, the term "reference genome" or "reference sequence" refers to any particular known genome sequence, whether partial or complete, of any organism or virus which may be used to reference identified sequences from a subject. For example, a reference genome used for human subjects as well as many other organisms is found at the National Center for Biotechnology Information at ncbi.nlm.nih.gov. A "genome" refers to the complete genetic information of an organism or virus, expressed in nucleic acid sequences.

[00129] In various embodiments, the reference sequence is significantly larger than the reads that are aligned to it. For example, it may be at least about 100 times larger, or at least about 1000 times larger, or at least about 10,000 times larger, or at least about 10 ⁵ times larger, or at least about 10 ⁶ times larger, or at least about 10 ⁷ times larger.

[00130] In one example, the reference sequence is that of a full length human genome. Such sequences may be referred to as genomic reference sequences. In another example, the reference sequence is limited to a specific human chromosome such as chromosome 13. In some embodiments, a reference Y chromosome is the Y chromosome sequence from human genome version hgl9. Such sequences may be referred to as chromosome reference sequences. Other examples of reference sequences include genomes of other species, as well as chromosomes, sub- chromosomal regions (such as strands), etc., of any species. [00131] In various embodiments, the reference sequence is a consensus sequence or other combination derived from multiple individuals. However, in certain applications, the reference sequence may be taken from a particular individual.

[00132] The term "clinically-relevant sequence" herein refers to a nucleic acid sequence that is known or is suspected to be associated or implicated with a genetic or disease condition. Determining the absence or presence of a clinically-relevant sequence can be useful in determining a diagnosis or confirming a diagnosis of a medical condition, or providing a prognosis for the development of a disease. [00133] The term "derived" when used in the context of a nucleic acid or a mixture of nucleic acids, herein refers to the means whereby the nucleic acid(s) are obtained from the source from which they originate. For example, in one embodiment, a mixture of nucleic acids that is derived from two different genomes means that the nucleic acids, e.g., cfDNA, were naturally released by cells through naturally occurring processes such as necrosis or apoptosis. In another embodiment, a mixture of nucleic acids that is derived from two different genomes means that the nucleic acids were extracted from two different types of cells from a subject.

[00134] The term "based on" when used in the context of obtaining a specific quantitative value, herein refers to using another quantity as input to calculate the specific quantitative value as an output.

[00135] The term "patient sample" herein refers to a biological sample obtained from a patient, i.e., a recipient of medical attention, care or treatment. The patient sample can be any of the samples described herein. In certain embodiments, the patient sample is obtained by non-invasive procedures, e.g., peripheral blood sample or a stool sample. The methods described herein need not be limited to humans. Thus, various veterinary applications are contemplated in which case the patient sample may be a sample from a non-human mammal (e.g., a feline, a porcine, an equine, a bovine, and the like).

[00136] The term "mixed sample" herein refers to a sample containing a mixture of nucleic acids, which are derived from different genomes.

[00137] The term "maternal sample" herein refers to a biological sample obtained from a pregnant subject, e.g., a woman. [00138] The term "biological fluid" herein refers to a liquid taken from a biological source and includes, for example, blood, serum, plasma, sputum, lavage fluid, cerebrospinal fluid, urine, semen, sweat, tears, saliva, and the like. As used herein, the terms "blood," "plasma" and "serum" expressly encompass fractions or processed portions thereof. Similarly, where a sample is taken from a biopsy, swab, smear, etc., the "sample" expressly encompasses a processed fraction or portion derived from the biopsy, swab, smear, etc.

[00139] The terms "maternal nucleic acids" and "fetal nucleic acids" herein refer to the nucleic acids of a pregnant female subject and the nucleic acids of the fetus being carried by the pregnant female, respectively.

[00140] As used herein, the term "corresponding to" sometimes refers to a nucleic acid sequence, e.g., a gene or a chromosome, that is present in the genome of different subjects, and which does not necessarily have the same sequence in all genomes, but serves to provide the identity rather than the genetic information of a sequence of interest, e.g., a gene or chromosome.

[00141] As used herein, the term "fetal fraction" refers to the fraction of fetal nucleic acids present in a sample comprising fetal and maternal nucleic acid. Fetal fraction is often used to characterize the cfDNA in a mother's blood.

[00142] As used herein the term "chromosome" refers to the heredity-bearing gene carrier of a living cell, which is derived from chromatin strands comprising DNA and protein components (especially histones). The conventional internationally recognized individual human genome chromosome numbering system is employed herein.

[00143] As used herein, the term "polynucleotide length" refers to the absolute number of nucleotides in a sequence or in a region of a reference genome. The term "chromosome length" refers to the known length of the chromosome given in base pairs, e.g., provided in the NCBI36/hgl8 assembly of the human chromosome found at |genome|.|ucsc|.|edu/cgi-bin/hgTracks?hgsid=167155613&ch romInfoPage= on the World Wide Web. [00144] The term "subject" herein refers to a human subject as well as a non- human subject such as a mammal, an invertebrate, a vertebrate, a fungus, a yeast, a bacterium, and a virus. Although the examples herein concern humans and the language is primarily directed to human concerns, the concepts disclosed herein are applicable to genomes from any plant or animal, and are useful in the fields of veterinary medicine, animal sciences, research laboratories and such.

[00145] The term "condition" herein refers to "medical condition" as a broad term that includes all diseases and disorders, but can include injuries and normal health situations, such as pregnancy, that might affect a person's health, benefit from medical assistance, or have implications for medical treatments.

[00146] The term "complete" when used in reference to a chromosomal aneuploidy herein refers to a gain or loss of an entire chromosome. [00147] The term "partial" when used in reference to a chromosomal aneuploidy herein refers to a gain or loss of a portion, i.e., segment, of a chromosome.

[00148] The term "mosaic" herein refers to denote the presence of two populations of cells with different karyotypes in one individual who has developed from a single fertilized egg. Mosaicism may result from a mutation during development which is propagated to only a subset of the adult cells.

[00149] The term "non-mosaic" herein refers to an organism, e.g., a human fetus, composed of cells of one karyotype.

[00150] The term "sensitivity" as used herein refers to the probability that a test result will be positive when the condition of interest is present. It may be calculated as the number of true positives divided by the sum of true positives and false negatives.

[00151] The term "specificity" as used herein refers to the probability that a test result will be negative when the condition of interest is absent. It may be calculated as the number of true negatives divided by the sum of true negatives and false positives.

[00152] The term "enrich" herein refers to the process of amplifying polymorphic target nucleic acids contained in a portion of a maternal sample, and combining the amplified product with the remainder of the maternal sample from which the portion was removed. For example, the remainder of the maternal sample can be the original maternal sample.

[00153] The term "original maternal sample" herein refers to a non-enriched biological sample obtained from a pregnant subject, e.g., a woman, who serves as the source from which a portion is removed to amplify polymorphic target nucleic acids. The "original sample" can be any sample obtained from a pregnant subject, and the processed fractions thereof, e.g., a purified cfDNA sample extracted from a maternal plasma sample.

[00154] The term "primer," as used herein refers to an isolated oligonucleotide that is capable of acting as a point of initiation of synthesis when placed under conditions inductive to synthesis of an extension product (e.g., the conditions include nucleotides, an inducing agent such as DNA polymerase, and a suitable temperature and pH). The primer is preferably single stranded for maximum efficiency in amplification, but may alternatively be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent. The exact lengths of the primers will depend on many factors, including temperature, source of primer, use of the method, and the parameters used for primer design.

Introduction and Context

[00155] CNV in the human genome significantly influence human diversity and predisposition to diseases (Redon et al., Nature 23 :444-454 [2006], Shaikh et al. Genome Res 19: 1682-1690 [2009]). Such diseases include, but are not limited to cancer, infectious and autoimmune diseases, diseases of the nervous system, metabolic and/or cardiovascular diseases, and the like.

[00156] CNVs have been known to contribute to genetic disease through different mechanisms, resulting in either imbalance of gene dosage or gene disruption in most cases. In addition to their direct correlation with genetic disorders, CNVs are known to mediate phenotypic changes that can be deleterious. Recently, several studies have reported an increased burden of rare or de novo CNVs in complex disorders such as Autism, ADHD, and schizophrenia as compared to normal controls, highlighting the potential pathogenicity of rare or unique CNVs (Sebat et al., 316:445 - 449 [2007]; Walsh et al., Science 320:539 - 543 [2008]). CNV arise from genomic rearrangements, primarily owing to deletion, duplication, insertion, and unbalanced translocation events. [00157] It has been shown that cfDNA fragments of fetal origin are shorter, on average, than those of maternal origin. NIPT (Non-invasive prenatal testing) based on NGS data has been successfully implemented. Current methodologies involve sequencing maternal samples using short reads (25bp-36bp), aligning to the genome, computing and normalizing sub-chromosomal coverage, and finally evaluating over- representation of target chromosomes (13 / 18 / 21 / X / Y) compared to the expected normalized coverage associated with a normal diploid genome. Thus, traditional NIPT assay and analysis relies on the counts or coverage to evaluate the likelihood of fetal aneuploidy. [00158] Since maternal plasma samples represent a mixture of maternal and fetal cfDNA, the success of any given NIPT method depends on its sensitivity to detect copy number changes in the low fetal fraction samples. For counting based methods, their sensitivity is determined by (a) sequencing depth and (b) ability of data normalization to reduce technical variance. This disclosure provides analytical methodology for NIPT and other applications by deriving fragment size information from, e.g., paired-end reads, and using this information in an analysis pipeline. Improved analytical sensitivity provides the ability to apply NIPT methods at reduced coverage (e.g., reduced sequencing depth) which enables the use of the technology for lower-cost testing of average risk pregnancies. [00159] Methods, apparatus, and systems are disclosed herein for determining copy number and copy number variations (CNV) of different sequences of interest in a test sample that comprises a mixture of nucleic acids derived from two or more different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. Copy number variations determined by the methods and apparatus disclosed herein include gains or losses of entire chromosomes, alterations involving very large chromosomal segments that are microscopically visible, and an abundance of sub-microscopic copy number variation of DNA segments ranging from single nucleotide, to kilobases (kb), to megabases (Mb) in size. [00160] In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples containing maternal and fetal cell free DNA. Some implementations use fragment length (or fragment size) of cfDNA to improve sensitivity and specificity for fetal aneuploidy detection from cfDNA in maternal plasma. Some embodiments are implemented with a PCR free library preparation coupled with paired end DNA sequencing. In some embodiments, both fragment size and coverage are utilized to enhance fetal aneuploidy detection. In some embodiments, the methods involve combining independent counting of shorter fragments with the relative fraction of shorter fragments in bins across the genome.

[00161] Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples.

[00162] Some embodiments disclosed provide methods to derive parameters with high signal to noise ratio from cell free nucleic acid fragments, for determining various genetic conditions related to copy number and CNV, with improved sensitivity, selectivity, and/or efficiency relative to conventional methods. The parameters include, but are not limited to, coverage, fragment size weighted coverage, fraction or ratio of fragments in a defined range, methylation level of fragments, t- statistics obtained from coverage, fetal fraction estimates obtained from coverage information, etc. The depicted process has been found particularly effective at improving the signal in samples having relatively low fractions of DNA from a genome under consideration (e.g., a genome of a fetus). An example of such sample is a maternal blood sample from an individual pregnant with fraternal twins, triplets, etc., where the process assesses copy number variation in the genome of one of the fetuses.

[00163] In some embodiments, high analytical sensitivities and specificities can be achieved with a simple library preparation using very low cfDNA input that does not require PCR amplification. The PCR free method simplifies the workflow, improves the turn-around time and eliminates biases that are inherent with PCR methods. In some embodiments, the detection of fetal aneuploidy from maternal plasma can be made more robust and efficient than conventional methods, requiring fewer unique cfDNA fragments. In combination, improved analytical sensitivity and specificity is achieved with a very fast turnaround time at a significantly lower number of cfDNA fragments. This potentially allows NIPT to be carried out at significantly lower costs to facilitate application in the general obstetric population. [00164] In various implementations, PCR-free library preparation is possible with the disclosed methods. Some implementations eliminate inherent biases of PCR methods, reduced assay complexity, reduce required sequencing depth (2.5X lower), provide faster turnaround time, e.g., turn around in one day, enable in-process fetal fraction (FF) measurement, facilitate discrimination between maternal and fetal/placental cfDNA using fragment size information.

Evaluating CNV

Methods for determination of CNV

[00165] Using the sequence coverage value, fragment size parameters, and/or methylation levels provided by the methods disclosed herein, one can determine various genetic conditions related to copy number and CNV of sequences, chromosomes, or chromosome segments with improved sensitivity, selectivity, and/or efficiency relative to using sequence coverage values obtained by conventional methods. For example, in some embodiments, the masked reference sequences are used for determining the presence or absence of any two or more different complete fetal chromosomal aneuploidies in a maternal test sample comprising fetal and maternal nucleic acid molecules. Exemplary methods provided below align reads to reference sequences (including reference genomes). The alignment can be performed on an unmasked or masked reference sequence, thereby yielding sequence tags mapped to the reference sequence. In some embodiments, only sequence tags falling on unmasked segments of the reference sequence are taken into account to determine copy number variation.

[00166] In some embodiments, assessing a nucleic acid sample for CNV involves characterizing the status of a chromosomal or segment aneuploidy by one of three types of calls: "normal" or "unaffected," "affected," and "no-call." Thresholds for calling normal and affected are typically set. A parameter related to aneuploidy or other copy number variation is measured in a sample and the measured value is compared to the thresholds. For duplication type aneuploidies, a call of affected is made if a chromosome or segment dose (or other measured value sequence content) is above a defined threshold set for affected samples. For such aneuploidies, a call of normal is made if the chromosome or segment dose is below a threshold set for normal samples. By contrast for deletion type aneuploidies, a call of affected is made if a chromosome or segment dose is below a defined threshold for affected samples, and a call of normal is made if the chromosome or segment dose is above a threshold set for normal samples. For example, in the presence of trisomy the "normal" call is determined by the value of a parameter, e.g., a test chromosome dose that is below a user-defined threshold of reliability, and the "affected" call is determined by a parameter, e.g., a test chromosome dose, that is above a user-defined threshold of reliability. A "no-call" result is determined by a parameter, e.g., a test chromosome dose that lies between the thresholds for making a "normal" or an "affected" call. The term "no-call" is used interchangeably with "unclassified". [00167] The parameters that may be used to determine CNV include, but are not limited to, coverage, fragment size biased/weighted coverage, fraction or ratio of fragments in a defined size range, and methylation level of fragments. As discussed herein, coverage is obtained from counts of reads aligned to a region of a reference genome and optionally normalized to produce sequence tag counts. In some embodiments, sequence tag counts can be weighted by fragment size.

[00168] In some embodiments, a fragment size parameter is biased toward fragment sizes characteristic of one of the genomes. A fragment size parameter is a parameter that relates to the size of a fragment. A parameter is biased toward a fragment size when: 1) the parameter is favorably weighted for the fragment size, e.g., a count weighted more heavily for the size than for other sizes; or 2) the parameter is obtained from a value that is favorably weighted for the fragment size, e.g., a ratio obtained from a count weighted more heavily for the size. A size is characteristic of a genome when the genome has an enriched or higher concentration of nucleic acid of the size relative to another genome or another portion of the same genome. [00169] In some embodiments, the method for determining the presence or absence of any complete fetal chromosomal aneuploidies in a maternal test sample comprises (a) obtaining sequence information for fetal and maternal nucleic acids in the maternal test sample; (b) using the sequence information and the method described above to identify a number of sequence tags, sequence coverage quantity, a fragment size parameter, or another parameter for each of the chromosomes of interest selected from chromosomes 1-22, X and Y and to identify a number of sequence tags or another parameter for one or more normalizing chromosome sequences; (c) using the number of sequence tags or the other parameter identified for each of the chromosomes of interest and the number of sequence tags or the other parameter identified for each of the normalizing chromosomes to calculate a single chromosome dose for each of the chromosomes of interests; and (d) comparing each chromosome dose to a threshold value, and thereby determining the presence or absence of any complete fetal chromosomal aneuploidies in the maternal test sample.

[00170] In some embodiments, step (a) described above can comprise sequencing at least a portion of the nucleic acid molecules of a test sample to obtain said sequence information for the fetal and maternal nucleic acid molecules of the test sample. In some embodiments, step (c) comprises calculating a single chromosome dose for each of the chromosomes of interest as the ratio of the number of sequence tags or the other parameter identified for each of the chromosomes of interest and the number of sequence tags or the other parameter identified for the normalizing chromosome sequence(s). In some other embodiments, chromosome dose is based on processed sequence coverage quantities derived from the number of sequence tags or another parameter. In some embodiments, only unique, non-redundant sequence tags are used to calculate the processed sequence coverage quantities or another parameter. In some embodiments, the processed sequence coverage quantity is a sequence tag density ratio, which is the number of sequence tag standardized by sequence length. In some embodiments, the processed sequence coverage quantity or the other parameter is a normalized sequence tag or another normalized parameter, which is the number of sequence tags or the other parameter of a sequence of interest divided by that of all or a substantial portion of the genome. In some embodiments, the processed sequence coverage quantity or the other parameter such as a fragment size parameter is adjusted according to a global profile of the sequence of interest. In some embodiments, the processed sequence coverage quantity or the other parameter is adjusted according to the within-sample correlation between the GC content and the sequence coverage for the sample being tested. In some embodiments, the processed sequence coverage quantity or the other parameter results from combinations of these processes, which are further described elsewhere herein. [00171] In some embodiments, a chromosome dose is calculated as the ratio of the processed sequence coverage or the other parameter for each of the chromosomes of interest and that for the normalizing chromosome sequence(s). [00172] In any one of the embodiments above, the complete chromosomal aneuploidies are selected from complete chromosomal trisomies, complete chromosomal monosomies and complete chromosomal polysomies. The complete chromosomal aneuploidies are selected from complete aneuploidies of any one of chromosome 1-22, X, and Y. For example, the said different complete fetal chromosomal aneuploidies are selected from trisomy 2, trisomy 8, trisomy 9, trisomy 20, trisomy 21, trisomy 13, trisomy 16, trisomy 18, trisomy 22, , 47,XXX, 47,XYY, and monosomy X.

[00173] In any one of the embodiments above, steps (a)-(d) are repeated for test samples from different maternal subjects, and the method comprises determining the presence or absence of any two or more different complete fetal chromosomal aneuploidies in each of the test samples.

[00174] In any one of the embodiments above, the method can further comprise calculating a normalized chromosome value (NCV), wherein the NCV relates the chromosome dose to the mean of the corresponding chromosome dose in a set of qualified samples as:

_{NCV =} i h where fij and σ, are the estimated mean and standard deviation, respectively, for the j- th chromosome dose in a set of qualified samples, and x _i; is the observed y ^' -th chromosome dose for test sample i.

[00175] In some embodiments, NCV can be calculated "on the fly" by relating the chromosome dose of a chromosome of interest in a test sample to the median of the corresponding chromosome dose in multiplexed samples sequenced on the same flow cells as:

where M _j is the estimated median for the j-th chromosome dose in a set of multiplexed samples sequenced on the same flow cell; <T _j is the standard deviation for the j-th chromosome dose in one or more sets of multiplexed samples sequenced on one or more flow cells, and X; is the observed j-th chromosome dose for test sample i. In this embodiment, test sample i is one of the multiplexed samples sequenced on the same flow cell from which M _j is determined.

[00176] In some embodiments, a method is provided for determining the presence or absence of different partial fetal chromosomal aneuploidies in a maternal test sample comprising fetal and maternal nucleic acids. The method involves procedures analogous to the method for detecting complete aneuploidy as outlined above. However, instead of analyzing a complete chromosome, a segment of a chromosome is analyzed. See US Patent Application Publication No. 2013/0029852, which is incorporated by reference. [00177] Figure 1 shows a method for determining the presence of copy number variation in accordance with some embodiments. Process 100 illustrated in Figure 1 uses sequence tag coverage based on the number of sequence tags (i.e., the sequence tag count) to determine CNV. However, similar to the description above for calculation of a NCV, other variables or parameters, such as size, size ratio, and methylation level, may be used instead of coverage. In some implementations, two or more variables are combined to determine a CNV. Furthermore, coverage and other parameters may be weighted based on the size of the fragments from which tags are derived. For ease of reading, only coverage is referred to in process 100 illustrated in Figure 1, but one should note that other parameters, such as size, size ratio, and methylation level, count weighted by size, etc. may be used in place of coverage.

[00178] In operations 130 and 135, qualified sequence tag coverages (or values of another parameter) and test sequence tag coverages (or values of another parameter) are determined. The present disclosure provides processes to determine coverage quantities that provide improved sensitivity and selectivity relative to conventional methods. Operation 130 and 135 are marked by asterisks and emphasized by boxes of heavy lines to indicate these operations contribute to improvement over prior art. In some embodiments, the sequence tag coverage quantities are normalized, adjusted, trimmed, and otherwise processed to improve the sensitivity and selectivity of the analysis. These processes are further described elsewhere herein.

[00179] From an over-view perspective, the method makes use of normalizing sequences of qualified training samples in determination of CNV of test samples. In some embodiments, the qualified training samples are unaffected and have normal copy number. Normalizing sequences provide a mechanism to normalize measurements for intra-run and inter-run variabilities. Normalizing sequences are identified using sequence information from a set of qualified samples obtained from subjects known to comprise cells having a normal copy number for any one sequence of interest, e.g., a chromosome or segment thereof. Determination of normalizing sequences is outlined in steps 110, 120, 130, 145 and 146 of the embodiment of the method depicted in Figure 1. In some embodiments, the normalizing sequences are used to calculate sequence dose for test sequences. See step 150. In some embodiments, normalizing sequences are also used to calculate a threshold against which the sequence dose of the test sequences is compared. See step 150. The sequence information obtained from the normalizing sequence and the test sequence is used for determining statistically meaningful identification of chromosomal aneuploidies in test samples (step 160). [00180] Turning to the details of the method for determining the presence of copy number variation according to some embodiments, Figure 1 provides a flow diagram 100 of an embodiment for determining a CNV of a sequence of interest, e.g., a chromosome or segment thereof, in a biological sample. In some embodiments, a biological sample is obtained from a subject and comprises a mixture of nucleic acids contributed by different genomes. The different genomes can be contributed to the sample by two individuals, e.g., the different genomes are contributed by the fetus and the mother carrying the fetus. Also, the different genomes can be contributed to the sample by three or more individuals, e.g., the different genomes are contributed by two or more fetuses and the mother carrying the fetuses. Alternatively, the genomes are contributed to the sample by aneuploid cancerous cells and normal euploid cells from the same subject, e.g., a plasma sample from a cancer patient.

[00181] Apart from analyzing a patient's test sample, one or more normalizing chromosomes or one or more normalizing chromosome segments are selected for each possible chromosome of interest. The normalizing chromosomes or segments are identified asynchronously from the normal testing of patient samples, which may take place in a clinical setting. In other words, the normalizing chromosomes or segments are identified prior to testing patient samples. The associations between normalizing chromosomes or segments and chromosomes or segments of interest are stored for use during testing. As explained below, such association is typically maintained over periods of time that span testing of many samples. The following discussion concerns embodiments for selecting normalizing chromosomes or chromosome segments for individual chromosomes or segments of interest. [00182] A set of qualified samples is obtained to identify qualified normalizing sequences and to provide variance values for use in determining statistically meaningful identification of CNV in test samples. In step 110, a plurality of biological qualified samples are obtained from a plurality of subjects known to comprise cells having a normal copy number for any one sequence of interest. In one embodiment, the qualified samples are obtained from mothers pregnant with a fetus that has been confirmed using cytogenetic means to have a normal copy number of chromosomes. The biological qualified samples may be a biological fluid, e.g., plasma, or any suitable sample as described below. In some embodiments, a qualified sample contains a mixture of nucleic acid molecules, e.g., cfDNA molecules. In some embodiments, the qualified sample is a maternal plasma sample that contains a mixture of fetal and maternal cfDNA molecules. Sequence information for normalizing chromosomes and/or segments thereof is obtained by sequencing at least a portion of the nucleic acids, e.g., fetal and maternal nucleic acids, using any known sequencing method. Preferably, any one of the Next Generation Sequencing (NGS) methods described elsewhere herein is used to sequence the fetal and maternal nucleic acids as single or clonally amplified molecules. In various embodiments, the qualified samples are processed as disclosed below prior to and during sequencing. They may be processed using apparatus, systems, and kits as disclosed herein.

[00183] In step 120, at least a portion of each of all the qualified nucleic acids contained in the qualified samples are sequenced to generate millions of sequence reads, e.g., 36bp reads, which are aligned to a reference genome, e.g., hgl8. In some embodiments, the sequence reads comprise about 20bp, about 25bp, about 30bp, about 35bp, about 40bp, about 45bp, about 50bp, about 55bp, about 60bp, about 65bp, about 70bp, about 75bp, about 80bp, about 85bp, about90bp, about 95bp, about lOObp, about 1 lObp, about 120bp, about 130, about 140bp, about 150bp, about 200bp, about 250bp, about 300bp, about 350bp, about 400bp, about 450bp, or about 500bp. It is expected that technological advances will enable single-end reads of greater than 500bp enabling for reads of greater than about lOOObp when paired end reads are generated. In one embodiment, the mapped sequence reads comprise 36bp. In another embodiment, the mapped sequence reads comprise 25bp.

[00184] Sequence reads are aligned to a reference genome, and the reads that are uniquely mapped to the reference genome are known as sequence tags. Sequence tags falling on masked segments of a masked reference sequence are not counted for analysis of CNV.

[00185] In one embodiment, at least about 3 x 106 qualified sequence tags, at least about 5 x 10 ⁶ qualified sequence tags, at least about 8 x 10 ⁶ qualified sequence tags, at least about 10 x 10 ⁶ qualified sequence tags, at least about 15 x 10 ⁶ qualified sequence tags, at least about 20 x 10 ⁶ qualified sequence tags, at least about 30 x 10 ⁶ qualified sequence tags, at least about 40 x 10 ⁶ qualified sequence tags, or at least about 50 x 10 ⁶ qualified sequence tags comprising between 20 and 40bp reads are obtained from reads that map uniquely to a reference genome.

[00186] In step 130, all the tags obtained from sequencing the nucleic acids in the qualified samples are counted to obtain a qualified sequence tag coverage. Similarly, in operation 135, all tags obtained from a test sample are counted to obtain a test sequence tag coverage. The present disclosure provides processes to determine coverage quantities that provides improved sensitivity and selectivity relative to conventional methods. Operation 130 and 135 are marked by asterisks and emphasized by boxes of heavy lines to indicate these operations contribute to improvement over prior art. In some embodiments, the sequence tag coverage quantities are normalized, adjusted, trimmed, and otherwise processed to improve the sensitivity and selectivity of the analysis. These processes are further described elsewhere herein. [00187] As all qualified sequence tags are mapped and counted in each of the qualified samples, the sequence tag coverage for a sequence of interest, e.g., a clinically-relevant sequence, in the qualified samples is determined, as are the sequence tag coverages for additional sequences from which normalizing sequences are identified subsequently. [00188] In some embodiments, the sequence of interest is a chromosome that is associated with a complete chromosomal aneuploidy, e.g., chromosome 21, and the qualified normalizing sequence is a complete chromosome that is not associated with a chromosomal aneuploidy and whose variation in sequence tag coverage approximates that of the sequence (i.e., chromosome) of interest, e.g., chromosome 21. The selected normalizing chromosome(s) may be the one or group that best approximates the variation in sequence tag coverage of the sequence of interest. Any one or more of chromosomes 1-22, X, and Y can be a sequence of interest, and one or more chromosomes can be identified as the normalizing sequence for each of the any one chromosomes 1-22, X and Y in the qualified samples. The normalizing chromosome can be an individual chromosome or it can be a group of chromosomes as described elsewhere herein. [00189] In another embodiment, the sequence of interest is a segment of a chromosome associated with a partial aneuploidy, e.g., a chromosomal deletion or insertion, or unbalanced chromosomal translocation, and the normalizing sequence is a chromosomal segment (or group of segments) that is not associated with the partial aneuploidy and whose variation in sequence tag coverage approximates that of the chromosome segment associated with the partial aneuploidy. The selected normalizing chromosome segment(s) may be the one or more that best approximates the variation in sequence tag coverage of the sequence of interest. Any one or more segments of any one or more chromosomes 1-22, X, and Y can be a sequence of interest. [00190] In other embodiments, the sequence of interest is a segment of a chromosome associated with a partial aneuploidy and the normalizing sequence is a whole chromosome or chromosomes. In still other embodiments, the sequence of interest is a whole chromosome associated with an aneuploidy and the normalizing sequence is a chromosomal segment or segments that are not associated with the aneuploidy.

[00191] Whether a single sequence or a group of sequences are identified in the qualified samples as the normalizing sequence(s) for any one or more sequences of interest, the qualified normalizing sequence may be chosen to have a variation in sequence tag coverage or a fragment size parameter that best or effectively approximates that of the sequence of interest as determined in the qualified samples. For example, a qualified normalizing sequence is a sequence that produces the smallest variability across the qualified samples when used to normalize the sequence of interest, i.e., the variability of the normalizing sequence is closest to that of the sequence of interest determined in qualified samples. Stated another way, the qualified normalizing sequence is the sequence selected to produce the least variation in sequence dose (for the sequence of interest) across the qualified samples. Thus, the process selects a sequence that when used as a normalizing chromosome is expected to produce the smallest variability in run-to-run chromosome dose for the sequence of interest.

[00192] The normalizing sequence identified in the qualified samples for any one or more sequences of interest remains the normalizing sequence of choice for determining the presence or absence of aneuploidy in test samples over days, weeks, months, and possibly years, provided that procedures needed to generate sequencing libraries, and sequencing the samples are essentially unaltered over time. As described above, normalizing sequences for determining the presence of aneuploidies are chosen for (possibly among other reasons as well) the variability in the number of sequence tags or values of the fragment size parameter that are mapped to it among samples, e.g., different samples, and sequencing runs, e.g., sequencing runs that occur on the same day and/or different days, that best approximates the variability of the sequence of interest for which it is used as a normalizing parameter. Substantial alterations in these procedures will affect the number of tags that are mapped to all sequences, which in turn will determine which one or group of sequences will have a variability across samples in the same and/or in different sequencing runs, on the same day or on different days that most closely approximates that of the sequence(s) of interest, which would require that the set of normalizing sequences be redetermined. Substantial alterations in procedures include changes in the laboratory protocol used for preparing the sequencing library, which includes changes related to preparing samples for multiplex sequencing instead of singleplex sequencing, and changes in sequencing platforms, which include changes in the chemistry used for sequencing.

[00193] In some embodiments, the normalizing sequence chosen to normalize a particular sequence of interest is a sequence that best distinguishes one or more qualified, samples from one or more affected samples, which implies that the normalizing sequence is a sequence that has the greatest differentiability, i.e., the differentiability of the normalizing sequence is such that it provides optimal differentiation to a sequence of interest in an affected test sample to easily distinguish the affected test sample from other unaffected samples. In other embodiments, the normalizing sequence is a sequence that has a combination of the smallest variability and the greatest differentiability.

[00194] The level of differentiability can be determined as a statistical difference between the sequence doses, e.g., chromosome doses or segment doses, in a population of qualified samples and the chromosome dose(s) in one or more test samples as described below and shown in the Examples. For example, differentiability can be represented numerically as a t-test value, which represents the statistical difference between the chromosome doses in a population of qualified samples and the chromosome dose(s) in one or more test samples. Similarly, differentiability can be based on segment doses instead of chromosome doses. Alternatively, differentiability can be represented numerically as a Normalized Chromosome Value (NCV), which is a z-score for chromosome doses as long as the distribution for the NCV is normal. Similarly, in the case where chromosome segments are the sequences of interest, differentiability of segment doses can be represented numerically as a Normalized Segment Value (NSV), which is a z-score for chromosome segment doses as long as the distribution for the NSV is normal. In determining the z-score, the mean and standard deviation of chromosome or segment doses in a set of qualified samples can be used. Alternatively, the mean and standard deviation of chromosome or segment doses in a training set comprising qualified samples and affected samples can be used. In other embodiments, the normalizing sequence is a sequence that has the smallest variability and the greatest differentiability or an optimal combination of small variability and large differentiability. [00195] The method identifies sequences that inherently have similar characteristics and that are prone to similar variations among samples and sequencing runs, and which are useful for determining sequence doses in test samples.

Determination of sequence doses

[00196] In some embodiments, chromosome or segment doses for one or more chromosomes or segments of interest are determined in all qualified samples as described in step 146 shown in Figure 1, and a normalizing chromosome or segment sequence is identified in step 145. Some normalizing sequences are provided before sequence doses are calculated. Then one or more normalizing sequences are identified according to various criteria as further described below, see step 145. In some embodiments, e.g., the identified normalizing sequence results in the smallest variability in sequence dose for the sequence of interest across all qualified samples. [00197] In step 146, based on the calculated qualified tag densities, a qualified sequence dose, i.e., a chromosome dose or a segment dose, for a sequence of interest is determined as the ratio of the sequence tag coverage for the sequence of interest and the qualified sequence tag coverage for additional sequences from which normalizing sequences are identified subsequently in step 145. The identified normalizing sequences are used subsequently to determine sequence doses in test samples.

[00198] In one embodiment, the sequence dose in the qualified samples is a chromosome dose that is calculated as the ratio of the number of sequence tags or fragment size parameter for a chromosome of interest and the number of sequence tags for a normalizing chromosome sequence in a qualified sample. The normalizing chromosome sequence can be a single chromosome, a group of chromosomes, a segment of one chromosome, or a group of segments from different chromosomes. Accordingly, a chromosome dose for a chromosome of interest is determined in a qualified sample as the ratio of the number of tags for a chromosome of interest and the number of tags for (i) a normalizing chromosome sequence composed of a single chromosome, (ii) a normalizing chromosome sequence composed of two or more chromosomes, (iii) a normalizing segment sequence composed of a single segment of a chromosome, (iv) a normalizing segment sequence composed of two or more segments form one chromosome, or (v) a normalizing segment sequence composed of two or more segments of two or more chromosomes. Examples for determining a chromosome dose for chromosome of interest 21 according to (i)-(v) are as follows: chromosome doses for chromosome of interest, e.g., chromosome 21, are determined as a ratio of the sequence tag coverage of chromosome 21 and one of the following sequence tag coverages: (i) each of all the remaining chromosomes, i.e., chromosomes 1-20, chromosome 22, chromosome X, and chromosome Y; (ii) all possible combinations of two or more remaining chromosomes; (iii) a segment of another chromosome, e.g., chromosome 9; (iv) two segments of one other chromosome, e.g., two segments of chromosome 9; (v) two segments of two different chromosomes, e.g., a segment of chromosome 9 and a segment of chromosome 14.

[00199] In another embodiment, the sequence dose in the qualified samples is a segment dose as opposed to a chromosome dose, which segment dose is calculated as the ratio of the number of sequence tags for a segment of interest, that is not a whole chromosome, and the number of sequence tags for a normalizing segment sequence in a qualified sample. The normalizing segment sequence can be any of the normalizing chromosome or segment sequences discussed above.

Identification of normalizing sequences [00200] In step 145, a normalizing sequence is identified for a sequence of interest. In some embodiments, e.g., the normalizing sequence is the sequence based on the calculated sequence doses, e.g., that result in the smallest variability in sequence dose for the sequence of interest across all qualified training samples. The method identifies sequences that inherently have similar characteristics and are prone to similar variations among samples and sequencing runs, and which are useful for determining sequence doses in test samples.

[00201] Normalizing sequences for one or more sequences of interest can be identified in a set of qualified samples, and the sequences that are identified in the qualified samples are used subsequently to calculate sequence doses for one or more sequences of interest in each of the test samples (step 150) to determine the presence or absence of aneuploidy in each of the test samples. The normalizing sequence identified for chromosomes or segments of interest may differ when different sequencing platforms are used and/or when differences exist in the purification of the nucleic acid that is to be sequenced and/or preparation of the sequencing library. The use of normalizing sequences according to the methods described herein provides specific and sensitive measure of a variation in copy number of a chromosome or segment thereof irrespective of sample preparation and/or sequencing platform that is used.

[00202] In some embodiments, more than one normalizing sequence is identified, i.e., different normalizing sequences can be determined for one sequence of interest, and multiple sequence doses can be determined for one sequence of interest. For example, the variation, e.g., coefficient of variation (CV= standard deviation/mean), in chromosome dose for chromosome of interest 21 is least when the sequence tag coverage of chromosome 14 is used. However, two, three, four, five, six, seven, eight or more normalizing sequences can be identified for use in determining a sequence dose for a sequence of interest in a test sample. As an example, a second dose for chromosome 21 in any one test sample can be determined using chromosome 7, chromosome 9, chromosome 11 or chromosome 12 as the normalizing chromosome sequence as these chromosomes all have CV close to that for chromosome 14.

[00203] In some embodiments, when a single chromosome is chosen as the normalizing chromosome sequence for a chromosome of interest, the normalizing chromosome sequence will be a chromosome that results in chromosome doses for the chromosome of interest that has the smallest variability across all samples tested, e.g., qualified samples. In some instances, the best normalizing chromosome may not have the least variation, but may have a distribution of qualified doses that best distinguishes a test sample or samples from the qualified samples, i.e., the best normalizing chromosome may not have the lowest variation, but may have the greatest differentiability.

[00204] In some embodiments, normalizing sequences include one or more robust autosomes sequences or segments thereof. In some embodiments, the robust autosomes include all autosomes except for the chromosome(s) of interest. In some embodiments, the robust autosomes include all autosomes except for chr X, Y, 13, 18, and 21. In some embodiments, the robust autosomes include all autosomes except those determined from a sample to be deviating from a normal diploid state, which can be useful in determining cancer genomes that have abnormal copy number relative to a normal diploid genome.

Determination of aneuploidies in test samples

[00205] Based on the identification of the normalizing sequence(s) in qualified samples, a sequence dose is determined for a sequence of interest in a test sample comprising a mixture of nucleic acids derived from genomes that differ in one or more sequences of interest.

[00206] In step 115, a test sample is obtained from a subject suspected or known to carry a clinically-relevant CNV of a sequence of interest. The test sample may be a biological fluid, e.g., plasma, or any suitable sample as described below. As explained, the sample may be obtained using a non-invasive procedure such as a simple blood draw. In some embodiments, a test sample contains a mixture of nucleic acid molecules, e.g., cfDNA molecules. In some embodiments, the test sample is a maternal plasma sample that contains a mixture of fetal and maternal cfDNA molecules.

[00207] In step 125, at least a portion of the test nucleic acids in the test sample is sequenced as described for the qualified samples to generate millions of sequence reads, e.g., 36bp reads. In various embodiments, 2x36 bp paired end reads are used for paired end sequencing. As in step 120, the reads generated from sequencing the nucleic acids in the test sample are uniquely mapped or aligned to a reference genome to produce tags. As described in step 120, at least about 3 x 10 ⁶ qualified sequence tags, at least about 5 x 10 ⁶ qualified sequence tags, at least about 8 x 10 ⁶ qualified sequence tags, at least about 10 x 10 ⁶ qualified sequence tags, at least about 15 x 10 ⁶ qualified sequence tags, at least about 20 x 10 ⁶ qualified sequence tags, at least about 30 x 10 ⁶ qualified sequence tags, at least about 40 x 10 ⁶ qualified sequence tags, or at least about 50 x 10 ⁶ qualified sequence tags comprising between 20 and 40bp reads are obtained from reads that map uniquely to a reference genome. In certain embodiments, the reads produced by sequencing apparatus are provided in an electronic format. Alignment is accomplished using computational apparatus as discussed below. Individual reads are compared against the reference genome, which is often vast (millions of base pairs) to identify sites where the reads uniquely correspond with the reference genome. In some embodiments, the alignment procedure permits limited mismatch between reads and the reference genome. In some cases, 1, 2, or 3 base pairs in a read are permitted to mismatch corresponding base pairs in a reference genome, and yet a mapping is still made.

[00208] In step 135, all or most of the tags obtained from sequencing the nucleic acids in the test samples are counted to determine a test sequence tag coverage using a computational apparatus as described below. In some embodiments, each read is aligned to a particular region of the reference genome (a chromosome or segment in most cases), and the read is converted to a tag by appending site information to the read. As this process unfolds, the computational apparatus may keep a running count of the number of tags/reads mapping to each region of the reference genome (chromosome or segment in most cases). The counts are stored for each chromosome or segment of interest and each corresponding normalizing chromosome or segment.

[00209] In certain embodiments, the reference genome has one or more excluded regions that are part of a true biological genome but are not included in the reference genome. Reads potentially aligning to these excluded regions are not counted. Examples of excluded regions include regions of long repeated sequences, regions of similarity between X and Y chromosomes, etc. Using a masked reference sequence obtained by masking techniques described above, only tags on unmasked segments of the reference sequence are taken into account for analysis of CNV.

[00210] In some embodiments, the method determines whether to count a tag more than once when multiple reads align to the same site on a reference genome or sequence. There may be occasions when two tags have the same sequence and therefore align to an identical site on a reference sequence. The method employed to count tags may under certain circumstances exclude from the count identical tags deriving from the same sequenced sample. If a disproportionate number of tags are identical in a given sample, it suggests that there is a strong bias or other defect in the procedure. Therefore, in accordance with certain embodiments, the counting method does not count tags from a given sample that are identical to tags from the sample that were previously counted.

[00211] Various criteria may be set for choosing when to disregard an identical tag from a single sample. In certain embodiments, a defined percentage of the tags that are counted must be unique. If more tags than this threshold are not unique, they are disregarded. For example, if the defined percentage requires that at least 50% are unique, identical tags are not counted until the percentage of unique tags exceeds 50% for the sample. In other embodiments, the threshold number of unique tags is at least about 60%. In other embodiments, the threshold percentage of unique tags is at least about 75%), or at least about 90%, or at least about 95%, or at least about 98%, or at least about 99%. A threshold may be set at 90% for chromosome 21. If 30M tags are aligned to chromosome 21, then at least 27M of them must be unique. If 3M counted tags are not unique and the 30 million and first tag is not unique, it is not counted. The choice of the particular threshold or other criterion used to determine when not to count further identical tags can be selected using appropriate statistical analysis. One factor influencing this threshold or other criterion is the relative amount of sequenced sample to the size of the genome to which tags can be aligned. Other factors include the size of the reads and similar considerations.

[00212] In one embodiment, the number of test sequence tags mapped to a sequence of interest is normalized to the known length of a sequence of interest to which they are mapped to provide a test sequence tag density ratio. As described for the qualified samples, normalization to the known length of a sequence of interest is not required, and may be included as a step to reduce the number of digits in a number to simplify it for human interpretation. As all the mapped test sequence tags are counted in the test sample, the sequence tag coverage for a sequence of interest, e.g., a clinically-relevant sequence, in the test samples is determined, as are the sequence tag coverages for additional sequences that correspond to at least one normalizing sequence identified in the qualified samples.

[00213] In step 150, based on the identity of at least one normalizing sequence in the qualified samples, a test sequence dose is determined for a sequence of interest in the test sample. In various embodiments, the test sequence dose is computationally determined using the sequence tag coverages of the sequence of interest and the corresponding normalizing sequence as described herein. The computational apparatus responsible for this undertaking will electronically access the association between the sequence of interest and its associated normalizing sequence, which may be stored in a database, table, graph, or be included as code in program instructions.

[00214] As described elsewhere herein, the at least one normalizing sequence can be a single sequence or a group of sequences. The sequence dose for a sequence of interest in a test sample is a ratio of the sequence tag coverage determined for the sequence of interest in the test sample and the sequence tag coverage of at least one normalizing sequence determined in the test sample, wherein the normalizing sequence in the test sample corresponds to the normalizing sequence identified in the qualified samples for the particular sequence of interest. For example, if the normalizing sequence identified for chromosome 21 in the qualified samples is determined to be a chromosome, e.g., chromosome 14, then the test sequence dose for chromosome 21 (sequence of interest) is determined as the ratio of the sequence tag coverage for chromosome 21 in and the sequence tag coverage for chromosome 14 each determined in the test sample. Similarly, chromosome doses for chromosomes 13, 18, X, Y, and other chromosomes associated with chromosomal aneuploidies are determined. A normalizing sequence for a chromosome of interest can be one or a group of chromosomes, or one or a group of chromosome segments. As described previously, a sequence of interest can be part of a chromosome, e.g., a chromosome segment. Accordingly, the dose for a chromosome segment can be determined as the ratio of the sequence tag coverage determined for the segment in the test sample and the sequence tag coverage for the normalizing chromosome segment in the test sample, wherein the normalizing segment in the test sample corresponds to the normalizing segment (single or a group of segments) identified in the qualified samples for the particular segment of interest. Chromosome segments can range from kilobases (kb) to megabases (Mb) in size (e.g., about lkb to 10 kb, or about 10 kb to 100 kb, or about lOOkb to 1 Mb).

[00215] In step 155, threshold values are derived from standard deviation values established for qualified sequence doses determined in a plurality of qualified samples and sequence doses determined for samples known to be aneuploid for a sequence of interest. Note that this operation is typically performed asynchronously with analysis of patient test samples. It may be performed, for example, concurrently with the selection of normalizing sequences from qualified samples. Accurate classification depends on the differences between probability distributions for the different classes, i.e., type of aneuploidy. In some examples, thresholds are chosen from empirical distribution for each type of aneuploidy, e.g., trisomy 21. Possible threshold values that were established for classifying trisomy 13, trisomy 18, trisomy 21, and monosomy X aneuploidies as described in the Examples, which describe the use of the method for determining chromosomal aneuploidies by sequencing cfDNA extracted from a maternal sample comprising a mixture of fetal and maternal nucleic acids. The threshold value that is determined to distinguish samples affected for an aneuploidy of a chromosome can be the same or can be different from the threshold for a different aneuploidy. As is shown in the Examples, the threshold value for each chromosome of interest is determined from the variability in the dose of the chromosome of interest across samples and sequencing runs. The less variable the chromosome dose for any chromosome of interest, the narrower the spread in the dose for the chromosome of interest across all the unaffected samples, which are used to set the threshold for determining different aneuploidies. [00216] Returning to the process flow associated with classifying a patient test sample, in step 160, the copy number variation of the sequence of interest is determined in the test sample by comparing the test sequence dose for the sequence of interest to at least one threshold value established from the qualified sequence doses. This operation may be performed by the same computational apparatus employed to measure sequence tag coverages and/or calculate segment doses.

[00217] In step 160, the calculated dose for a test sequence of interest is compared to that set as the threshold values that are chosen according to a user- defined "threshold of reliability" to classify the sample as a "normal" an "affected" or a "no call." The "no call" samples are samples for which a definitive diagnosis cannot be made with reliability. Each type of affected sample (e.g., trisomy 21, partial trisomy 21, monosomy X) has its own thresholds, one for calling normal (unaffected) samples and another for calling affected samples (although in some cases the two thresholds coincide). As described elsewhere herein, under some circumstances a no-call can be converted to a call (affected or normal) if fetal fraction of nucleic acid in the test sample is sufficiently high. The classification of the test sequence may be reported by the computational apparatus employed in other operations of this process flow. In some cases, the classification is reported in an electronic format and may be displayed, emailed, texted, etc. to interest persons. [00218] In some embodiments, the determination of CNV comprises calculating a NCV or NSV that relates the chromosome or segment dose to the mean of the corresponding chromosome or segment dose in a set of qualified samples as described above. Then CNV can be determined by comparing the NCV/NSV to a predetermined copy number evaluation threshold value. [00219] The copy number evaluation threshold can be chosen to optimize the rate of false positives and false negatives. The higher the copy number evaluation threshold, the less likely the occurrence of a false positive. Similarly, the lower the threshold, the less likely the occurrence of a false negative. Thus, a trade-off exists between a first ideal threshold above which only true positives are classified, and a second ideal threshold below which only true negatives are classified.

[00220] Thresholds are set largely depending on the variability in chromosome doses for a particular chromosome of interest as determined in a set of unaffected samples. The variability is dependent on a number of factors, including the fraction of fetal cDNA present in a sample. The variability (CV) is determined by the mean or median and standard deviation for chromosome doses across a population of unaffected samples. Thus, the threshold (s) for classifying aneuploidy use NCVs, according to :

[00221] NCVij = - ^X ^-

(where flj and σ, are the estimated mean and standard deviation, respectively, for the y ^' -th chromosome dose in a set of qualified samples, and x _i; is the observed y ^' -th chromosome dose for test sample / ^' .)

with an associated fetal fraction as:

NCVijxdj

[00222] FFij = 2 X = 2 X NCV X CV

[00223] Thus, for every NCV of a chromosome of interest, an expected fetal fraction associated with the given NCV value can be calculated from the CV based on the mean and standard deviation of the chromosome ratio for the chromosome of interest across a population of unaffected samples.

[00224] Subsequently, based on the relationship between fetal fraction and NCV values, a decision boundary can be chosen above which samples are determined to be positive (affected) based on the normal distribution quantiles. As described above, in some embodiments, a threshold is set for optimal trade-off between the detection of true positives and rate of false negative results. Namely, the threshold is chosen to maximize the sum of true positives and true negatives, or minimize the sum of the false positives and false negatives.

[00225] Certain embodiments provide a method for providing prenatal diagnosis of a fetal chromosomal aneuploidy in a biological sample comprising fetal and maternal nucleic acid molecules. The diagnosis is made based on obtaining sequence information from at least a portion of the mixture of the fetal and maternal nucleic acid molecules derived from a biological test sample, e.g., a maternal plasma sample, computing from the sequencing data a normalizing chromosome dose for one or more chromosomes of interest, and/or a normalizing segment dose for one or more segments of interest, and determining a statistically significant difference between the chromosome dose for the chromosome of interest and/or the segment dose for the segment of interest, respectively, in the test sample and a threshold value established in a plurality of qualified (normal) samples, and providing the prenatal diagnosis based on the statistical difference. As described in step 160 of the method, a diagnosis of normal or affected is made. A "no call" is provided in the event that the diagnosis for normal or affected cannot be made with confidence.

[00226] In some embodiments, two thresholds can be chosen. A first threshold is chosen to minimize the false positive rate, above which samples will be classified as "Affected", and a second threshold is chosen to minimize the false negative rate, below which samples will be classified as "unaffected". Samples having NCVs above the second threshold but below the first threshold can be classified as "Aneuploidy suspected" or "No call" samples, for which the presence or absence of aneuploidy can be confirmed by independent means. The region between the first and second thresholds can be referred to as a "no call" region.

[00227] In some embodiments, the suspected and no call thresholds are shown in Table 1. As can be seen, the thresholds of NCV vary across different chromosomes. In some embodiments, the thresholds vary according to the FF for the sample as explained above. Threshold techniques applied here contribute to improved sensitivity and selectivity in some embodiments.

TABLE 1. Suspected and Affected NCV Thresholds Bracketing

No-Call Ranges

Fragment Size and Sequence Coverage Analyses [00228] As mentioned above, fragment size parameters, as well as coverage, may be used to evaluate CNV. Fragment size of a cell free nucleic acid fragment, e.g., a cfDNA fragment may be obtained by pair end sequencing, electrophoresis (e.g., microchip-based capillary electrophoresis), and other methods known in the art. Figure 2A thematically illustrates how paired end sequencing may be used to determine both fragment size and sequence coverage. [00229] The top half of Figure 2A a shows a diagram of a fetal cell free DNA fragment and a maternal cell free DNA fragment providing a template for a paired end sequencing process. Conventionally, long nucleic acid sequences are fragmented into shorter sequences to be read in a paired end sequencing process. Such fragments are also referred to as inserts. Fragmenting is unnecessary for cell free DNA because they already exist in fragments mostly shorter than 300 base pairs. It has been shown that fetal cell free DNA fragments in maternal plasma are longer than maternal cell free DNA fragments. As shown at the top of figure 2A, cell free DNA of fetal origin have an average length of about 167 base pairs, while cell free DNA of maternal origin have an average length of about 175 base pairs. In paired end sequencing on certain platforms, such as the Illumina's sequencing by synthesis platform as described further hereinafter, adaptor sequences, index sequences, and/or prime sequences are ligated to the two ends of a fragment (not shown in Figure 2A). A fragment is first read in one direction, providing read 1 from one end of the fragment. Then a second read starts from the opposite end of the fragment, providing the rea 2 sequence. The correspondence between read 1 and read 2 can be identified by their coordinates in the flow cell. Then read 1 and read 2 are mapped to a reference sequence as a pair of tags that are near each other, as shown in the bottom half of Figure 2A. In some embodiments, if the reads are long enough, the two reads can overlap in middle portion of the insert. After the pair is aligned to the reference sequence, the relative distance between the two reads and the length of the fragment can be determined from the positions of the two reads. Because paired end reads provide twice as many base pairs as single end reads of the same read length, they help to improve alignment qualities, especially for sequences with many repeats or non-unique sequences. In many embodiments, a reference sequence is divided into bins, such as 100 K base pair bins. After paired end reads are aligned to the reference sequence, the number of reads aligned to a bin can be determined. The number as well as the lengths of inserts (e.g., cfDNA fragments) can also be determined for a bin. In some embodiments, if an insert straddles two bins, half of an insert may be attributed to each bin.

[00230] Figure 2B shows an embodiment providing process 220 for using size- based coverage to determine a copy number variation of a nucleic acid sequence of interest in a test sample including cell-free nucleic acid fragments originating from two or more genomes. As disclosed herein, a parameter is "biased toward a fragment size or size range" when: 1) the parameter is favorably weighted for the fragment size or size range, e.g., a count weighted more heavily when associated with fragments of the size or size range than for other sizes or ranges; or 2) the parameter is obtained from a value that is favorably weighted for the fragment size or size range, e.g., a ratio obtained from a count weighted more heavily when associated with fragments of the size or size range. A fragment size or size range may be a characteristic of a genome or a portion thereof when the genome produces nucleic acid fragments enriched in or having a higher concentration of the size or size range relative to nucleic acid fragments from another genome or another portion of the same genome.

[00231] Process 220 starts by receiving sequence reads obtained by sequencing the cell-free nucleic acid fragments in the test sample. See block 222. The two or more genomes in the test sample may be a genome of a pregnant mother and a genome of a fetus carried by the pregnant mother. In other applications, the test sample includes cell free DNA from tumor cells and unaffected cells. In some embodiments, because of the high signal to noise ratio provided by the size-biased coverage, the sequencing of the cell free nucleic acid fragments are performed without the need to amplify the nucleic acid fragments using PCR. Process 200 further involves aligning the sequence reads of the cell-free nucleic acid fragments to a reference genome that includes the sequence of interest and is divided into a plurality of bins. Successful alignment results in test sequence tags, which include sequence and its location on the reference sequence. See block 224. Then process 220 proceeds by determining sizes of the cell-free nucleic acid fragments existing in the test sample. Some embodiments applying paired end sequencing provide the length of an insert associated with a sequence tag. See block 226. The terms "size" and "length" are used interchangeably when they are used with reference to nucleic acid sequences or fragments. In the embodiment illustrated here, process 220 further involves weighting the test sequence tags based on the sizes of cell-free nucleic acid fragments from which the tags are obtained. See block 228. As used herein, "weighting" refers to modifying a quantity using one or more variables or functions. The one or more variables or functions are considered a "weight." In many embodiments, the variable is multiplied by the weight. In other embodiments, the variable may be modified exponentially or otherwise. In some embodiments, weighting the test sequence tags is performed by biasing the coverages toward test sequence tags obtained from cell-free nucleic acid fragments of a size or a size range characteristic of one genome in the test sample. As disclosed herein, a size is characteristic of a genome when the genome has an enriched or higher concentration of nucleic acid of the size relative to another genome or another portion of the same genome.

[00232] In some embodiments, weighting function may be a linear or nonlinear function. Examples of applicable non-linear functions include, but are not limited to Heaviside step functions, box-car functions, stair-case functions, or sigmoidal functions. In some embodiments, a Heaviside function or a box-car function is used, such that a tag in a specific size range is multiplied by a weight of 1, and tags outside of the range is multiplied by a weight of 0. In some embodiments, fragments between 80 and 150 base pairs are given a weight of 1, while fragments outside of this range is given a weight of 0. In these examples, the weighting is discreet, being zero or one depending on whether the parameter of all the value falls inside or outside a particular range. Alternatively, weights are calculated as a continuous function of the fragment size or other aspect of the associated parameter value.

[00233] In some embodiments, the weights for fragments in one size range are positive, and those in another range are negative. This may be used to help enhance signal when the directions of the difference between two genomes have the opposite signs. For instance, read counts have a weight of 1 for 80-150 base-pair insert, and a weight of -1 for 160-200 base-pair insert.

[00234] Weighs may be given to counts, as well as other parameters. For instance, weighting may also be applied to the fractional or ratio parameters that use fragment size. For example, the ratio may give fragments in certain sub-ranges greater weight than fragments and other size bins. [00235] Then coverages are calculated for the bins based on the weighted test sequence tags. See block 230. Such coverages are considered size-biased. As explained above a value is biased toward a fragment size or size range when the parameter is favorably weighted for the fragment size or size range. Process 200 further involves identifying a copy number variation in the sequence of interest from the calculated coverages. See block 232. In some embodiments, as further explained hereinafter in connection with Figures 2C, 3A-3K, and 4, the coverages may be adjusted or corrected to remove noise in the data, thereby increasing the signal-to- noise ratio. In some applications, the coverage based on the weighted tags obtained in process 220 provides both a higher sensitivity and/or a higher selectivity compared to un-weighted coverages in determining the copy number variation. In some applications, the example workflow provided below can further improve the sensitivity and selectivity for CNV analysis.

Workflow Example for Analyzing Fragment Size and/or Sequence Coverage

[00236] Some embodiments disclosed provide methods to determine sequence coverage quantities with low noise and/or high signal, providing data to determine various genetic conditions related to copy number and CNV with improved sensitivity, selectivity, and/or efficiency relative to sequence coverage quantities obtained by conventional methods. In certain embodiments, sequences from a test sample are processed to obtain sequence coverage quantities.

[00237] The process makes use of certain information available from other sources. In some implementations, all of this information is obtained from a training set of samples known to be unaffected (e.g., not aneuploid). In other embodiments, some or all of the information is obtained from other test samples, which may be provided "on-the-fly" as multiple samples are analyzed in the same process.

[00238] In certain embodiments, sequence masks are employed to reduce data noise. In some embodiments, both the sequence of interest and its normalizing sequences are masked. In some embodiments, different masks may be employed when different chromosomes or segments of interest are considered. For example one mask (or group of masks) may be employed when chromosome 13 is the chromosome of interest and a different mask (or group of masks) may be employed with chromosome 21 is the chromosome of interest. In certain embodiments, the masks are defined at the resolution of bins. Therefore, in one example, the mask resolution is 100 kb. In some embodiments, a distinct mask may be applied to chromosome Y. The masked exclusion regions for chromosome Y may be provided at a finer resolution (lkb) than for other chromosomes of interest, as described in US Provisional Patent Application No. 61/836,057, filed June 17, 2013 [attorney docket no. ARTEP008P]. The masks are provided in the form of files identifying excluded genomic regions.

[00239] In certain embodiments, the process utilizes an expectation value of normalized coverage to remove bin-to-bin variation in the profile of a sequence of interest, which variation is uninformative for determination of CNV for the test sample. The process adjusts normalized coverage quantities according to the expectation value of normalized coverage for each bin across the entire genome, or at least the bins of the robust chromosomes in the reference genome (for use in operation 317 below). Parameters other than coverage may be improved by this process as well. The expectation value may be determined from a training set of unaffected samples. As an example, the expectation value may be a median value across the training set samples. The expected coverage values of the samples may be determined as the number of unique non-redundant tags aligned to a bin divided by the total number of unique non-redundant tags aligned to all bins in the robust chromosomes of the reference genome.

[00240] Figure 2C depicts a flowchart of a process 200 for determining a fragment size parameter for a sequence of interest, which parameter is used to evaluate the copy number of the sequence of interest in a test sample in block 214. This process removes systematic variation common across unaffected training samples, which variation increases noise in the analysis for CNV evaluation. It also removes GC bias specific to a test sample, thereby increasing the signal-to-noise ratio in data analysis. It is worth noting that process 200 may also be applied to coverage, regardless of if the coverage is biased by size or not. Similarly, the processes in Figures 2D, 3, and 4 are equally applicable to coverage, fragment size weighted coverage, fragment size, fraction or ratio of fragments in a defined size range, methylation level of fragments, etc. [00241] The process 200 starts by providing sequence reads of the test sample as indicated in block 202. In some embodiments the sequence reads are obtained by sequencing DNA segments obtained from a pregnant woman's blood including cfDNA of the mother and the fetus. The process proceeds to align the sequence reads to a reference genome including the sequence of interest, providing test sequence tags. Block 204. In some embodiments, reads that are aligned to more than one site are excluded. In some embodiments multiple reads align to the same site are excluded or reduced to a single read count. In some embodiments, reads aligned to excluded sites are also excluded. Therefore, in some embodiments, only the uniquely aligned, non- redundant tags aligned to non-excluded sites are counted to provide a non-excluded site count (NES count) for determining the coverage or other parameters of each bin.

[00242] Process 200 provides sizes of the cell-free nucleic acid fragments existing in the test sample. In some embodiments using paired end sequencing, an insert size/length can be obtained from the locations of a pair of reads at the ends of the insert. Other techniques can be used to determine fragment size. See block 205. Then, in bins of the reference genome, including bins in the sequence of interest, process 200 determines values of a fragment size parameter biased toward fragment sizes characteristic of one of the genomes. The term "fragment size parameter" refers to a parameter that relates to the size or length of a fragment or a collection of fragments of nucleic acid fragments; e.g., cfDNA fragments obtained from a bodily fluid. As used herein, a parameter is "biased toward a fragment size or size range" when: 1) the parameter is favorably weighted for the fragment size or size range, e.g., a count weighted more heavily when associated with fragments of the size or size range than for other sizes or ranges; or 2) the parameter is obtained from a value that is favorably weighted for the fragment size or size range, e.g., a ratio obtained from a count weighted more heavily when associated with fragments of the size or size range. A fragment size or size range may be a characteristic of a genome or a portion thereof when the genome produces nucleic acid fragments enriched in or having a higher concentration of the size or size range relative to nucleic acid fragments from another genome or another portion of the same genome.

[00243] In some embodiments, the fragment size parameter is a size-weighted count. In some embodiments a fragment is weighted 1 in a range, and 0 outside of the range. In other embodiments, the fragment size parameter is a fraction or a ratio of fragments in a size range. See block 206. In some embodiments, the value of the fragment size parameter (or coverage, as noted above) of each bin is divided by the value of the parameter of the normalizing sequence in the same sample, providing a normalized parameter. [00244] Process 200 then provides a global profile of the sequence of interest. The global profile comprises an expected parameter value in each bin obtained from a training set of unaffected training samples. Block 208. Process 200 removes variation common in the training sample by adjusting the normalized parameter values of the test sequence tags according to the expected parameter values to obtain a global- profile-corrected values of the parameter for the sequence of interest. Block 210. In some embodiments, the expected value of the parameter obtained from the training set provided in block 208 is a median of across the training samples. In some embodiments, operation 2010 adjusts the normalized value of the parameter by subtracting the expected value of the parameter from the normalized value of the parameter. In other embodiments, operation 210 divides the normalized value of the parameter by the expected value of the parameter of each bin to produce global- profile corrected value of the parameter.

[00245] In addition to or instead of global profile correction, process 200 removes GC bias specific to the test sample by adjusting the parameter value. As shown in block 212, the process adjusts the global-profile-corrected parameter value based on the relation between GC content level and the global-profile-corrected coverage existing in the test sample, thereby obtaining a sample-GC-corrected value of the fragment size parameter. After adjusting for systematic variation common in the unaffected training samples and within-subject GC bias, the process provides fragment size value corrected for global profile and/or GC variance, which value is used to evaluate CNV of the sample with improved sensitivity and specificity. In some implementations, the fragment size value may be adjusted using a principal component analysis method to remove components of variance unrelated to copy number variation of the sequence of interest as further described with reference to block 719 of Figure 2F. In some implementations, the fragment size value may be curated by removing outlier bins of within a sample as described with reference to block 321 of Figure 3 A. Multi-pass Process for Copy Number Determination Using Multiple Parameters

[00246] As emphasized above, the processes disclosed herein are suitable for determining CNV using multiple parameters, including but not limited to coverage, fragment size weighted coverage, fragment size, fraction or ratio of fragments in a defined size range, methylation level of fragments, etc. Each of these parameters may be separately processed to individually contribute to a final copy number variation determination.

[00247] In some embodiments, similar processes may be applied to a size- weighted coverage analysis and a fragment size analysis, both of which are fragment size parameters. Figure 2D shows a flow chart of two overlapping passes of work flow 600, pass 1 for size-weighted coverage, and pass 2 for fragment size analysis. In another embodiment not shown here, methylation level can be processed in one additional pass. The two passes can include comparable operations to obtain adjusted coverage information, on which determination of CNV is based.

[00248] An initial single pass portion of the process starts by receiving sequencing data, see block 602, and continues through computing counts as described above, see block 612. After this point, the depicted process splits into two passes, as described above. Returning to the initial portion of the process, the workflow converts sequencing data into sequence reads. When the sequencing data is derived from multiplex sequencing, the sequence reads are also de-multiplexed to identify the source of the data. See block 604. The sequence reads are then aligned to a reference sequence, where the aligned sequence reads are provided as sequence tags. See block 606. Then sequence tags are filtered to obtain non-excluded sites (NESs), which are unambiguously mapped, non-duplicated sequence tags. Sequence tags are organized into bins of specific sequence length, such as 1 kb, 100 kb, or 1 Mb. See block 610. In some embodiments involving analysis of syndrome specific regions, the bins are 100 kb. In some embodiments, bins exhibiting high variability may be masked using a sequence mask obtained from a plurality of unaffected samples in a manner as described in Figure 3A, block 313. Then the tags in the NESs are counted to provide coverages to be normalized and adjusted for analysis of CNV. See block 612. [00249] In the depicted embodiment, operations 604, 606, 610, and 612 are performed once and most of the remaining operations are performed twice, once for a size-weighted coverage analysis (pass 1) and once for a fragment size analysis (pass 2). In other embodiments, one or more of the operations shown as being performed in two passes are performed only once and the results are shared in both processes.

Examples of such shared operations include operations 614, 616, and 618.

[00250] In the depicted embodiments, the obtained coverages (size weighted counts) or fragment size parameter (size fractions or ratios) of NESs are normalized by, e.g., dividing the value NES of a bin by the total NESs of the genome or a set of normalizing chromosomes. In some embodiments, only the coverage is normalized, while the fragment size parameter does not need to be normalized, because it is not affected by sequencing depth the same way as coverage. See block 614. Then, in some embodiments, the variance common to a training set including unaffected samples is removed, which variance is unrelated to the CNV of interest. In the depicted embodiment, the common variance is represented as a global wave profile obtained from unaffected samples in the manner similar to the global wave profile described above. In some embodiments as illustrated in Figure 6, the unaffected samples used to obtain a global wave profile include samples coming from the same flow cell or processing batch. See block 616. The calculation of the flow cell specific global wave is further explained hereinafter. In the depicted embodiment, after the global wave profile has been removed, coverages are corrected for GC level on a sample-specific basis. See block 616. Some algorithms for GC correction are described in further details hereinafter in the text associated with Figure 3A, block 319. [00251] In the depicted embodiment, in both pass 1 for weighted coverage analysis and pass 2 for fragment size analysis, data may be further filtered for noise specific to an individual sample, e.g., data of outlier bins that have coverages extremely different from other bins may be removed from analysis, which difference cannot be attributed to the copy number variation of interest. See block 622. This within-sample filtering operation may correspond to block 321 in Figure 3A.

[00252] In some embodiments, after single sample filtering, the weighted coverage values of pass 1 and the fragment size parameter of pass 2 are both enriched in target signal over reference. See blocks 624 and 628. Then, the coverage and the fragment size parameter for the chromosome each is used to calculate a chromosome dose and a normalized chromosome value (NCV) as described above. The NCV then may be compared to a criterion to determine a score indicating a probability of a CNV. See blocks 626 and 630. The scores from the two passes can then be combined to provide a composite, final score, which determines whether an aneuploidy should be called. In some embodiments, the scores of 626 and 630 are t- test statistics or Z values. In some embodiments, the final score is a chi square value. In other embodiments, the final score is a root mean square of the two t values or z scores. Other means to combine the two scores from the two paths may be used to improve the overall sensitivity and selectivity in CNV detection. Alternatively, one may combine the two scores from the two passes by logical operations, e.g., AND operation or OR operation. For instance, when a high sensitivity is preferred to ensure low false negative, a CNV call can be made when the score from pass 1 OR pass 2 meets a call criterion. On the other hand, if high selectivity is desired to ensure low false positive, a CNV call can be made only if the score from both pass 1 AND pass 2 meet a call criterion.

[00253] It is notable that there is a trade-off between sensitivity and selectivity using such logical operations above. In some embodiments, a two-step sequencing approach is applied to overcome the trade-off as further described hereinafter. Briefly, the initial scoring of a sample is compared against a relatively low, first threshold designed to increase sensitivity, and if the sample scores higher than the first threshold, it undergoes a second round of sequencing, which is deeper than the first one. Such a sample is then re-processed and analyzed in a workflow similar to that described above. Then the resulting score is compared to a relatively high, second threshold designed to improve the sensitivity. In some embodiments, the samples undergoing a second round of sequencing score relatively low among those that score above the first threshold, thereby reducing the number of samples that need to be resequenced.

[00254] In some embodiments, a 3rd pass using a 3rd parameter can be employed. One example of this 3rd pass is methylation. The methylation may be determined directly through measuring the methylation of the nucleic acids from the sample or indirectly as a parameter that correlates with fragment size of the cell free nucleic acids. [00255] In some embodiments, this 3rd parameter is a 2nd coverage or count based parameter, where the counts are based on fragment sizes outside the primary fragment size used in the first count based parameter. When fragments between 80 and 150 base pairs are used for generating the count or coverage parameter, they exclude about 70% of the reads from a sequencing. To the extent that these excluded reads still have some potentially useful signal, they may be used in a 3rd parameter which includes the excluded reads or reads in a size-based fraction that is outside of or overlaps with the size-based fraction used in the first parameter. In this regard, the reads and associated coverage values taken from the excluded fragments may be given a lower weight. In other words, the copy number variation parameter calculated using these reads may be ascribed less importance in making a final copy number variation call. Alternatively, as described above, the tags outside of the size range in the first parameter may take on a negative value when the two genomes have opposite characteristics in the two size ranges. [00256] In various implementations, the coverages in processes 200, 220, and

600 are biased toward tags from fragments at a shorter end of a fragment size spectrum. In some embodiments, the coverages are biased toward tags from fragments of sizes shorter than a specified value. In some embodiments, the coverages are biased toward tags from fragments in a range of fragment sizes, and the upper end of the range is about 150 base pairs or fewer.

[00257] In various implementations of processes 200, 220, and 600, the sequence reads are obtained by sequencing the cell-free nucleic acid fragments without first using PCR to amplify nucleic acids of the cell-free nucleic acid fragments. In various embodiments, the sequencing reads are obtained by sequencing the cell-free nucleic acid fragments to a depth of no greater than about 6 M fragments per sample. In some embodiments, the sequencing depth is no greater than about 1 M fragments per sample. In some embodiments, sequencing reads are obtained by multiplex sequencing, and the number of samples multiplexed is at least about 24.

[00258] In various implementations of processes 200, 220, and 600, the test sample comprises plasma from an individual. In some embodiments, the processes further comprising obtaining the cell-free nucleic acid from the test sample. In some embodiments, the processes further comprising sequencing the cell-free nucleic acid fragments originating from two or more genomes. [00259] In various implementations of processes 200, 220, and 600, the two or more genomes comprise genomes from a mother and a fetus. In some implementations, the copy number variation in the sequence of interest comprises aneuploidy in the genome of the fetus. [00260] In some implementations of processes 200, 220, and 600, the two or more genomes comprise genomes from cancer and somatic cells. In some implementations, the processes comprising using a copy number variation in the cancer genome to diagnose cancer, monitor the progress of cancer, and/or determine a treatment for cancer. In some implementations, the copy number variation causes a genetic abnormality.

[00261] In some implementations of processes 200, 220, and 600, the coverages are biased toward tags from fragments at a longer end of a fragment size spectrum. In some implementations, the coverages are biased toward tags from fragments of sizes longer than a specified value. In some implementations, coverages are biased toward tags from fragments in a range of fragment sizes, and wherein the lower end of the range is about 150 base pairs or more.

[00262] In some implementations of processes 200, 220, and 600, the processes further involves: determining, in bins of the reference genome, including the sequence of interest, levels of methylation of the cell-free nucleic acid fragments in said bins, and using the levels of methylation, in addition to or instead of the calculated coverages or the values of the fragment size parameter to identify a copy number variation. In some implementation, using the methylation levels to identify a copy number variation involves providing a global methylation profile for the bins of the sequence of interest. The global methylation profile includes expected levels of methylation in at least bins of the sequence of interest. In some implementations, the expected levels of methylation are obtained from lengths of cell-free nucleic acid fragments in a training set of unaffected training samples comprising nucleic acids sequenced and aligned in substantially the same manner as the nucleic acid fragments of the test sample, the expected levels of methylation exhibiting variation from bin to bin. In some implementations, the processes involve adjusting the value of the levels of methylation using the expected levels of methylation in the bins of at least the sequence of interest, thereby obtaining global-profile-corrected values of the levels of methylation for the sequence of interest, the processes further involve identifying a copy number variation using global-profile-corrected coverages and the global- profile-corrected levels of methylation. In some implementations, identifying a copy number variation using the global-profile-corrected coverages and the global-profile- corrected levels of methylation further comprises: adjusting the global-profile- corrected coverages and the global-profile-corrected levels of methylation based on GC content levels, thereby obtaining GC-corrected coverages and GC-corrected values of the levels of methylation for the sequence of interest; and identifying a copy number variation using the GC-corrected coverages and the GC-corrected levels of methylation. [00263] In some implementations of processes 200, 220, and 600, the fragment size parameter comprises a fraction or ratio including a portion of the cell-free nucleic acid fragments in the test sample having fragment sizes shorter or longer than a threshold value. In some implementations, the fragment size parameter includes a fraction including (i) a number of fragments in the test sample within a first size range including 110 base pairs, and (ii) a number of fragments in the test sample within a second size range comprising the first size range and sizes outside the first size range.

Copy Number Determination Using a Three-pass Process, Likelihood Ratios, T Statistics, and/or Fetal Fractions

[00264] Figure 2E shows a flow chart of a three-pass process for evaluating copy number. It includes three overlapping passes of work flow 700, which includes pass 1 (or 713 A) analysis of coverage of reads associated with fragments of all sizes, pass 2 (or 713B) analysis of coverage of reads associated with shorter fragments, and pass 3 (or 713C) analysis of relative frequency of shorter reads relative to all reads.

[00265] Process 700 is similar to process 600 in its overall organization. Operations indicated by blocks 702, 704, 706, 710, 712 may be performed in the same or a similar manner to operations indicated by blocks 602, 604, 606, and 610, and 612. After read counts are obtained, coverage is determined using reads from fragments of all sizes in pass 713 A. Coverage is determined using reads from short fragments in pass 713B. Frequency of reads from short fragments relative to all reads is determined in pass 713C. The relative frequency is also referred to as a size ratio or a size fraction elsewhere herein. It is an example of a fragment size characteristic. In some implementations, short fragments are fragments shorter than about 150 base pairs. In various implementations, short fragments can be in the size ranges of about 50-150, 80-150, or 110-150 base pairs. In some implementations, the third pass, or pass 713C, is optional.

[00266] The data of the three passes 713A, 713B, and 713C all undergo normalization operations 714, 716, 718, 719, and 722 to remove variance unrelated to copy number of the sequence of interest. These normalization operations are boxed in blocks 723. Operation 714 involves normalizing the analyzed quantity of the sequence of interest by dividing the analyzed quantity by the total value of the quantity of the reference sequence. This normalization step uses values obtained from a test sample. Similarly, operations 718 and 722 normalize the analyzed quantity using values obtained from the test sample. Operations 716 and 719 use values obtained from a training set of unaffected samples.

[00267] Operation 716 removes variance of a global wave obtained from the training set of unaffected samples, which uses the same or similar methods as described with reference to block 616. Operation 718 removes variance of individual- specific GC variance using the same or similar manner methods as described with reference to block 618.

[00268] Operation 719 removes further variance using a principal component analysis (PCA) method. The variance removed by the PCA methods is due to factors unrelated to copy number of the sequence of interest. The analyzed quantity in each bin (coverage, fragment size ratio, etc.) provides an independent variable for the PCA, and the samples of the unaffected training set supply values for these independent variables. The samples of the training set all include samples having the same copy number of the sequence of interest, e.g., two copies of a somatic chromosome, one copy of the X chromosome (when male samples are used as unaffected samples), or two copies of the X chromosome (when female samples are used as unaffected samples). Thus, variance in the samples does not result from an aneuploidy or other difference in copy number. The PCA of the training set yields principal components that are unrelated to copy number of the sequence of interest. The principal components can then be used to remove variance in a test sample unrelated to the copy number of the sequence of interest. [00269] In certain embodiments, the variance of one or more of the principal components is removed from the test sample's data using the coefficients estimated from unaffected samples' data in a region outside of the sequence of interest. In some implementations, the region represents all robust chromosomes. For instance, a PCA is performed on normalized bin coverage data of training normal samples, thereby providing principal components corresponding to dimensions in which most variance in the data can be captured. Variance so captured is unrelated to copy number variation in the sequence of interest. After the principal components have been obtained from the training normal samples, they are applied to test data. A linear regression model with test sample as response variable and principal components as dependent variables is generated across bins from a region outside of the sequence of interest. Resulting regression coefficients are used to normalize the bin coverage of the region of interest by subtracting the linear combination of principal components defined by the estimated regression coefficients. This removes variance unrelated to CNV from the sequence of interest. See block 719. The residual data is used for downstream analysis. Additionally, operation 722 removes outlier data points using methods described with reference to block 622.

[00270] After undergoing the normalization operations in block 723, the coverage values of all bins have been "normalized" to remove sources of variation other than aneuploidy or other copy number variations. In a sense, the bins of the sequence of interest are enriched or altered relative to other bins for purposes of copy number variation detection. See block 724, which is not an operation but represents the resulting coverage values. The normalization operations in large block 723 may increase the signal and/or reduce the noise of the quantity under analysis. Similarly, the coverage values of short fragments for the bins have been normalized to remove sources of variation other than aneuploidy or other copy number variations as shown in block 728, and the relative frequency of short fragments (or size ratio) for the bins have been similarly normalized to remove sources of variation other than aneuploidy or other copy number variations as shown in block 732. As with block 724, blocks 728 and 732 are not operations but represents the coverage and relative frequency values after the processing large block 723. It should be understood, that the operations in large block 723 may be modified, rearranged, or removed. For example, in some embodiments, PCA operation 719 is not performed. In other embodiments, the correcting for GC operation 718 is not performed. In other embodiments, the order of the operations is changed; e.g., PCA operation 719 is performed prior to correct for GC operation 718,

[00271] The coverage of all fragments after normalization and variance removal shown in block 724 is used to obtain a t-statistic in block 726. Similarly, the coverage of short fragments after normalization and variance removal shown in block 728 is used to obtain a t-statistic in block 730, and the relative frequency of short fragments after normalization and variance removal shown in block 732 is used to obtain a t-statistic in block 734. [00272] Figure 2F demonstrates why applying a t-statistic to copy number analysis can help to improve the accuracy of the analysis. Figure 2F shows, in each panel, the frequency distributions of normalized bin coverage of a sequence of interest and a reference sequence, with the sequence of interest distribution overlapping and obscuring the reference sequence distribution. In the top panel, bin coverage for a sample having higher coverage is shown, having over 6 million reads; in the bottom panel, bin coverage for a sample having lower coverage is shown, having fewer than 2 million reads. The horizontal axis indicates coverage normalized relative to the mean coverage of the reference sequence. The vertical axis indicates relative probability density related to numbers of bins having the mean coverage values. Figure 2F is thus a type of histogram. The distribution for the sequence of interest is shown to the front, and the distribution of the reference sequence is shown to the back. The mean for the distribution of the sequence of interest is lower than that of the reference sequence, indicating a lowered copy number in the sample. The mean difference between the sequence of interest and the reference sequence is similar for the high coverage sample in the top panel and the low coverage sample in the bottom panel. Thus, the difference in mean may, in some implementations, be used to identify a copy number variation in the sequence of interest. Note that the distributions of the high coverage sample have variances smaller than those of the low coverage sample. Using only the mean to distinguish the two distributions does not capture the difference between the two distributions as well as using both mean and variance. A t- statistic can reflect both the mean and variance of the distribution.

[00273] In some implementations, operation 726 calculates a t-statistic as follows:

[00275] where x ₁ is the bin coverage of the sequence of interest, x ₂ being the bin coverage of the reference region/sequence, si being the standard deviation of the coverages of the sequence of interest, s ₂ being the standard deviation of the coverages of the reference region, ni being the number of bins of the sequence of interest; and n ₂ being the number of the bins of the reference region.

[00276] In some implementations, the reference region includes all robust chromosomes (e.g., chromosomes other than those most likely to harbor an aneuploidy). In some implementations, the reference region includes at least one chromosome outside of the sequence of interest. In some imitations, the reference region includes robust chromosomes not including the sequence of interest. In other implementations, the reference region includes a set of chromosomes (e.g., a subset of chromosomes selected from the robust chromosomes) that have been determined to provide the best signal detection ability for a set of training samples. In some embodiments, the signal detection ability is based on the ability of the reference region to discriminate bins harboring copy number variations from bins that do not harbor copy number variations. In some embodiments, the reference region is identified in a manner similar to that employed to determine a "normalizing sequence" or a "normalizing chromosome" as described in the section titled "Identification of Normalizing Sequences."

[00277] Returning to Figure 2E, one or more fetal fraction estimates (block

735) may be combined with any of the t statistics in block 726, 730 and 734 to obtain a likelihood estimate for a ploidy case. See block 736. In some implementations, the one or more fetal fractions of block 740 are obtained by any of process 800 in Figures 2G, process 900 in Figure 2H, or process 1000 of Figure 21. The processes may be implemented in parallel using a workflow as workflow 1100 in Figure 2 J.

[00278] Figure 2G shows an example process 800 for determining fetal fraction from coverage information according to some implementations of the disclosure. Process 800 starts by obtaining coverage information (e.g., sequence dose values) of training samples from a training set. See block 802. Each sample of the training set is obtained from a pregnant woman known to be carrying a male fetus. Namely, the sample contains cfDNA of the male fetus. In some implementations, operation 802 may obtain sequence coverage normalized in ways different from sequence dose as described herein, or it may obtain other coverage values.

[00279] Process 800 then involves calculating fetal fractions of the training samples. In some implementations, fetal fraction may be calculated from the sequence dose values:

[00281] where Rx _j is the sequence dose for a male sample, medi (Rx ) being the median of the sequence doses for female samples. In other implementations, mean or other central tendency measures may be used. In some implementations, the FF may be obtained by other methods, such as the relative frequency of X and Y chromosomes. See block 804.

[00282] Process 800 further involves dividing the reference sequence into multiple bins of subsequences. In some implementations, the reference sequence is a complete genome. In some implementations, the bins are 100 kb bins. In some implementations, the genome is divided into about 25,000 bins. The process then obtains coverages of the bins. See block 806. In some implementations, the coverages used in block 806 are obtained after undergoing normalizing operations shown in block 1123 of Figure 2J. In other implementations, coverages from different size range may be used.

[00283] Each bin is associated with coverages of the samples in the training set. Therefore, for each bin a correlation may be obtained between the coverage of the samples and the fetal fractions of the samples. Process 800 involves obtaining correlations between fetal fraction and coverage for all the bins. See block 808. Then the process selects the bins having correlation values above a threshold. See block 810. In some implementations, bins having the 6000 highest correlation values are selected. The purpose is to identify bins that demonstrate high correlation between coverage and fetal fraction in the training samples. Then the bins may be used to predict fetal fraction in the test sample. Although the training samples are male samples, the correlation between fetal fraction and coverage may be generalized to male and female test samples. [00284] Using the selected bins having high correlation values, the process obtains a linear model relating fetal fraction to coverage. See block 812. Each selected bin provides an independent variable for the linear model. Therefore, the obtained linear model also includes a parameter or weight for each bin. The weights of the bins are adjusted to fit the model to the data. After obtaining the linear model, process 800 involves applying coverage data of the test sample to the model to determine the fetal fraction for the test sample. See block 814. The applied coverage data of the test sample are for the bins that have high correlations between fetal fraction and coverage. [00285] Figure 2 J shows workflow 1100 for processing sequence reads information of which can be used to obtain fetal fraction estimates. The workflow 1100 shares similar processing steps as workflow 600 in Figure 2D. Blocks 1102, 1104, 1106, 1110, 1112, 1123, 1114, 1116, 1118, and 1122 respectively correspond to blocks 602, 604, 606, 610, 612, 623, 614, 616, 618, and 622. In some implementations, one or more normalizing operations in the 123 block are optional. Pass 1 provides coverage information, which may be used in block 806 of process 800 shown in Figure 2G. Process 800 then can yield a fetal fraction estimate 1150 in Figure 2J.

[00286] In some implementations, a plurality of fetal fraction estimates (e.g., 1150 and 1152 in Figure 2J) may be combined to provide a composite fetal fraction estimate (e.g., 1154). Various methods may be used to obtain fetal fraction estimates.

For instance, fetal fraction may be obtained from coverage information. See block

1150 of Figure 2J and process 800 of Figure 2G. In some implementations, fetal fraction can also be estimated from size distribution of fragments. See block 1152 of Figure 2J and process 900 of Figure 2H. In some implementations, fetal fraction can also be estimated from 8-mer frequency distribution. See block 1152 of Figure 2J and process 1000 of Figure 21.

[00287] In a test sample including cfDNA of male fetus, fetal fraction may also be estimated from the coverage of the Y chromosome and/or the X chromosome. In some implementations, a composite estimate of fetal fraction (see, e.g., block 1155) for a putatively male fetus is obtained by using information selected from the group consisting of: a fetal fraction obtained from coverage information of bins, a fetal fraction obtained from fragment size information, a fetal fraction obtained from coverage of the Y chromosome, a fetal fraction obtained from the X chromosome, and any combinations thereof. In some implementations, the putative sex of the fetus is obtained by using the coverage of the Y chromosome. Two or more fetal fractions (e.g., 1150 and 1152) may be combined in various ways to provide a composite estimate of fetal fraction (e.g., 1155). For instance, an average or a weighted average approach may be used in some implementations, wherein weighting can be based on the statistical confidence of the fetal fraction estimate.

[00288] In some implementations, a composite estimate of fetal fraction for a putatively female fetus is obtained by using information selected from the group consisting of: a fetal fraction obtained from coverage information of bins, a fetal fraction obtained from fragment size information, and any combinations thereof.

[00289] Figure 2H shows a process for determining fetal fraction from size distribution information according to some implementations. Process 900 starts by obtaining coverage information (e.g., sequence dose values) of male training samples from a training set. See block 902. Process 900 then involves calculating fetal fractions of the training samples using methods described above with reference to block 804. See block 904.

[00290] Process 900 proceeds to divide a size range into a plurality of bins to provide fragment-size-based bins and determine frequencies of reads for the fragment-size-based bins. See block 906. In some implementations, the frequencies of fragment-size-based bins are obtained without normalizing for factors shown in block 1123. See path 1124 of Figure 2J. In some implementations, the frequencies of fragment-size-based bins are obtained after optionally undergoing normalizing operations shown in block 1123 of Figure 2J. In some implementations, the size range is divided into 40 bins. In some implementations, the bin at the low end includes fragments of size smaller than about 55 base pairs. In some implementations, the bin at the low end includes fragments of size in the range of about 50-55 base pairs, which excludes information for reads shorter than 50 bp. In some implementations, the bin at the high end includes fragments of size larger than about 245 base pairs. In some implementations, the bin at the high end includes fragments of size in the range of about 245-250 base pairs, which excludes information for reads longer than 250 bp. [00291] Process 900 proceeds by obtaining a linear model relating fetal fraction to frequencies of reads for the fragment-size-based bins, using data of the training samples. See block 908. The obtained linear model includes independent variables for the frequencies of reads of the size-based bins. The model also includes a parameter or weight for each size-based bin. The weights of the bins are adjusted to fit the model to the data. After obtaining the linear model, process 900 involves applying read frequency data of the test sample to the model to determine the fetal fraction for the test sample. See block 910.

[00292] In some implementations, an 8-mer frequency may be used to calculate fetal fraction. Figure 21 shows an example process 1000 for determining fetal fraction from 8-mer frequency information according to some implementations of the disclosure. Process 1000 starts by obtaining coverage information (e.g., sequence dose values) of male training samples from a training set. See block 1002. Process 1000 then involves calculating fetal fractions of the training samples using any of the methods described for block 804. See block 1004.

[00293] Process 1000 further involves obtaining the frequencies of 8-mers

(e.g., all possible permutations of 4 nucleotides at 8 positions) from the reads of each training sample. See block 1006. In some implementations, up to 65,536 or close to that many 8-mers and their frequencies are obtained. In some implementations, the frequencies of 8-mers are obtained without normalizing for factors shown in block 1123. See path 1124 of Figure 2J. In some implementations, 8-mer frequencies are obtained after optionally undergoing normalizing operations shown in block 1123 of Figure 2J.

[00294] Each 8-mer is associated with frequencies of the samples in the training set. Therefore, for each 8-mer a correlation may be obtained between the 8- mer frequency of the samples and the fetal fractions of the samples. Process 1000 involves obtaining correlations between fetal fraction and 8-mer frequencies for all the 8-mers. See block 1008. Then the process selects the 8-mers having correlation values above a threshold. See block 1010. The purpose is to identify 8-mers that demonstrate high correlation between 8-mer frequency and fetal fraction in the training samples. Then the bins may be used to predict fetal fraction in the test sample. Although the training samples are male samples, the correlation between fetal fraction and 8-mer frequency may be generalized to male and female test samples.

[00295] Using the selected 8-mers having high correlation values, the process obtains a linear model relating fetal fraction to 8-mer frequency. See block 1012. Each selected bin provides an independent variable for the linear model. Therefore, the obtained linear model also includes a parameter or weight for each bin. After obtaining the linear model, process 1000 involves applying 8-mer frequency data of the test sample to the model to determine the fetal fraction for the test sample. See block 1014.

[00296] Returning to Figure 2E, in some implementations, process 700 involves obtaining a final ploidy likelihood in operation 736 using the t-statistic based on the coverage of all fragments provided by operation 726, the fetal fraction estimate provided by operation 726, and the t-statistic based on the coverage of the short fragments provided by operation 730. These implementations combine the results from pass 1 and pass 2 using a multivariate normal models. In some implementations for evaluating CNV, the ploidy likelihood is an aneuploidy likelihood, which is a likelihood of a model having an aneuploid assumption (e.g., trisomy or monosomy) minus the likelihood of a model having an euploid assumption wherein the model uses the t-statistic based on the coverage of all fragments, the fetal fraction estimate, and the t-statistic based on the coverage of the short fragments as an input and provides a likelihood as an output.

[00297] In some implementations, the ploidy likelihood is expressed as a likelihood ratio. In some implementations, likelihood ratio is modeled as:

∑ff _total <l(ff total)*Vi (J short? all \ff est)

[00298] LR =

Vo(J short? all)

[00299] Wwhere pi represents the likelihood that data come from a multivariate normal distribution representing a 3-copy or 1-copy model, po represents the likelihood that data come from a multivariate normal distribution representing a 2- copy model, T _S hort, T _all are T scores calculated from chromosomal coverage generated from short and all fragments, while q(ff total) being the density distribution of fetal fraction (estimated from training data) considering the error associated with fetal fraction estimation. The model combine coverage generated from short fragments with coverage generated by all fragments, which helps improving separation between coverage scores of affected and unaffected samples. In the depicted embodiment, the model also makes use of fetal fraction, thereby further improves the ability to discriminate between affected and unaffected samples. Here, the likelihood ratio is calculated using t-statistic based on coverage of all fragments (726), t-statistic based on coverage of short fragments (730), and a fetal fraction estimate provided by processes 800 (or block 726), 900, or 1000 as described above. In some implementations, this likelihood ratio is used to analyze chromosomes 13, 18, and 21.

[00300] some implementation, a ploidy likelihood obtained by operation 736 uses only the t-statistics obtained based on relative frequency of short fragments provided by operation 734 of pass 3 and the fetal fraction estimate provided by operation 726, processes 800, 900, or 1000. The likelihood ratio may be calculated according to the following equation:

∑ff total q(fftotad*Pl {Tshort_ freq West)

[00301] LR =

Po(T short Jreq)

[00302] where pi represents the likelihood that data come from a multivariate normal distribution representing a 3-copy or 1-copy model, po represents the likelihood that data come from a multivariate normal distribution representing a 2- copy model, T _S hort-freq is a T score calculated from relative frequency of short fragments, while q(ff total) being the density distribution of fetal fraction (estimated from training data) considering the error associated with fetal fraction estimation. Here, the likelihood ratio is calculated using t-statistic based on relative frequency of short fragments (734) and a fetal fraction estimate provided by processes 800 (or block 726), 900, or 1000 as described above. In some implementations, this likelihood ratio is used to analyze chromosome X.

[00303] In some implementations, the likelihood ratio is calculated using t- statistic based on coverage of all fragments (726), t-statistic based on coverage of short fragments (730), and relative frequency of short fragments (734). Moreover, fetal fraction obtained as describe above may be combined with t-statistics to calculate likelihood ration. By combining information from any of the three passes 713A, 713B, and 713C, the discriminative ability of the ploidy evaluation can be improved. See, e.g., Example 2 and Figure 12. In some implementations, different combinations may be used to obtain likelihood ratios for a chromosome, e.g., t statistics from all three passes, t statistics from the first and second passes, fetal fraction and three t-statistics, fetal fraction and one t statistic, etc. Then an optimal combination can be selected based on the models performance.

[00304] In some implementations for evaluating autosomes, the modeled likelihood ratio represents the likelihood of the modeled data having been obtained from a trisomy or monosomy sample relative to the likelihood of the modeled data having been obtained from a diploid sample. Such likelihood ratio may be used to determine trisomy or monosomy of the autosomes in some implementations.

[00305] In some implementations for evaluating the sex chromosome, the likelihood ratio for monosomy X and the likelihood ratio for trisomy X are evaluated. Moreover, a chromosome coverage measurement (e.g., CNV or coverage z score) for chromosome X and one for chromosome Y are also evaluated. In some implementations, the four values are evaluated using a decision tree to determine copy number of the sex chromosome. In some implementations, the decision tree allows determination of a ploidy case of XX, XY, X, XXY, XXX, or XYY. [00306] In some implementations, the likelihood ratio is transformed into a log likelihood ratio, and a criterion or threshold for calling an aneuploidy or a copy number variation can be empirically set to obtain a particular sensitivity and selectivity. For instance, a log likelihood ratio of 1.5 may be set for calling a trisomy 13 or a trisomy 18 based on a model's sensitivity and selectivity when applied to a training set. Moreover, for instance, a call criterion value of 3 may be set for a trisomy of chromosome 21 in some applications.

Details of an Exemplary Process for Determining Sequence

Coverage

[00307] Figure 3A presents an example of a process 301 for reducing the noise in sequence data from a test sample. Figures 3B-3J present data analyses at various stages of the process. This provides one example of a process flow that may be used in a multipass process such as depicted in Figure 2D.

[00308] Process 301 illustrated in Figure 3A uses sequence tag coverage based on the number of sequence tags to evaluate copy number. However, similar to the description above regarding process 100 for determining CNV with reference to Figure 1, other variables or parameters, such as size, size ratio, and methylation level, may be used instead of coverage for process 400. In some implementations, two or more variables can separately undergo the same process to derive two scores indicative of probability of CNV, as shown above with reference to Figure 2D. Then the two scores may be combined to determine a CNV. Furthermore, coverage and other parameters may be weighted based on the size of the fragments from which tags are derived. For ease of reading, only coverage is referred to in process 300, but one should note that other parameters, such as size, size ratio, and methylation level, count weighted by size, etc. may be used in place of coverage.

[00309] As shown in Figure 3A, the depicted process begins with extraction of cfDNA from one or more samples. See block 303. Suitable extraction processes and apparatus are described elsewhere herein. In some embodiments, a process described in US Patent Application No. 61/801,126, filed March 15, 2013 (incorporated herein by reference in its entirety) extracts cfDNA. In some implementations, the apparatus processes cfDNA from multiple samples together to provide multiplexed libraries and sequence data. See blocks 305 and 307 in Figure 3A. In some embodiments, the apparatus processes cfDNA from eight or more test samples in parallel. As described elsewhere herein, a sequencing system may process extracted cfDNA to produce a library of coded (e.g., bar coded) cfDNA fragments. A sequencer sequences library of cfDNA to produce a very large number of sequence reads. Per sample coding allows demultiplexing of the reads in multiplexed samples. Each of the eight or more samples may have hundreds of thousands or millions of reads. The process may filter the reads prior to additional operations in Figure 3A. In some embodiments, read filtering is a quality-filtering process enabled by software programs implemented in the sequencer to filter out erroneous and low quality reads. For example, Illumina' s Sequencing Control Software (SCS) and Consensus Assessment of Sequence and Variation software programs filter out erroneous and low quality reads by converting raw image data generated by the sequencing reactions into intensity scores, base calls, quality scored alignments, and additional formats to provide biologically relevant information for downstream analysis.

[00310] After the sequencer or other apparatus generates the reads for a sample, an element of the system computationally aligns the reads to a reference genome. See block 309. Alignment is described elsewhere herein. The alignment produces tags, which contain read sequences with annotated location information specifying unique positions on the reference genome. In certain implementations, the system conducts a first pass alignment without regard for duplicate reads - two or more reads having identical sequences - and subsequently removes duplicated reads or counts duplicate reads as a single read to produce non-duplicated sequence tags. In other implementations, the system does not remove duplicated reads. In some embodiments, the process removes from consideration reads that are aligned to multiple locations on the genome to produce uniquely aligned tags. In some embodiments, uniquely aligned, non-redundant sequence tags mapped to non- excluded sites (NESs) are accounted for to yield non-excluded site counts (NES counts), which provide data to estimate coverage. [00311] As explained elsewhere, excluded sites are sites found in regions of a reference genome that have been excluded for the purpose of counting sequence tags. In some embodiments, excluded sites are found in regions of chromosomes that contain repetitive sequences, e.g., centromeres and telomeres, and regions of chromosomes that are common to more than one chromosome, e.g., regions present on the Y-chromosome that are also present on the X chromosome. Non-excluded sites (NESs) are sites that are not excluded in a reference genome for the purpose of counting sequence tags.

[00312] Next, the system divides the aligned tags into bins on the reference genome. See block 311. The bins are spaced along the length of the reference genome. In some embodiments, the entire reference genome is divided into contiguous bins, which may have defined equal size (e.g., 100 kb). Alternatively, the bins may have a length determined dynamically, possibly on a per-sample basis. Sequencing depth impacts optimal bin size selection. Dynamically sized bins may have their size determined by the library size. For example, the bin size may be determined to be the sequence length required to accommodate 1000 tags, on average.

[00313] Each bin has a number of tags from a sample under consideration.

This number of tags, which reflects the "coverage" of the aligned sequence, serves as a starting point for filtering and otherwise cleaning the sample data to reliably determine copy number variation in the sample. Figure 3A shows the cleaning operations in blocks 313 to 321.

[00314] In the embodiment depicted in Figure 3A, the process applies a mask to the bins of the reference genome. See block 313. The system may exclude coverage in masked bins from consideration in some or all of the following process operations. In many cases, coverage values from masked bins are not considered any of the remaining operations in Figure 3 A.

[00315] In various implementations, one or more masks are applied to remove bins for regions of the genome found to exhibit high variability from sample to sample. Such masks are provided for both chromosomes of interest (e.g., chrl3, 18, and 21) and other chromosomes. As explained elsewhere, a chromosome of interest is the chromosome under consideration as potentially harboring a copy number variation or other aberration. [00316] In some implementations, masks are identified from a training set of qualified samples using the following approach. Initially, each training set sample is processed and filtered according to operations 315 through 319 in Figure 3 A. The normalized and corrected coverage quantities are then noted for each bin and statistics such as standard deviation, median absolute deviation, and/or coefficient of variation are calculated for each bin. Various filter combinations may be evaluated for each chromosome of interest. The filter combinations provide one filter for the bins of the chromosome of interest and a different filter for the bins of all other chromosomes.

[00317] In some implementations, the choice of a normalizing chromosome (or group of chromosomes) is reconsidered after obtaining masks (e.g., by choosing cut- offs for a chromosome of interest as described above). After applying the sequence mask, the process of choosing a normalizing chromosome or chromosomes may be conducted as described elsewhere herein. For example, all possible combinations of chromosomes are evaluated as normalizing chromosomes and ranked according to their ability to discriminate affected and unaffected samples. This process may (or may not) find a different optimal normalizing chromosome or group of chromosomes. In other embodiments, normalizing chromosomes are those that result in the smallest variability in sequence dose for the sequence of interest across all qualified samples. If a different normalizing chromosome or group of chromosomes is identified, the process optionally executes the above described identification of bins to filter. Possibly the new normalizing chromosome(s) result in different cut-offs.

[00318] In certain embodiments, a different mask is applied for chromosome Y.

An example of a suitable chromosome Y mask is described in US Provisional Patent Application No. 61/836,057, filed June 17, 2013 [attorney docket no. ARTEP008P], which is incorporated herein by reference for all purposes.

[00319] After the system computationally masks the bins, it computationally normalizes the coverage values in the bins that are not excluded by the masks. See block 315. In certain embodiments, the system normalizes the test sample coverage values in each bin (e.g., NES counts per bin) against most or all of the coverage in reference genome or a portion thereof (e.g., the coverage in the robust chromosomes of the reference genome). In some cases, the system normalizes the test sample coverage values (per bin) by dividing the count for the bin under consideration by the total number of all non-excluded sites aligning to all robust chromosomes in the reference genome. In some embodiments, the system normalizes the test sample coverage values (per bin) by performing a linear regression. For instance, the system first calculates coverages for a subset of bins in robust chromosomes as y _a = intercept + slope * gwp _a , where y _a is coverage for bin a, and gwp _a is the global profile for the same bin. The system then calculates the normalized coverages Z as: Z = y _b / (intercept + slope * gwp _b ) - 1.

[00320] As explained above, a robust chromosome is one that is unlikely to be aneuploid. In certain embodiments, the robust chromosomes are all autosomal chromosomes other than chromosomes 13, 18, and 21. In some embodiments, the robust chromosomes are all autosomal chromosomes other than chromosomes determined to deviate from a normal diploid genome.

[00321] A bin's transformed count value or coverage is referred to as a "normalized coverage quantity" for further processing. The normalization is performed using information unique to each sample. Typically, no information from a training set is used. Normalization allows coverage quantities from samples having different library sizes (and consequently different numbers of reads and tags) to be treated on equal footing. Some of the subsequent process operations use coverage quantities derived from training samples which may be sequenced from libraries that are larger or smaller than the libraries used for a test sample under consideration. Without normalization based on the number of reads aligned to the entire reference genome (or at least the robust chromosomes), treatment using parameters derived from a training set might not be reliable or generalizable in some implementations. [00322] Figure 3B illustrates the coverage across chromosomes 21, 13, and 18 for many samples. Some of the samples were processed differently from one another. As a consequence, one can see a wide sample-to- sample variation at any given genomic position. Normalization removes some of the sample-to-sample variation. The left panel of Figure 3C depicts normalized coverage quantities across an entire genome.

[00323] In the embodiment of Figure 3A, the system removes or reduces a

"global profile" from the normalized coverage quantities produced in operation 315. See block 317. This operation removes systematic biases in the normalized coverage quantities arising from the structure of the genome, the library generation process, and the sequencing process. In addition, this operation is designed to correct for any systematic linear deviation from the expected profile in any given sample.

[00324] In some implementations, the global profile removal involves dividing the normalized coverage quantity of each bin by a corresponding expected value of each bin. In other embodiments, the global profile removal involves subtracting an expected value of each bin from the normalized coverage quantity of each bin. The expected value may be obtained from a training set of unaffected samples (or unaffected female samples for the X chromosome). Unaffected samples are samples from individuals known not to have an aneuploidy for the chromosome of interest. In some implementations, the global profile removal involves subtracting the expected value of each bin (obtained from a training set) from the normalized coverage quantity of each bin. In some embodiments, the process uses median values of normalized coverage quantities for each bin as determined using the training set. In other words, the median values are the expected values. [00325] In some embodiments, the global profile removal is implemented using a linear correction for the dependence of the sample coverage on the global profile. As indicated, the global profile is an expected value for each bin as determined from the training set (for example the median value for each bin). These embodiments may employ a robust linear model obtained by fitting the test sample's normalized coverage quantities against the global median profile obtained for each bin. In some embodiments, the linear model is obtained by regressing the sample's observed normalized coverage quantities against the global median (or other expectation value) profile. [00326] The linear model is based on an assumption that sample coverage quantities have a linear relationship with the global profile values, which linear relationship should hold for both robust chromosomes/regions and a sequence of interest. See Figure 3D. In such case, a regression of the sample normalized coverage quantities on the global profile's expected coverage quantities will produce a line having a slope and intercept. In certain embodiments, the slope and intercept of such line is used to calculate a "predicted" coverage quantity from the global profile value for a bin. In some implementations, a global profile correction involves modeling each bin's normalized coverage quantity by the predicted coverage quantities for the bin. In some implementations, coverages of the test sequence tags are adjusted by: (i) obtaining a mathematical relation between the coverage of the test sequence tags versus the expected coverage in a plurality of bins in one or more robust chromosomes or regions, and (ii) applying the mathematical relation to bins in the sequence of interest. In some implementations, the coverages in a test sample are corrected for variation using a linear relationship between the expected coverage values from unaffected training samples and coverage values for the test sample in robust chromosomes or other robust regions of the genome. The adjustment results in global-profile-corrected coverages. In some cases, the adjustment involves obtaining coverages for a test sample for a subset of bins in robust chromosomes or regions as follows: y _a = intercept + slope * gwp _a where ya is coverage of bin a for the test sample in one or more robust chromosomes or regions, and gwpa is the global profile for bin a for unaffected training samples. The process then computes a global-profile-corrected coverage zb for a sequence or region of interest as: zb = yb / (intercept + slope * gwpb) - 1 where yb is the observed coverage of bin b for the test sample in the sequence of interest (which may reside outside a robust chromosome or region), and gwpb is the global profile for bin b for unaffected training samples. The denominator (intercept + slope * gwpb) is the coverage for bin b that is predicted to be observed in unaffected test samples based on the relationship estimated from robust regions of the genome. In the case of a sequence of interest harboring a copy number variation, the observed coverage and hence the global-profile-corrected coverage value for bin b will deviate significantly from the coverage of an unaffected sample. For example, the corrected coverage zb would be proportional to fetal fraction in the case of trisomic sample for bins on the affected chromosome. This process normalizes within sample by computing intercept and slope on robust chromosomes, and then evaluates how the genomic region of interest deviates from a relationship (as described by the slope and the intercept) that holds for robust chromosomes within the same sample.

[00327] The slope and intercept are obtained from a line as shown in Figure

3D. An example of global profile removal is depicted in Figure 3C. The left panel shows a high bin-to-bin variation in normalized coverage quantities across many samples. The right panel shows the same normalized coverage quantities after global profile removal as described above.

[00328] After the system removes or reduces the global profile variations at block 317, it corrects for in-sample GC (guanine-cytosine) content variations. See block 319. Every bin has its own fractional contribution from GC. The fraction is determined by dividing the number of G and C nucleotides in a bin by the total number of nucleotides in a bin (e.g., 100,000). Some bins will have greater GC fractions than others. As shown in Figures 3E and 3F, different samples exhibit different GC biases. These differences and their corrections will be explained further below. Figures 3E-G show global profile corrected, normalized coverage quantity (per bin) as a function of GC fraction (per bin). Surprisingly, different samples exhibit different GC dependence. Some samples show monotonically decreasing dependence (as in Figure 3E), while others exhibit a comma shaped dependence (as in Figure 3F and 3G). Because these profiles may be unique for each sample, the correction described in this step is performed separately and uniquely for each sample.

[00329] In some embodiments, the system computationally arranges bins on the basis of GC fraction as illustrated in Figures 3E-G. It then corrects the global profile corrected, normalized coverage quantity of a bin using information from other bins with similar GC contents. This correction is applied to each unmasked bin.

[00330] In some processes, each bin is corrected for GC content in the following way. The system computationally selects bins having GC fractions similar to those of a bin under consideration and then determines a correction parameter from information in the selected bins. In some embodiments, those bins having similar GC fractions are selected using an arbitrarily defined cut-off value of similarity. In one example, 2% of all bins are selected. These bins are the 2% having GC content bins most similar to the bin under consideration. For example, the 1% of bins having slightly more GC content and 1% having slightly less GC content are selected.

[00331] Using the selected bins, the system computationally determines a correction parameter. In one example, the correction parameter is a representative value of the normalized coverage quantities (after global profile removal) in the selected bins. Examples of such representative value include the median or mean of the normalized coverage quantities in the selected bins. The system applies a calculated correction parameter for a bin under consideration to the normalized coverage quantity (after global profile removal) for the bin under consideration. In some implementations, a representative value (e.g., median value) is subtracted from the normalized coverage quantity of the bin under consideration. In some embodiments, the median value (or other representative value) of normalized coverage quantities is selected using only the coverage quantities for robust autosomal chromosomes (all autosomes other than chromosomes 13, 18, and 21).

[00332] In one example using, e.g., lOOkb bins, each bin will have a unique value of GC fraction, and the bins are divided into groups based on their GC fraction content. For example, the bins are divided into 50 groups, where group boundaries correspond to (0, 2, 4, 6, and 100) quantiles of the %GC distribution. A median normalized coverage quantity is calculated for each group of bins from the robust autosomes mapping to the same GC group (in the sample), and then the median value is subtracted from the normalized coverage quantities (for all bins across the entire genome in the same GC group). This applies a GC correction estimated from robust chromosomes within any given sample to the potentially affected chromosomes within the same sample. For example, all bins on robust chromosomes having a GC content between 0.338660 and 0.344720 are grouped together, the median is calculated for this group and is subtracted from the normalized coverage of the bins within this GC range, which bins may be found anywhere on the genome (excluding chromosomes 13, 18, 21, and X). In certain embodiments, chromosome Y is excluded from this GC correction process. [00333] Figure 3G shows application of a GC correction using median normalized coverage quantities as a correction parameter as just described. The left panel shows the uncorrected coverage quantities versus GC fraction profile. As shown, the profile has a non-linear shape. The right panel shows the corrected coverage quantities. Figure 3H shows the normalized coverages for many samples before GC fraction correction (left panel) and after GC fraction correction (right panel). Figure 31 shows the coefficient of variation (CV) of the normalized coverages for many test samples before GC fraction correction (red) and after GC fraction correction (green), where GC correction leads to substantially smaller variation in normalized coverages.

[00334] The above process is a relatively simple implementation of the GC correction. Alternative approaches to correcting for GC bias employ a spline or other non-linear fitting technique, which may be applied in the continuous GC space and does not involve binning coverage quantities by GC content. Examples of suitable techniques include continuous loess correction and smooth spline correction. A fitting function may be derived from bin-by-bin normalized coverage quantity versus GC content for the sample under consideration. The correction for each bin is calculated by applying the GC content for bin under consideration to the fitting function. For instance, the normalized coverage quantity may be adjusted by subtracting the expected coverage value of a spline at the GC content of the bin under consideration. Alternatively, the adjustment may be achieved by division of the expected coverage value according to the spline fit.

[00335] After correcting the GC-dependence in operation 319, the system computationally removes outlier bins in sample under consideration -See block 321. This operation may be referred to as single sample filtering or trimming. Figure 3J shows that even after GC correction, the coverage still has sample-specific variation within small regions. See for example the coverage at position 1.1 e8 on chromosome 12 where an unexpectedly high deviation from the expected value results. It is possible that this deviation results from a small copy number variation in the material genome. Alternatively, this may be due to technical reasons in sequencing unrelated to copy number variation. Typically, this operation is only applied to the robust chromosomes. [00336] As one example, the systems computationally filters any bins having a

GC corrected normalized coverage quantity of more than 3 median absolute deviations from the median of the GC corrected normalized coverage quantity across all bins in the chromosome harboring the bin under consideration for filtering. In one example, the cut-off value is defined as 3 median absolute deviations adjusted to be consistent with the standard deviation, so actually the cut-off is 1.4826*median absolute deviations from the median. In certain embodiments, this operation is applied to all chromosomes in the sample, including both the robust chromosomes and the chromosomes suspected of aneuploidy. [00337] In certain implementations, an additional operation which may be characterized as quality control is performed. See block 323. In some embodiments, a quality control metric involves detection of whether any potential denominator chromosomes i.e. "normalizing chromosomes" or "robust chromosomes" are aneuploid or otherwise inappropriate for determining whether the test sample has a copy number variation in a sequence of interest. When the process determines that a robust chromosome is inappropriate, the process may disregard the test sample and make no call. Alternatively, a failure of this QC metric may trigger use of an alternate set of normalizing chromosomes for calling. In one example, a quality control method compares actual normalized coverage values for robust chromosomes against expectation values for robust autosomal chromosomes. The expectation values can be obtained by fitting a multivariate normal model to the normalized profiles of unaffected training samples, selecting the best model structure according to the likelihood of the data or Bayesian criteria (e.g., the model is selected using Akaike information criterion or possibly Bayesian information criterion), and fixing the best model for use in QC. The normal models of the robust chromosomes can be obtained by, for example, using a clustering technique that identifies a probability function having a mean and standard deviation for the chromosome coverages in the normal samples. Of course, other model forms may be used. The process evaluates the likelihood of observed normalized coverage in any incoming test sample given the fixed model parameters. It may do this by scoring each incoming test sample with the model to obtain likelihood and thereby identify outliers relative to normal sample set. Deviation in the likelihood of the test sample from that of the training samples may suggest either an abnormality in normalizing chromosomes or a sample handling / assay processing artifact that may result in incorrect sample classification. This QC metric can be used to reduce errors in classification associated with either of these sample artifacts. Figure 3K, right panel, shows on the x-axis chromosome number and the y-axis shows normalized chromosome coverage based on a comparison with a QC model obtained as described above. The graphs shows one sample with an excessive coverage for chromosome 2 and other sample with an excessive coverage for chromosome 20. These samples would be eliminated using the QC metric described here or diverted to use an alternate set of normalizing chromosomes. The left panel of Figure 3K shows NCV versus likelihood for a chromosome. [00338] The sequence depicted in Figure 3 A may be used for all bins of all chromosomes in the genome. In certain embodiments, a different process is applied to chromosome Y. To calculate chromosome or segment dose, NCV, and/or NSV, the corrected normalized coverage quantities (as determined in Figure 3A) from bins in the chromosomes or segments used in the expressions for dose, NCV, and/or NSV are used. See block 325. In certain embodiments, a mean normalized coverage quantity is calculated from all bins in a chromosome of interest, normalizing chromosome, segment of interest, and/or normalizing segment is used to calculate sequence dose, NCV, and/or NSV as described elsewhere herein.

[00339] In certain embodiments, chromosome Y is treated differently. It may be filtered by masking a set of bins unique to the Y chromosome. In some embodiments, the Y chromosome filter is determined according the process in US

Provisional Patent Application No. 61/836,057, previously incorporated by reference.

In some embodiments, the filter masks bins that are smaller than those in the filter of the other chromosomes. For example, the Y chromosome mask may filter at the 1 kb level, while the other chromosome masks may filter at the 100 kb level. Nevertheless, the Y chromosome may be normalized at the same bin size as the other chromosomes

(e.g., 100 kb).

[00340] In certain embodiments, the filtered Y chromosome is normalized as described above in operation 315 of Figure 3 A. However, otherwise, the Y chromosome is not further corrected. Thus, the Y chromosome bins are not subjected to global profile removal. Similarly, the Y chromosome bins are not subjected to GC correction or other filtering steps performed thereafter. This is because when the sample is processed, the process does not know whether the sample is male or female. A female sample should have no reads aligning to the Y reference chromosome.

Creating a Sequence Mask

[00341] Some embodiments disclosed herein employ a strategy for filtering out (or masking) non-discriminant sequence reads on a sequence of interest using sequence masks, which leads to higher signal and lower noise, relatively to values calculated by conventional methods, in the coverage values used for CNV evaluation. Such masks can be identified by various techniques. In one embodiment, a mask is identified using a technique illustrated in Figures 4A-4B as explained below in further details.

[00342] In some implementations, the mask is identified using a training set of representative samples known to have normal copy number of the sequence of interest. Masks may be identified using a technique that first normalizes the training set samples, then corrects for systematic variation across a range of sequence (e.g., a profile), and then corrects them for GC variability as described below. The normalization and correction are performed on samples from a training set, not test samples. The mask is identified once and then applied to many test samples.

[00343] Figure 4A shows a flow chart of a process 400 for creating such a sequence mask, which can be applied to one or more test samples to remove bins on a sequence of interest from consideration in evaluation of copy number. Process 400 illustrated in Figure 4 uses sequence tag coverage based on the number of sequence tags to obtain a sequence mask. However, similar to the description above regarding process 100 for determining CNV with reference to Figure 1, other variables or parameters, such as size, size ratio, and methylation level, may be used in addition to or instead of coverage for process 400. In some implementations, one mask is generated for each of two or more parameters. Furthermore, coverage and other parameters may be weighted based on the size of the fragments from which tags are derived. For ease of reading, only coverage is referred to in process 400, but one should note that other parameters, such as size, size ratio, and methylation level, count weighted by size, etc. may be used in the place of coverage.

[00344] Process 400 starts by providing a training set including sequence reads from a plurality of unaffected training samples. Block 402. The process then align the sequence reads of the training set to a reference genome comprising the sequence of interest, thereby providing training sequence tags for the training samples. Block 404. In some embodiments, only uniquely aligned non-redundant tags mapped to non-excluded sites are used for further analysis. The process involves dividing the reference genome into a plurality of bins and determining for each unaffected training sample a coverage of training sequence tags in each bin for each training sample. Block 406. The process also determines for each bin an expected coverage of the training sequence tags across all training samples. Block 408. In some embodiments, the expected coverage of each bin is the median or means across the training samples. The expected coverages constitutes a global profile. The process then adjust the coverage of the training sequence tags in each bin for each training sample by removing the variation in the global profile, thereby obtaining global-profile-corrected coverages of the training sequence tags in the bins for each training sample. The process then creates a sequence mask comprising unmasked and masked bins across the reference genome. Each masked bin has a distribution characteristic exceeding a masking threshold. The distribution characteristic is provided for the adjusted coverages of the training sequence tags in the bin across training samples. In some implementations, the masking threshold may relate to the observed variation in normalized coverage within a bin across training samples. Bins with high coefficients of variation or median absolute deviation of normalized coverage across samples may be identified based on an empirical distribution of the respective metrics. In some alternative implementations, the masking threshold may relate to the observed variation in normalized coverage within a bin across training samples. Bins with high coefficients of variation or median absolute deviation of normalized coverage across samples may be masked based on an empirical distribution of the respective metrics.

[00345] In some implementations, separate cut-offs for identifying masked bins, i.e., masking thresholds, are defined for the chromosome of interest and for all other chromosomes. Further, separate masking thresholds may be defined for each chromosome of interest separately, and a single masking threshold for the set of all non-affected chromosomes. As an example, a mask based on a certain masking threshold is defined for chromosome 13 and another masking threshold is used to define a mask for the other chromosomes. Non-affected chromosomes may also have their masking thresholds defined per chromosome. [00346] Various masking threshold combinations may be evaluated for each chromosome of interest. The masking threshold combinations provide one mask for the bins of the chromosome of interest and a different mask for the bins of all other chromosomes. [00347] In one approach, a range of values for coefficient of variation (CV) or measure of sample distribution cut-offs is defined as percentiles (e.g., 95, 96, 97, 98, 99) of the empirical distribution of bin CV values and these cut-off values are applied to all autosomes excluding chromosomes of interest. Further, a range of percentile cut-off values for CV is defined for the empirical CV distribution and these cut-off values are applied to a chromosome of interest (e.g., chr 21). In some embodiments, the chromosomes of interest are the X chromosome and chromosomes 13, 18, and 21. Of course, other approaches may be considered; for example, a separate optimization may be performed for each chromosome. Together, the ranges to be optimized in parallel (e.g., one range for a chromosome of interest under consideration and another range for all other chromosomes) define a grid of CV cut-off combinations. See Figure 4B. Performance of the system on the training set is evaluated across the two cut-offs (one for normalizing chromosomes (or autosomes other than the chromosome of interest) and one for chromosome of interest), and the best performing combination is chosen for final configuration. This combination may be different for each of the chromosomes of interest. In certain embodiments, performance is evaluated on a validation set instead of the training set, namely, cross-validation is used to evaluate performance.

[00348] In some embodiments, the performance optimized to determine cut-off ranges is the coefficient of variation of chromosome doses (based on a tentative selection of normalizing chromosomes). The process selects the combination of cutoffs that minimize the CV of the chromosome dose (e.g., ratio) of the chromosome of interest using a currently a selected normalizing chromosome (or chromosomes). In one approach, the process tests the performance of each combination of cut-offs in the grid as follows: (1) apply the combination of cut-offs to define masks for all chromosomes and apply those masks to filter the tags of a training set; (2) calculate normalized coverages across the training set of unaffected samples by applying the process of Figure 3 A to the filtered tags; (3) determine a representative normalized coverage per chromosome by, e.g., summing the bin's normalized coverages for a chromosome under consideration; (4) calculate chromosome doses using the current normalizing chromosomes, and (5) determine the CVs of the chromosome doses. The process may assess the performance of the selected filters by applying them to a set of test samples separated from an original portion of the training set. That is, the process splits the original training set into training and testing subsets. The training subset is used to define the mask cut-offs as described above.

[00349] In alternative embodiments, instead of defining masks based on CV of coverages, the masks may be defined by a distribution of mapping quality scores from the alignment results across training samples within the bins. A mapping quality score reflects the uniqueness with which a read is mapped to the reference genome. In other words, mapping quality scores quantify the probability that a read is misaligned. A low mapping quality score is associated low uniqueness (high probability of misalignment). The uniqueness accounts for one or more errors in the read sequence (as generated by the sequencer). A detailed description of mapping quality scores is presented in Li H, Ruan J, Durbin R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-8, which is incorporated herein by reference in its entirety. In some implementation, the mapping quality score herein is referred to as a MapQ score. Figure 4B shows that MapQ score has a strong monotonous correlation with CV of processed coverages. For instance, bins with CV higher than 0.4 almost completely cluster on the left of the plot in Figure 4B, having MapQ scores lower than about 4. Therefore, masking bins with small MapQ can yield a mask quite similar to one defined by masking bins with high CV.

Samples and Sample Processing Samples

[00350] Samples that are used for determining a CNV, e.g., chromosomal aneuploidies, partial aneuploidies, and the like, can include samples taken from any cell, tissue, or organ in which copy number variations for one or more sequences of interest are to be determined. Desirably, the samples contain nucleic acids that are that are present in cells and/or nucleic acids that are "cell-free" (e.g., cfDNA).

[00351] In some embodiments it is advantageous to obtain cell-free nucleic acids, e.g., cell-free DNA (cfDNA). Cell-free nucleic acids, including cell-free DNA, can be obtained by various methods known in the art from biological samples including but not limited to plasma, serum, and urine (see, e.g., Fan et al., Proc Natl Acad Sci 105: 16266-16271 [2008]; Koide et al., Prenatal Diagnosis 25:604-607 [2005]; Chen et al., Nature Med. 2: 1033-1035 [1996]; Lo et al., Lancet 350: 485-487 [1997]; Botezatu et al., Clin Chem. 46: 1078-1084, 2000; and Su et al., J Mol. Diagn. 6: 101-107 [2004]). To separate cell-free DNA from cells in a sample, various methods including, but not limited to fractionation, centrifugation (e.g., density gradient centrifugation), DNA-specific precipitation, or high-throughput cell sorting and/or other separation methods can be used. Commercially available kits for manual and automated separation of cfDNA are available (Roche Diagnostics, Indianapolis, IN, Qiagen, Valencia, CA, Macherey-Nagel, Duren, DE). Biological samples comprising cfDNA have been used in assays to determine the presence or absence of chromosomal abnormalities, e.g., trisomy 21, by sequencing assays that can detect chromosomal aneuploidies and/or various polymorphisms. [00352] In various embodiments the cfDNA present in the sample can be enriched specifically or non-specifically prior to use (e.g., prior to preparing a sequencing library). Non-specific enrichment of sample DNA refers to the whole genome amplification of the genomic DNA fragments of the sample that can be used to increase the level of the sample DNA prior to preparing a cfDNA sequencing library. Non-specific enrichment can be the selective enrichment of one of the two genomes present in a sample that comprises more than one genome. For example, non-specific enrichment can be selective of the fetal genome in a maternal sample, which can be obtained by known methods to increase the relative proportion of fetal to maternal DNA in a sample. Alternatively, non-specific enrichment can be the non- selective amplification of both genomes present in the sample. For example, nonspecific amplification can be of fetal and maternal DNA in a sample comprising a mixture of DNA from the fetal and maternal genomes. Methods for whole genome amplification are known in the art. Degenerate oligonucleotide-primed PCR (DOP), primer extension PCR technique (PEP) and multiple displacement amplification (MDA) are examples of whole genome amplification methods. In some embodiments, the sample comprising the mixture of cfDNA from different genomes is un-enriched for cfDNA of the genomes present in the mixture. In other embodiments, the sample comprising the mixture of cfDNA from different genomes is non-specifically enriched for any one of the genomes present in the sample.

[00353] The sample comprising the nucleic acid(s) to which the methods described herein are applied typically comprises a biological sample ("test sample"), e.g., as described above. In some embodiments, the nucleic acid(s) to be screened for one or more CNVs is purified or isolated by any of a number of well-known methods.

[00354] Accordingly, in certain embodiments the sample comprises or consists of a purified or isolated polynucleotide, or it can comprise samples such as a tissue sample, a biological fluid sample, a cell sample, and the like. Suitable biological fluid samples include, but are not limited to blood, plasma, serum, sweat, tears, sputum, urine, sputum, ear flow, lymph, saliva, cerebrospinal fluid, ravages, bone marrow suspension, vaginal flow, trans-cervical lavage, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, amniotic fluid, milk, and leukophoresis samples. In some embodiments, the sample is a sample that is easily obtainable by non-invasive procedures, e.g., blood, plasma, serum, sweat, tears, sputum, urine, sputum, ear flow, saliva or feces. In certain embodiments the sample is a peripheral blood sample, or the plasma and/or serum fractions of a peripheral blood sample. In other embodiments, the biological sample is a swab or smear, a biopsy specimen, or a cell culture. In another embodiment, the sample is a mixture of two or more biological samples, e.g., a biological sample can comprise two or more of a biological fluid sample, a tissue sample, and a cell culture sample. As used herein, the terms "blood," "plasma" and "serum" expressly encompass fractions or processed portions thereof. Similarly, where a sample is taken from a biopsy, swab, smear, etc., the "sample" expressly encompasses a processed fraction or portion derived from the biopsy, swab, smear, etc.

[00355] In certain embodiments, samples can be obtained from sources, including, but not limited to, samples from different individuals, samples from different developmental stages of the same or different individuals, samples from different diseased individuals (e.g., individuals with cancer or suspected of having a genetic disorder), normal individuals, samples obtained at different stages of a disease in an individual, samples obtained from an individual subjected to different treatments for a disease, samples from individuals subjected to different environmental factors, samples from individuals with predisposition to a pathology, samples individuals with exposure to an infectious disease agent (e.g., HIV), and the like.

[00356] In one illustrative, but non-limiting embodiment, the sample is a maternal sample that is obtained from a pregnant female, for example a pregnant woman. In this instance, the sample can be analyzed using the methods described herein to provide a prenatal diagnosis of potential chromosomal abnormalities in the fetus. The maternal sample can be a tissue sample, a biological fluid sample, or a cell sample. A biological fluid includes, as non-limiting examples, blood, plasma, serum, sweat, tears, sputum, urine, sputum, ear flow, lymph, saliva, cerebrospinal fluid, ravages, bone marrow suspension, vaginal flow, transcervical lavage, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, and leukophoresis samples.

[00357] In another illustrative, but non-limiting embodiment, the maternal sample is a mixture of two or more biological samples, e.g., the biological sample can comprise two or more of a biological fluid sample, a tissue sample, and a cell culture sample. In some embodiments, the sample is a sample that is easily obtainable by non-invasive procedures, e.g., blood, plasma, serum, sweat, tears, sputum, urine, milk, sputum, ear flow, saliva and feces. In some embodiments, the biological sample is a peripheral blood sample, and/or the plasma and serum fractions thereof. In other embodiments, the biological sample is a swab or smear, a biopsy specimen, or a sample of a cell culture. As disclosed above, the terms "blood," "plasma" and "serum" expressly encompass fractions or processed portions thereof. Similarly, where a sample is taken from a biopsy, swab, smear, etc., the "sample" expressly encompasses a processed fraction or portion derived from the biopsy, swab, smear, etc.

[00358] In certain embodiments samples can also be obtained from in vitro cultured tissues, cells, or other polynucleotide-containing sources. The cultured samples can be taken from sources including, but not limited to, cultures (e.g., tissue or cells) maintained in different media and conditions (e.g., pH, pressure, or temperature), cultures (e.g., tissue or cells) maintained for different periods of length, cultures (e.g., tissue or cells) treated with different factors or reagents (e.g., a drug candidate, or a modulator), or cultures of different types of tissue and/or cells. [00359] Methods of isolating nucleic acids from biological sources are well known and will differ depending upon the nature of the source. One of skill in the art can readily isolate nucleic acid(s) from a source as needed for the method described herein. In some instances, it can be advantageous to fragment the nucleic acid molecules in the nucleic acid sample. Fragmentation can be random, or it can be specific, as achieved, for example, using restriction endonuclease digestion. Methods for random fragmentation are well known in the art, and include, for example, limited DNAse digestion, alkali treatment and physical shearing. In one embodiment, sample nucleic acids are obtained from as cfDNA, which is not subjected to fragmentation. Sequencing Library Preparation

[00360] In one embodiment, the methods described herein can utilize next generation sequencing technologies (NGS), that allow multiple samples to be sequenced individually as genomic molecules (i.e., singleplex sequencing) or as pooled samples comprising indexed genomic molecules (e.g., multiplex sequencing) on a single sequencing run. These methods can generate up to several hundred million reads of DNA sequences. In various embodiments the sequences of genomic nucleic acids, and/or of indexed genomic nucleic acids can be determined using, for example, the Next Generation Sequencing Technologies (NGS) described herein. In various embodiments analysis of the massive amount of sequence data obtained using NGS can be performed using one or more processors as described herein.

[00361] In various embodiments the use of such sequencing technologies does not involve the preparation of sequencing libraries.

[00362] However, in certain embodiments the sequencing methods contemplated herein involve the preparation of sequencing libraries. In one illustrative approach, sequencing library preparation involves the production of a random collection of adapter-modified DNA fragments (e.g., polynucleotides) that are ready to be sequenced. Sequencing libraries of polynucleotides can be prepared from DNA or RNA, including equivalents, analogs of either DNA or cDNA, for example, DNA or cDNA that is complementary or copy DNA produced from an RNA template, by the action of reverse transcriptase. The polynucleotides may originate in double- stranded form (e.g., dsDNA such as genomic DNA fragments, cDNA, PCR amplification products, and the like) or, in certain embodiments, the polynucleotides may originated in single-stranded form (e.g., ssDNA, RNA, etc.) and have been converted to dsDNA form. By way of illustration, in certain embodiments, single stranded mRNA molecules may be copied into double-stranded cDNAs suitable for use in preparing a sequencing library. The precise sequence of the primary polynucleotide molecules is generally not material to the method of library preparation, and may be known or unknown. In one embodiment, the polynucleotide molecules are DNA molecules. More particularly, in certain embodiments, the polynucleotide molecules represent the entire genetic complement of an organism or substantially the entire genetic complement of an organism, and are genomic DNA molecules (e.g., cellular DNA, cell free DNA (cfDNA), etc.), that typically include both intron sequence and exon sequence (coding sequence), as well as non-coding regulatory sequences such as promoter and enhancer sequences. In certain embodiments, the primary polynucleotide molecules comprise human genomic DNA molecules, e.g., cfDNA molecules present in peripheral blood of a pregnant subject. [00363] Preparation of sequencing libraries for some NGS sequencing platforms is facilitated by the use of polynucleotides comprising a specific range of fragment sizes. Preparation of such libraries typically involves the fragmentation of large polynucleotides (e.g. cellular genomic DNA) to obtain polynucleotides in the desired size range. [00364] Fragmentation can be achieved by any of a number of methods known to those of skill in the art. For example, fragmentation can be achieved by mechanical means including, but not limited to nebulization, sonication and hydroshear. However mechanical fragmentation typically cleaves the DNA backbone at C-O, P-0 and C-C bonds resulting in a heterogeneous mix of blunt and 3' - and 5 '-overhanging ends with broken C-O, P-0 and/ C-C bonds (see, e.g., Alnemri and Liwack, J Biol. Chem 265: 17323-17333 [1990]; Richards and Boyer, J Mol Biol 11 :327-240 [1965]) which may need to be repaired as they may lack the requisite 5 '-phosphate for the subsequent enzymatic reactions, e.g., ligation of sequencing adaptors, that are required for preparing DNA for sequencing. [00365] In contrast, cfDNA, typically exists as fragments of less than about 300 base pairs and consequently, fragmentation is not typically necessary for generating a sequencing library using cfDNA samples. [00366] Typically, whether polynucleotides are forcibly fragmented (e.g., fragmented in vitro), or naturally exist as fragments, they are converted to blunt-ended DNA having 5'-phosphates and 3'-hydroxyl. Standard protocols, e.g., protocols for sequencing using, for example, the Illumina platform as described elsewhere herein, instruct users to end-repair sample DNA, to purify the end-repaired products prior to dA-tailing, and to purify the dA-tailing products prior to the adaptor-ligating steps of the library preparation.

[00367] Various embodiments of methods of sequence library preparation described herein obviate the need to perform one or more of the steps typically mandated by standard protocols to obtain a modified DNA product that can be sequenced by NGS. An abbreviated method (ABB method), a 1-step method, and a 2-step method are examples of methods for preparation of a sequencing library, which can be found in patent application 13/555,037 filed on July 20, 2012, which is incorporated by reference by its entirety. Marker Nucleic Acids for tracking and verifying sample integrity

[00368] In various embodiments verification of the integrity of the samples and sample tracking can be accomplished by sequencing mixtures of sample genomic nucleic acids, e.g., cfDNA, and accompanying marker nucleic acids that have been introduced into the samples, e.g., prior to processing. [00369] Marker nucleic acids can be combined with the test sample (e.g., biological source sample) and subjected to processes that include, for example, one or more of the steps of fractionating the biological source sample, e.g., obtaining an essentially cell-free plasma fraction from a whole blood sample, purifying nucleic acids from a fractionated, e.g., plasma, or unfractionated biological source sample, e.g., a tissue sample, and sequencing. In some embodiments, sequencing comprises preparing a sequencing library. The sequence or combination of sequences of the marker molecules that are combined with a source sample is chosen to be unique to the source sample. In some embodiments, the unique marker molecules in a sample all have the same sequence. In other embodiments, the unique marker molecules in a sample are a plurality of sequences, e.g., a combination of two, three, four, five, six, seven, eight, nine, ten, fifteen, twenty, or more different sequences. [00370] In one embodiment, the integrity of a sample can be verified using a plurality of marker nucleic acid molecules having identical sequences. Alternatively, the identity of a sample can be verified using a plurality of marker nucleic acid molecules that have at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17m, at least 18, at least 19, at least 20, at least 25, at least 30, at least 35, at least 40, at least 50, or more different sequences. Verification of the integrity of the plurality of biological samples, i.e., two or more biological samples, requires that each of the two or more samples be marked with marker nucleic acids that have sequences that are unique to each of the plurality of test sample that is being marked. For example, a first sample can be marked with a marker nucleic acid having sequence A, and a second sample can be marked with a marker nucleic acid having sequence B. Alternatively, a first sample can be marked with marker nucleic acid molecules all having sequence A, and a second sample can be marked with a mixture of sequences B and C, wherein sequences A, B and C are marker molecules having different sequences.

[00371] The marker nucleic acid(s) can be added to the sample at any stage of sample preparation that occurs prior to library preparation (if libraries are to be prepared) and sequencing. In one embodiment, marker molecules can be combined with an unprocessed source sample. For example, the marker nucleic acid can be provided in a collection tube that is used to collect a blood sample. Alternatively, the marker nucleic acids can be added to the blood sample following the blood draw. In one embodiment, the marker nucleic acid is added to the vessel that is used to collect a biological fluid sample, e.g., the marker nucleic acid(s) are added to a blood collection tube that is used to collect a blood sample. In another embodiment, the marker nucleic acid(s) are added to a fraction of the biological fluid sample. For example, the marker nucleic acid is added to the plasma and/or serum fraction of a blood sample, e.g., a maternal plasma sample. In yet another embodiment, the marker molecules are added to a purified sample, e.g., a sample of nucleic acids that have been purified from a biological sample. For example, the marker nucleic acid is added to a sample of purified maternal and fetal cfDNA. Similarly, the marker nucleic acids can be added to a biopsy specimen prior to processing the specimen. In some embodiments, the marker nucleic acids can be combined with a carrier that delivers the marker molecules into the cells of the biological sample. Cell-delivery carriers include pH-sensitive and cationic liposomes.

[00372] In various embodiments, the marker molecules have antigenomic sequences, that are sequences that are absent from the genome of the biological source sample. In an exemplary embodiment, the marker molecules that are used to verify the integrity of a human biological source sample have sequences that are absent from the human genome. In an alternative embodiment, the marker molecules have sequences that are absent from the source sample and from any one or more other known genomes. For example, the marker molecules that are used to verify the integrity of a human biological source sample have sequences that are absent from the human genome and from the mouse genome. The alternative allows for verifying the integrity of a test sample that comprises two or more genomes. For example, the integrity of a human cell-free DNA sample obtained from a subject affected by a pathogen, e.g., a bacterium, can be verified using marker molecules having sequences that are absent from both the human genome and the genome of the affecting bacterium. Sequences of genomes of numerous pathogens, e.g., bacteria, viruses, yeasts, fungi, protozoa etc., are publicly available on the World Wide Web at ncbi.nlm.nih.gov/genomes. In another embodiment, marker molecules are nucleic acids that have sequences that are absent from any known genome. The sequences of marker molecules can be randomly generated algorithmically.

[00373] In various embodiments the marker molecules can be naturally- occurring deoxyribonucleic acids (DNA), ribonucleic acids or artificial nucleic acid analogs (nucleic acid mimics) including peptide nucleic acids (PNA), morpholino nucleic acid, locked nucleic acids, glycol nucleic acids, and threose nucleic acids, which are distinguished from naturally-occurring DNA or RNA by changes to the backbone of the molecule or DNA mimics that do not have a phosphodiester backbone. The deoxyribonucleic acids can be from naturally-occurring genomes or can be generated in a laboratory through the use of enzymes or by solid phase chemical synthesis. Chemical methods can also be used to generate the DNA mimics that are not found in nature. Derivatives of DNA are that are available in which the phosphodiester linkage has been replaced but in which the deoxyribose is retained include but are not limited to DNA mimics having backbones formed by thioformacetal or a carboxamide linkage, which have been shown to be good structural DNA mimics. Other DNA mimics include morpholino derivatives and the peptide nucleic acids (PNA), which contain an N-(2-aminoethyl)glycine-based pseudopeptide backbone (Ann Rev Biophys Biomol Struct 24: 167-183 [1995]). PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion (Mol Biotechnol 26:233-248 [2004]. Another good structural mimic/analog of DNA analog that can be used as a marker molecule is phosphorothioate DNA in which one of the non-bridging oxygens is replaced by a sulfur. This modification reduces the action of endo-and exonucleases2 including 5' to 3' and 3' to 5' DNA POL 1 exonuclease, nucleases SI and PI, RNases, serum nucleases and snake venom phosphodiesterase.

[00374] The length of the marker molecules can be distinct or indistinct from that of the sample nucleic acids, i.e., the length of the marker molecules can be similar to that of the sample genomic molecules, or it can be greater or smaller than that of the sample genomic molecules. The length of the marker molecules is measured by the number of nucleotide or nucleotide analog bases that constitute the marker molecule. Marker molecules having lengths that differ from those of the sample genomic molecules can be distinguished from source nucleic acids using separation methods known in the art. For example, differences in the length of the marker and sample nucleic acid molecules can be determined by electrophoretic separation, e.g., capillary electrophoresis. Size differentiation can be advantageous for quantifying and assessing the quality of the marker and sample nucleic acids. Preferably, the marker nucleic acids are shorter than the genomic nucleic acids, and of sufficient length to exclude them from being mapped to the genome of the sample. For example, as a 30 base human sequence is needed to uniquely map it to a human genome. Accordingly in certain embodiments, marker molecules used in sequencing bioassays of human samples should be at least 30 bp in length.

[00375] The choice of length of the marker molecule is determined primarily by the sequencing technology that is used to verify the integrity of a source sample. The length of the sample genomic nucleic acids being sequenced can also be considered. For example, some sequencing technologies employ clonal amplification of polynucleotides, which can require that the genomic polynucleotides that are to be clonally amplified be of a minimum length. For example, sequencing using the Illumina GAII sequence analyzer includes an in vitro clonal amplification by bridge PCR (also known as cluster amplification) of polynucleotides that have a minimum length of 1 lObp, to which adaptors are ligated to provide a nucleic acid of at least 200 bp and less than 600 bp that can be clonally amplified and sequenced. In some embodiments, the length of the adaptor-ligated marker molecule is between about 200bp and about 600bp, between about 250bp and 550bp, between about 300bp and 500bp, or between about 350 and 450. In other embodiments, the length of the adaptor-ligated marker molecule is about 200bp. For example, when sequencing fetal cfDNA that is present in a maternal sample, the length of the marker molecule can be chosen to be similar to that of fetal cfDNA molecules. Thus, in one embodiment, the length of the marker molecule used in an assay that comprises massively parallel sequencing of cfDNA in a maternal sample to determine the presence or absence of a fetal chromosomal aneuploidy, can be about 150 bp, about 160bp, 170 bp, about 180bp, about 190bp or about 200bp; preferably, the marker molecule is about 170 pp. Other sequencing approaches, e.g., SOLiD sequencing, Polony Sequencing and 454 sequencing use emulsion PCR to clonally amplify DNA molecules for sequencing, and each technology dictates the minimum and the maximum length of the molecules that are to be amplified. The length of marker molecules to be sequenced as clonally amplified nucleic acids can be up to about 600bp. In some embodiments, the length of marker molecules to be sequenced can be greater than 600bp.

[00376] Single molecule sequencing technologies, that do not employ clonal amplification of molecules, and are capable of sequencing nucleic acids over a very broad range of template lengths, in most situations do not require that the molecules to be sequenced be of any specific length. However, the yield of sequences per unit mass is dependent on the number of 3' end hydroxyl groups, and thus having relatively short templates for sequencing is more efficient than having long templates. If starting with nucleic acids longer than 1000 nt, it is generally advisable to shear the nucleic acids to an average length of 100 to 200 nt so that more sequence information can be generated from the same mass of nucleic acids. Thus, the length of the marker molecule can range from tens of bases to thousands of bases. The length of marker molecules used for single molecule sequencing can be up to about 25bp, up to about 50bp, up to about 75bp, up to about lOObp, up to about 200bp, up to about 300bp, up to about 400bp, up to about 500bp, up to about 600bp, up to about 700bp, up to about 800 bp, up to about 900bp, up to about lOOObp, or more in length.

[00377] The length chosen for a marker molecule is also determined by the length of the genomic nucleic acid that is being sequenced. For example, cfDNA circulates in the human bloodstream as genomic fragments of cellular genomic DNA. Fetal cfDNA molecules found in the plasma of pregnant women are generally shorter than maternal cfDNA molecules (Chan et al., Clin Chem 50:8892 [2004]). Size fractionation of circulating fetal DNA has confirmed that the average length of circulating fetal DNA fragments is <300 bp, while maternal DNA has been estimated to be between about 0.5 and 1 Kb (Li et al., Clin Chem, 50: 1002-1011 [2004]). These findings are consistent with those of Fan et al., who determined using NGS that fetal cfDNA is rarely >340bp (Fan et al., Clin Chem 56: 1279-1286 [2010]). DNA isolated from urine with a standard silica-based method consists of two fractions, high molecular weight DNA, which originates from shed cells and low molecular weight (150-250 base pair) fraction of transrenal DNA (Tr-DNA) (Botezatu et al., Clin Chem. 46: 1078-1084, 2000; and Su et al., J Mol. Diagn. 6: 101-107, 2004). The application of newly developed technique for isolation of cell-free nucleic acids from body fluids to the isolation of transrenal nucleic acids has revealed the presence in urine of DNA and RNA fragments much shorter than 150 base pairs (U.S. Patent Application Publication No. 20080139801). In embodiments, wherein cfDNA is the genomic nucleic acid that is sequenced, marker molecules that are chosen can be up to about the length of the cfDNA. For example, the length of marker molecules used in maternal cfDNA samples to be sequenced as single nucleic acid molecules or as clonally amplified nucleic acids can be between about 100 bp and 600. In other embodiments, the sample genomic nucleic acids are fragments of larger molecules. For example, a sample genomic nucleic acid that is sequenced is fragmented cellular DNA. In embodiments, when fragmented cellular DNA is sequenced, the length of the marker molecules can be up to the length of the DNA fragments. In some embodiments, the length of the marker molecules is at least the minimum length required for mapping the sequence read uniquely to the appropriate reference genome. In other embodiments, the length of the marker molecule is the minimum length that is required to exclude the marker molecule from being mapped to the sample reference genome. [00378] In addition, marker molecules can be used to verify samples that are not assayed by nucleic acid sequencing, and that can be verified by common bio- techniques other than sequencing, e.g., real-time PCR.

Sample controls (e.g., in process positive controls for sequencing and/or analysis).

[00379] In various embodiments marker sequences introduced into the samples, e.g., as described above, can function as positive controls to verify the accuracy and efficacy of sequencing and subsequent processing and analysis.

[00380] Accordingly, compositions and method for providing an in-process positive control (IPC) for sequencing DNA in a sample are provided. In certain embodiments, positive controls are provided for sequencing cfDNA in a sample comprising a mixture of genomes are provided. An IPC can be used to relate baseline shifts in sequence information obtained from different sets of samples, e.g., samples that are sequenced at different times on different sequencing runs. Thus, for example, an IPC can relate the sequence information obtained for a maternal test sample to the sequence information obtained from a set of qualified samples that were sequenced at a different time.

[00381] Similarly, in the case of segment analysis, an IPC can relate the sequence information obtained from a subject for particular segment(s) to the sequence obtained from a set of qualified samples (of similar sequences) that were sequenced at a different time. In certain embodiments an IPC can relate the sequence information obtained from a subject for particular cancer-related loci to the sequence information obtained from a set of qualified samples (e.g., from a known amplification/deletion, and the like). [00382] In addition, IPCs can be used as markers to track sample(s) through the sequencing process. IPCs can also provide a qualitative positive sequence dose value, e.g., NCV, for one or more aneuploidies of chromosomes of interest, e.g., trisomy 21, trisomy 13, trisomy 18 to provide proper interpretation, and to ensure the dependability and accuracy of the data. In certain embodiments IPCs can be created to comprise nucleic acids from male and female genomes to provide doses for chromosomes X and Y in a maternal sample to determine whether the fetus is male. [00383] The type and the number of in-process controls depends on the type or nature of the test needed. For example, for a test requiring the sequencing of DNA from a sample comprising a mixture of genomes to determine whether a chromosomal aneuploidy exists, the in-process control can comprise DNA obtained from a sample known comprising the same chromosomal aneuploidy that is being tested. In some embodiments, the IPC includes DNA from a sample known to comprise an aneuploidy of a chromosome of interest. For example, the IPC for a test to determine the presence or absence of a fetal trisomy, e.g., trisomy 21, in a maternal sample comprises DNA obtained from an individual with trisomy 21. In some embodiments, the IPC comprises a mixture of DNA obtained from two or more individuals with different aneuploidies. For example, for a test to determine the presence or absence of trisomy 13, trisomy 18, trisomy 21, and monosomy X, the IPC comprises a combination of DNA samples obtained from pregnant women each carrying a fetus with one of the trisomies being tested. In addition to complete chromosomal aneuploidies, IPCs can be created to provide positive controls for tests to determine the presence or absence of partial aneuploidies.

[00384] An IPC that serves as the control for detecting a single aneuploidy can be created using a mixture of cellular genomic DNA obtained from a two subjects one being the contributor of the aneuploid genome. For example, an IPC that is created as a control for a test to determine a fetal trisomy, e.g., trisomy 21, can be created by combining genomic DNA from a male or female subject carrying the trisomic chromosome with genomic DNA with a female subject known not to carry the trisomic chromosome. Genomic DNA can be extracted from cells of both subjects, and sheared to provide fragments of between about 100 - 400 bp, between about 150- 350 bp, or between about 200-300 bp to simulate the circulating cfDNA fragments in maternal samples. The proportion of fragmented DNA from the subject carrying the aneuploidy, e.g., trisomy 21, is chosen to simulate the proportion of circulating fetal cfDNA found in maternal samples to provide an IPC comprising a mixture of fragmented DNA comprising about 5%, about 10%, about 15%, about 20%, about 25%), about 30%>, of DNA from the subject carrying the aneuploidy. The IPC can comprise DNA from different subjects each carrying a different aneuploidy. For example, the IPC can comprise about 80%> of the unaffected female DNA, and the remaining 20%> can be DNA from three different subjects each carrying a trisomic chromosome 21, a trisomic chromosome 13, and a trisomic chromosome 18. The mixture of fragmented DNA is prepared for sequencing. Processing of the mixture of fragmented DNA can comprise preparing a sequencing library, which can be sequenced using any massively parallel methods in singleplex or multiplex fashion. Stock solutions of the genomic IPC can be stored and used in multiple diagnostic tests.

[00385] Alternatively the IPC can be created using cfDNA obtained from a mother known to carry a fetus with a known chromosomal aneuploidy. For example, cfDNA can be obtained from a pregnant woman carrying a fetus with trisomy 21. The cfDNA is extracted from the maternal sample, and cloned into a bacterial vector and grown in bacteria to provide an ongoing source of the IPC. The DNA can be extracted from the bacterial vector using restriction enzymes. Alternatively, the cloned cfDNA can be amplified by, e.g., PCR. The IPC DNA can be processed for sequencing in the same runs as the cfDNA from the test samples that are to be analyzed for the presence or absence of chromosomal aneuploidies.

[00386] While the creation of IPCs is described above with respect to trisomies, it will be appreciated that IPCs can be created to reflect other partial aneuploidies including for example, various segment amplification and/or deletions. Thus, for example, where various cancers are known to be associated with particular amplifications (e.g., breast cancer associated with 20Q13) IPCs can be created that incorporate those known amplifications.

Sequencing Methods

[00387] As indicated above, the prepared samples (e.g., Sequencing Libraries) are sequenced as part of the procedure for identifying copy number variation(s). Any of a number of sequencing technologies can be utilized.

[00388] Some sequencing technologies are available commercially, such as the sequencing-by-hybridization platform from Affymetrix Inc. (Sunnyvale, CA) and the sequencing-by-synthesis platforms from 454 Life Sciences (Bradford, CT), Illumina/Solexa (Hayward, CA) and Helicos Biosciences (Cambridge, MA), and the sequencing-by-ligation platform from Applied Biosy stems (Foster City, CA), as described below. In addition to the single molecule sequencing performed using sequencing-by-synthesis of Helicos Biosciences, other single molecule sequencing technologies include, but are not limited to, the SMRT™ technology of Pacific Biosciences, the ION TORRENT™ technology, and nanopore sequencing developed for example, by Oxford Nanopore Technologies.

[00389] While the automated Sanger method is considered as a 'first generation' technology, Sanger sequencing including the automated Sanger sequencing, can also be employed in the methods described herein. Additional suitable sequencing methods include, but are not limited to nucleic acid imaging technologies, e.g., atomic force microscopy (AFM) or transmission electron microscopy (TEM). Illustrative sequencing technologies are described in greater detail below.

[00390] In one illustrative, but non-limiting, embodiment, the methods described herein comprise obtaining sequence information for the nucleic acids in a test sample, e.g., cfDNA in a maternal sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using Illumina's sequencing-by-synthesis and reversible terminator-based sequencing chemistry (e.g. as described in Bentley et al., Nature 6:53-59 [2009]). Template DNA can be genomic DNA, e.g., cellular DNA or cfDNA. In some embodiments, genomic DNA from isolated cells is used as the template, and it is fragmented into lengths of several hundred base pairs. In other embodiments, cfDNA is used as the template, and fragmentation is not required as cfDNA exists as short fragments. For example fetal cfDNA circulates in the bloodstream as fragments approximately 170 base pairs (bp) in length (Fan et al., Clin Chem 56: 1279-1286 [2010]), and no fragmentation of the DNA is required prior to sequencing. Illumina's sequencing technology relies on the attachment of fragmented genomic DNA to a planar, optically transparent surface on which oligonucleotide anchors are bound. Template DNA is end-repaired to generate 5'-phosphorylated blunt ends, and the polymerase activity of Klenow fragment is used to add a single A base to the 3' end of the blunt phosphorylated DNA fragments. This addition prepares the DNA fragments for ligation to oligonucleotide adapters, which have an overhang of a single T base at their 3' end to increase ligation efficiency. The adapter oligonucleotides are complementary to the flow-cell anchor oligos (not to be confused with the anchor/anchored reads in the analysis of repeat expansion). Under limiting- dilution conditions, adapter-modified, single-stranded template DNA is added to the flow cell and immobilized by hybridization to the anchor oligos. Attached DNA fragments are extended and bridge amplified to create an ultra-high density sequencing flow cell with hundreds of millions of clusters, each containing about 1,000 copies of the same template. In one embodiment, the randomly fragmented genomic DNA is amplified using PCR before it is subjected to cluster amplification. Alternatively, an amplification-free (e.g., PCR free) genomic library preparation is used, and the randomly fragmented genomic DNA is enriched using the cluster amplification alone (Kozarewa et al., Nature Methods 6:291-295 [2009]). The templates are sequenced using a robust four-color DNA sequencing-by-synthesis technology that employs reversible terminators with removable fluorescent dyes. High-sensitivity fluorescence detection is achieved using laser excitation and total internal reflection optics. Short sequence reads of about tens to a few hundred base pairs are aligned against a reference genome and unique mapping of the short sequence reads to the reference genome are identified using specially developed data analysis pipeline software. After completion of the first read, the templates can be regenerated in situ to enable a second read from the opposite end of the fragments. Thus, either single-end or paired end sequencing of the DNA fragments can be used.

[00391] Various embodiments of the disclosure may use sequencing by synthesis that allows paired end sequencing. In some embodiments, the sequencing by synthesis platform by Illumina involves clustering fragments. Clustering is a process in which each fragment molecule is isothermally amplified. In some embodiments, as the example described here, the fragment has two different adaptors attached to the two ends of the fragment, the adaptors allowing the fragment to hybridize with the two different oligos on the surface of a flow cell lane. The fragment further includes or is connected to two index sequences at two ends of the fragment, which index sequences provide labels to identify different samples in multiplex sequencing. In some sequencing platforms, a fragment to be sequenced is also referred to as an insert.

[00392] In some implementation, a flow cell for clustering in the Illumina platform is a glass slide with lanes. Each lane is a glass channel coated with a lawn of two types of oligos. Hybridization is enabled by the first of the two types of oligos on the surface. This oligo is complementary to a first adapter on one end of the fragment. A polymerase creates a compliment strand of the hybridized fragment. The double- stranded molecule is denatured, and the original template strand is washed away. The remaining strand, in parallel with many other remaining strands, is clonally amplified through bridge application.

[00393] In bridge amplification, a strand folds over, and a second adapter region on a second end of the strand hybridizes with the second type of oligos on the flow cell surface. A polymerase generates a complimentary strand, forming a double- stranded bridge molecule. This double-stranded molecule is denatured resulting in two single-stranded molecules tethered to the flow cell through two different oligos. The process is then repeated over and over, and occurs simultaneously for millions of clusters resulting in clonal amplification of all the fragments. After bridge amplification, the reverse strands are cleaved and washed off, leaving only the forward strands. The 3' ends are blocked to prevent unwanted priming.

[00394] After clustering, sequencing starts with extending a first sequencing primer to generate the first read. With each cycle, fluorescently tagged nucleotides compete for addition to the growing chain. Only one is incorporated based on the sequence of the template. After the addition of each nucleotide, the cluster is excited by a light source, and a characteristic fluorescent signal is emitted. The number of cycles determines the length of the read. The emission wavelength and the signal intensity determine the base call. For a given cluster all identical strands are read simultaneously. Hundreds of millions of clusters are sequenced in a massively parallel manner. At the completion of the first read, the read product is washed away.

[00395] In the next step of protocols involving two index primers, an index 1 primer is introduced and hybridized to an index 1 region on the template. Index regions provide identification of fragments, which is useful for de-multiplexing samples in a multiplex sequencing process. The index 1 read is generated similar to the first read. After completion of the index 1 read, the read product is washed away and the 3' end of the strand is de-protected. The template strand then folds over and binds to a second oligo on the flow cell. An index 2 sequence is read in the same manner as index 1. Then an index 2 read product is washed off at the completion of the step. [00396] After reading two indices, read 2 initiates by using polymerases to extend the second flow cell oligos, forming a double-stranded bridge. This double- stranded DNA is denatured, and the 3' end is blocked. The original forward strand is cleaved off and washed away, leaving the reverse strand. Read 2 begins with the introduction of a read 2 sequencing primer. As with read 1, the sequencing steps are repeated until the desired length is achieved. The read 2 product is washed away. This entire process generates millions of reads, representing all the fragments. Sequences from pooled sample libraries are separated based on the unique indices introduced during sample preparation. For each sample, reads of similar stretches of base calls are locally clustered. Forward and reversed reads are paired creating contiguous sequences. These contiguous sequences are aligned to the reference genome for variant identification. [00397] The sequencing by synthesis example described above involves paired end reads, which is used in many of the embodiments of the disclosed methods. Paired end sequencing involves 2 reads from the two ends of a fragment. When a pair of reads are mapped to a reference sequence, the base-pair distance between the two reads can be determined, which distance can then be used to determine the length of the fragments from which the reads were obtained. In some instances, a fragment straddling two bins would have one of its pair-end read aligned to one bin, and another to an adjacent bin. This gets rarer as the bins get longer or the reads get shorter. Various methods may be used to account for the bin-membership of these fragments. For instance, they can be omitted in determining fragment size frequency of a bin; they can be counted for both of the adjacent bins; they can be assigned to the bin that encompasses the larger number of base pairs of the two bins; or they can be assigned to both bins with a weight related to portion of base pairs in each bin.

[00398] Paired end reads may use insert of different length (i.e., different fragment size to be sequenced). As the default meaning in this disclosure, paired end reads are used to refer to reads obtained from various insert lengths. In some instances, to distinguish short-insert paired end reads from long-inserts paired end reads, the latter is also referred to as mate pair reads. In some embodiments involving mate pair reads, two biotin junction adaptors first are attached to two ends of a relatively long insert (e.g., several kb). The biotin junction adaptors then link the two ends of the insert to form a circularized molecule. A sub-fragment encompassing the biotin junction adaptors can then be obtained by further fragmenting the circularized molecule. The sub-fragment including the two ends of the original fragment in opposite sequence order can then be sequenced by the same procedure as for short- insert paired end sequencing described above. Further details of mate pair sequencing using an Illumina platform is shown in an online publication at the following URL, which is incorporated by reference by its entirety: res| . |illumina| . |com/documents/products/technotes/technote_nextera_matepair_ data _pr ocessing. Additional information about paired end sequencing can be found in US Patent No. 7601499 and US Patent Publication No. 2012/0,053,063, which are incorporated by reference with regard to materials on paired end sequencing methods and apparatuses.

[00399] After sequencing of DNA fragments, sequence reads of predetermined length, e.g., 100 bp, are mapped or aligned to a known reference genome. The mapped or aligned reads and their corresponding locations on the reference sequence are also referred to as tags. In one embodiment, the reference genome sequence is the NCBI36/hgl8 sequence, which is available on the world wide web at genome dot ucsc dot edu/cgi-bin/hgGateway ?org=Human&db=hg 18&hgsid= 166260105). Alternatively, the reference genome sequence is the GRCh37/hgl9, which is available on the world wide web at genome dot ucsc dot edu/cgi-bin/hgGateway. Other sources of public sequence information include GenBank, dbEST, dbSTS, EMBL (the European Molecular Biology Laboratory), and the DDBJ (the DNA Databank of Japan). A number of computer algorithms are available for aligning sequences, including without limitation BLAST (Altschul et al., 1990), BLITZ (MPsrch) (Sturrock & Collins, 1993), FASTA (Person & Lipman, 1988), BOWTIE (Langmead et al., Genome Biology 10:R25.1-R25.10 [2009]), or ELAND (Illumina, Inc., San Diego, CA, USA). In one embodiment, one end of the clonally expanded copies of the plasma cfDNA molecules is sequenced and processed by bioinformatics alignment analysis for the Illumina Genome Analyzer, which uses the Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) software.

[00400] In one illustrative, but non-limiting, embodiment, the methods described herein comprise obtaining sequence information for the nucleic acids in a test sample, e.g., cfDNA in a maternal sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using single molecule sequencing technology of the Helicos True Single Molecule Sequencing (tSMS) technology (e.g. as described in Harris T.D. et al., Science 320: 106-109 [2008]). In the tSMS technique, a DNA sample is cleaved into strands of approximately 100 to 200 nucleotides, and a polyA sequence is added to the 3' end of each DNA strand. Each strand is labeled by the addition of a fluorescently labeled adenosine nucleotide. The DNA strands are then hybridized to a flow cell, which contains millions of oligo-T capture sites that are immobilized to the flow cell surface. In certain embodiments the templates can be at a density of about 100 million templates/cm ² . The flow cell is then loaded into an instrument, e.g., HeliScope™ sequencer, and a laser illuminates the surface of the flow cell, revealing the position of each template. A CCD camera can map the position of the templates on the flow cell surface. The template fluorescent label is then cleaved and washed away. The sequencing reaction begins by introducing a DNA polymerase and a fluorescently labeled nucleotide. The oligo- T nucleic acid serves as a primer. The polymerase incorporates the labeled nucleotides to the primer in a template directed manner. The polymerase and unincorporated nucleotides are removed. The templates that have directed incorporation of the fluorescently labeled nucleotide are discerned by imaging the flow cell surface. After imaging, a cleavage step removes the fluorescent label, and the process is repeated with other fluorescently labeled nucleotides until the desired read length is achieved. Sequence information is collected with each nucleotide addition step. Whole genome sequencing by single molecule sequencing technologies excludes or typically obviates PCR-based amplification in the preparation of the sequencing libraries, and the methods allow for direct measurement of the sample, rather than measurement of copies of that sample.

[00401] In another illustrative, but non-limiting embodiment, the methods described herein comprise obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using the 454 sequencing (Roche) (e.g. as described in Margulies, M. et al. Nature 437:376-380 [2005]). 454 sequencing typically involves two steps. In the first step, DNA is sheared into fragments of approximately 300-800 base pairs, and the fragments are blunt-ended. Oligonucleotide adaptors are then ligated to the ends of the fragments. The adaptors serve as primers for amplification and sequencing of the fragments. The fragments can be attached to DNA capture beads, e.g., streptavidin-coated beads using, e.g., Adaptor B, which contains 5'-biotin tag. The fragments attached to the beads are PCR amplified within droplets of an oil-water emulsion. The result is multiple copies of clonally amplified DNA fragments on each bead. In the second step, the beads are captured in wells (e.g., picoliter-sized wells). Pyrosequencing is performed on each DNA fragment in parallel. Addition of one or more nucleotides generates a light signal that is recorded by a CCD camera in a sequencing instrument. The signal strength is proportional to the number of nucleotides incorporated. Pyrosequencing makes use of pyrophosphate (PPi) which is released upon nucleotide addition. PPi is converted to ATP by ATP sulfurylase in the presence of adenosine 5' phosphosulfate. Luciferase uses ATP to convert luciferin to oxyluciferin, and this reaction generates light that is measured and analyzed. [00402] In another illustrative, but non-limiting, embodiment, the methods described herein comprises obtaining sequence information for the nucleic acids in the test sample , e.g., cfDNA in a maternal test sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using the SOLiD™ technology (Applied Biosystems). In SOLiD™ sequencing-by-ligation, genomic DNA is sheared into fragments, and adaptors are attached to the 5' and 3' ends of the fragments to generate a fragment library. Alternatively, internal adaptors can be introduced by ligating adaptors to the 5' and 3' ends of the fragments, circularizing the fragments, digesting the circularized fragment to generate an internal adaptor, and attaching adaptors to the 5' and 3' ends of the resulting fragments to generate a mate-paired library. Next, clonal bead populations are prepared in microreactors containing beads, primers, template, and PCR components. Following PCR, the templates are denatured and beads are enriched to separate the beads with extended templates. Templates on the selected beads are subjected to a 3' modification that permits bonding to a glass slide. The sequence can be determined by sequential hybridization and ligation of partially random oligonucleotides with a central determined base (or pair of bases) that is identified by a specific fluorophore. After a color is recorded, the ligated oligonucleotide is cleaved and removed and the process is then repeated.

[00403] In another illustrative, but non-limiting, embodiment, the methods described herein comprise obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using the single molecule, real-time (SMRT™) sequencing technology of Pacific Biosciences. In SMRT sequencing, the continuous incorporation of dye-labeled nucleotides is imaged during DNA synthesis. Single DNA polymerase molecules are attached to the bottom surface of individual zero-mode wavelength detectors (ZMW detectors) that obtain sequence information while phospholinked nucleotides are being incorporated into the growing primer strand. A ZMW detector comprises a confinement structure that enables observation of incorporation of a single nucleotide by DNA polymerase against a background of fluorescent nucleotides that rapidly diffuse in an out of the ZMW (e.g., in microseconds). It typically takes several milliseconds to incorporate a nucleotide into a growing strand. During this time, the fluorescent label is excited and produces a fluorescent signal, and the fluorescent tag is cleaved off. Measurement of the corresponding fluorescence of the dye indicates which base was incorporated. The process is repeated to provide a sequence.

[00404] In another illustrative, but non-limiting embodiment, the methods described herein comprise obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using nanopore sequencing (e.g. as described in Soni GV and Meller A. Clin Chem 53 : 1996-2001 [2007]). Nanopore sequencing DNA analysis techniques are developed by a number of companies, including, for example, Oxford Nanopore Technologies (Oxford, United Kingdom), Sequenom, NABsys, and the like. Nanopore sequencing is a single-molecule sequencing technology whereby a single molecule of DNA is sequenced directly as it passes through a nanopore. A nanopore is a small hole, typically of the order of 1 nanometer in diameter. Immersion of a nanopore in a conducting fluid and application of a potential (voltage) across it results in a slight electrical current due to conduction of ions through the nanopore. The amount of current that flows is sensitive to the size and shape of the nanopore. As a DNA molecule passes through a nanopore, each nucleotide on the DNA molecule obstructs the nanopore to a different degree, changing the magnitude of the current through the nanopore in different degrees. Thus, this change in the current as the DNA molecule passes through the nanopore provides a read of the DNA sequence. [00405] In another illustrative, but non-limiting, embodiment, the methods described herein comprises obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, cfDNA or cellular DNA in a subject being screened for a cancer, and the like, using the chemical-sensitive field effect transistor (chemFET) array (e.g., as described in U.S. Patent Application Publication No. 2009/0026082). In one example of this technique, DNA molecules can be placed into reaction chambers, and the template molecules can be hybridized to a sequencing primer bound to a polymerase. Incorporation of one or more triphosphates into a new nucleic acid strand at the 3' end of the sequencing primer can be discerned as a change in current by a chemFET. An array can have multiple chemFET sensors. In another example, single nucleic acids can be attached to beads, and the nucleic acids can be amplified on the bead, and the individual beads can be transferred to individual reaction chambers on a chemFET array, with each chamber having a chemFET sensor, and the nucleic acids can be sequenced.

[00406] In another embodiment, the present method comprises obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, using transmission electron microscopy (TEM). The method, termed Individual Molecule Placement Rapid Nano Transfer (EVIPRNT), comprises utilizing single atom resolution transmission electron microscope imaging of high- molecular weight (150kb or greater) DNA selectively labeled with heavy atom markers and arranging these molecules on ultra-thin films in ultra-dense (3nm strand- to-strand) parallel arrays with consistent base-to-base spacing. The electron microscope is used to image the molecules on the films to determine the position of the heavy atom markers and to extract base sequence information from the DNA. The method is further described in PCT patent publication WO 2009/046445. The method allows for sequencing complete human genomes in less than ten minutes.

[00407] In another embodiment, the DNA sequencing technology is the Ion

Torrent single molecule sequencing, which pairs semiconductor technology with a simple sequencing chemistry to directly translate chemically encoded information (A, C, G, T) into digital information (0, 1) on a semiconductor chip. In nature, when a nucleotide is incorporated into a strand of DNA by a polymerase, a hydrogen ion is released as a byproduct. Ion Torrent uses a high-density array of micro-machined wells to perform this biochemical process in a massively parallel way. Each well holds a different DNA molecule. Beneath the wells is an ion-sensitive layer and beneath that an ion sensor. When a nucleotide, for example a C, is added to a DNA template and is then incorporated into a strand of DNA, a hydrogen ion will be released. The charge from that ion will change the pH of the solution, which can be detected by Ion Torrent's ion sensor. The sequencer— essentially the world's smallest solid-state pH meter— calls the base, going directly from chemical information to digital information. The Ion personal Genome Machine (PGM™) sequencer then sequentially floods the chip with one nucleotide after another. If the next nucleotide that floods the chip is not a match. No voltage change will be recorded and no base will be called. If there are two identical bases on the DNA strand, the voltage will be double, and the chip will record two identical bases called. Direct detection allows recordation of nucleotide incorporation in seconds.

[00408] In another embodiment, the present method comprises obtaining sequence information for the nucleic acids in the test sample, e.g., cfDNA in a maternal test sample, using sequencing by hybridization. Sequencing-by- hybridization comprises contacting the plurality of polynucleotide sequences with a plurality of polynucleotide probes, wherein each of the plurality of polynucleotide probes can be optionally tethered to a substrate. The substrate might be flat surface comprising an array of known nucleotide sequences. The pattern of hybridization to the array can be used to determine the polynucleotide sequences present in the sample. In other embodiments, each probe is tethered to a bead, e.g., a magnetic bead or the like. Hybridization to the beads can be determined and used to identify the plurality of polynucleotide sequences within the sample. [00409] In some embodiments of the methods described herein, the mapped sequence tags comprise sequence reads of about 20bp, about 25bp, about 30bp, about 35bp, about 40bp, about 45bp, about 50bp, about 55bp, about 60bp, about 65bp, about 70bp, about 75bp, about 80bp, about 85bp, about90bp, about 95bp, about lOObp, about HObp, about 120bp, about 130, about 140bp, about 150bp, about 200bp, about 250bp, about 300bp, about 350bp, about 400bp, about 450bp, or about 500bp. It is expected that technological advances will enable single-end reads of greater than 500bp enabling for reads of greater than about lOOObp when paired end reads are generated. In one embodiment, the mapped sequence tags comprise sequence reads that are 36bp. Mapping of the sequence tags is achieved by comparing the sequence of the tag with the sequence of the reference to determine the chromosomal origin of the sequenced nucleic acid (e.g. cfDNA) molecule, and specific genetic sequence information is not needed. A small degree of mismatch (0-2 mismatches per sequence tag) may be allowed to account for minor polymorphisms that may exist between the reference genome and the genomes in the mixed sample.

[00410] A plurality of sequence tags are typically obtained per sample. In some embodiments, at least about 3 x 10 ⁶ sequence tags, at least about 5 x 10 ⁶ sequence tags, at least about 8 x 10 ⁶ sequence tags, at least about 10 x 10 ⁶ sequence tags, at least about 15 x 10 ⁶ sequence tags, at least about 20 x 10 ⁶ sequence tags, at least about 30 x 10 ⁶ sequence tags, at least about 40 x 10 ⁶ sequence tags, or at least about 50 x 10 ⁶ sequence tags comprising between 20 and 40bp reads, e.g., 36bp, are obtained from mapping the reads to the reference genome per sample. In one embodiment, all the sequence reads are mapped to all regions of the reference genome. In one embodiment, the tags that have been mapped to all regions, e.g., all chromosomes, of the reference genome are counted, and the CNV, i.e., the over- or under-representation of a sequence of interest, e.g., a chromosome or portion thereof, in the mixed DNA sample is determined. The method does not require differentiation between the two genomes.

[00411] The accuracy required for correctly determining whether a CNV, e.g., aneuploidy, is present or absent in a sample, is predicated on the variation of the number of sequence tags that map to the reference genome among samples within a sequencing run (inter-chromosomal variability), and the variation of the number of sequence tags that map to the reference genome in different sequencing runs (inter- sequencing variability). For example, the variations can be particularly pronounced for tags that map to GC-rich or GC-poor reference sequences. Other variations can result from using different protocols for the extraction and purification of the nucleic acids, the preparation of the sequencing libraries, and the use of different sequencing platforms. The present method uses sequence doses (chromosome doses, or segment doses) based on the knowledge of normalizing sequences (normalizing chromosome sequences or normalizing segment sequences), to intrinsically account for the accrued variability stemming from interchromosomal (intra-run), and inter-sequencing (inter- run) and platform-dependent variability. Chromosome doses are based on the knowledge of a normalizing chromosome sequence, which can be composed of a single chromosome, or of two or more chromosomes selected from chromosomes 1- 22, X, and Y. Alternatively, normalizing chromosome sequences can be composed of a single chromosome segment, or of two or more segments of one chromosome or of two or more chromosomes. Segment doses are based on the knowledge of a normalizing segment sequence, which can be composed of a single segment of any one chromosome, or of two or more segments of any two or more of chromosomes 1- 22, X, and Y. CNV and Prenatal Diagnoses

[00412] Cell-free fetal DNA and RNA circulating in maternal blood can be used for the early non-invasive prenatal diagnosis (NIPD) of an increasing number of genetic conditions, both for pregnancy management and to aid reproductive decisionmaking. The presence of cell-free DNA circulating in the bloodstream has been known for over 50 years. More recently, presence of small amounts of circulating fetal DNA was discovered in the maternal bloodstream during pregnancy (Lo et al., Lancet 350:485-487 [1997]). Thought to originate from dying placental cells, cell- free fetal DNA (cfDNA) has been shown to consists of short fragments typically fewer than 200 bp in length Chan et al., Clin Chem 50:88-92 [2004]), which can be discerned as early as 4 weeks gestation (Illanes et al., Early Human Dev 83 :563-566 [2007]), and known to be cleared from the maternal circulation within hours of delivery (Lo et al., Am J Hum Genet 64:218-224 [1999]). In addition to cfDNA, fragments of cell-free fetal RNA (cfRNA) can also be discerned in the maternal bloodstream, originating from genes that are transcribed in the fetus or placenta. The extraction and subsequent analysis of these fetal genetic elements from a maternal blood sample offers novel opportunities for NIPD.

[00413] The present method is a polymorphism-independent method that for use in NIPD and that does not require that the fetal cfDNA be distinguished from the maternal cfDNA to enable the determination of a fetal aneuploidy. In some embodiments, the aneuploidy is a complete chromosomal trisomy or monosomy, or a partial trisomy or monosomy. Partial aneuploidies are caused by loss or gain of part of a chromosome, and encompass chromosomal imbalances resulting from unbalanced translocations, unbalanced inversions, deletions and insertions. By far, the most common known aneuploidy compatible with life is trisomy 21, i.e., Down Syndrome (DS), which is caused by the presence of part or all of chromosome 21. Rarely, DS can be caused by an inherited or sporadic defect whereby an extra copy of all or part of chromosome 21 becomes attached to another chromosome (usually chromosome 14) to form a single aberrant chromosome. DS is associated with intellectual impairment, severe learning difficulties and excess mortality caused by long-term health problems such as heart disease. Other aneuploidies with known clinical significance include Edward syndrome (trisomy 18) and Patau Syndrome (trisomy 13), which are frequently fatal within the first few months of life. Abnormalities associated with the number of sex chromosomes are also known and include monosomy X, e.g., Turner syndrome (XO), and triple X syndrome (XXX) in female births and Kleinefelter syndrome (XXY) and XYY syndrome in male births, which are all associated with various phenotypes including sterility and reduction in intellectual skills. Monosomy X [45, X] is a common cause of early pregnancy loss accounting for about 7% of spontaneous abortions. Based on the liveborn frequency of 45,X (also called Turner syndrome) of 1-2/10,000, it is estimated that less than 1% of 45, X conceptions will survive to term. About 30% of Turners syndrome patients are mosaic with both a 45, X cell line and either a 46,XX cell line or one containing a rearranged X chromosome (Hook and Warburton 1983). The phenotype in a liveborn infant is relatively mild considering the high embryonic lethality and it has been hypothesized that possibly all liveborn females with Turner syndrome carry a cell line containing two sex chromosomes. Monosomy X can occur in females as 45, X or as 45,X/46XX, and in males as 45,X/46XY. Autosomal monosomies in human are generally suggested to be incompatible with life; however, there is quite a number of cytogenetic reports describing full monosomy of one chromosome 21 in live born children (Vosranova let al., Molecular Cytogen. 1 : 13 [2008]; Joosten et al., Prenatal Diagn. 17:271-5 [1997]. The method described herein can be used to diagnose these and other chromosomal abnormalities prenatally. [00414] According to some embodiments the methods disclosed herein can determine the presence or absence of chromosomal trisomies of any one of chromosomes 1-22, X and Y. Examples of chromosomal trisomies that can be detected according to the present method include without limitation trisomy 21 (T21; Down Syndrome), trisomy 18 (T18; Edward's Syndrome), trisomy 16 (T16), trisomy 20 (T20), trisomy 22 (T22; Cat Eye Syndrome), trisomy 15 (T15; Prader Willi Syndrome), trisomy 13 (T13; Patau Syndrome), trisomy 8 (T8; Warkany Syndrome), trisomy 9, and the XXY (Kleinefelter Syndrome), XYY, or XXX trisomies. Complete trisomies of other autosomes existing in a non-mosaic state are lethal, but can be compatible with life when present in a mosaic state. It will be appreciated that various complete trisomies, whether existing in a mosaic or non-mosaic state, and partial trisomies can be determined in fetal cfDNA according to the teachings provided herein. [00415] Non-limiting examples of partial trisomies that can be determined by the present method include, but are not limited to, partial trisomy lq32-44, trisomy 9 p, trisomy 4 mosaicism, trisomy 17p, partial trisomy 4q26-qter, partial 2p trisomy, partial trisomy lq, and/or partial trisomy 6p/monosomy 6q.

[00416] The methods disclosed herein can be also used to determine chromosomal monosomy X, chromosomal monosomy 21, and partial monosomies such as, monosomy 13, monosomy 15, monosomy 16, monosomy 21, and monosomy 22, which are known to be involved in pregnancy miscarriage. Partial monosomy of chromosomes typically involved in complete aneuploidy can also be determined by the method described herein. Non-limiting examples of deletion syndromes that can be determined according to the present method include syndromes caused by partial deletions of chromosomes. Examples of partial deletions that can be determined according to the methods described herein include without limitation partial deletions of chromosomes 1, 4, 5, 7, 11, 18, 15, 13, 17, 22 and 10, which are described in the following. [00417] 1 q21.1 deletion syndrome or lq21.1 (recurrent) microdeletion is a rare aberration of chromosome 1. Next to the deletion syndrome, there is also a lq21.1 duplication syndrome. While there is a part of the DNA missing with the deletion syndrome on a particular spot, there are two or three copies of a similar part of the DNA on the same spot with the duplication syndrome. Literature refers to both the deletion and the duplication as the lq21.1 copy -number variations (CNV). The lq21.1 deletion can be associated with the TAR Syndrome (Thrombocytopenia with Absent radius).

[00418] Wolf-Hirschhorn syndrome (WHS) (OMIN #194190) is a contiguous gene deletion syndrome associated with a hemizygous deletion of chromosome 4pl6.3. Wolf-Hirschhorn syndrome is a congenital malformation syndrome characterized by pre- and postnatal growth deficiency, developmental disability of variable degree, characteristic craniofacial features ('Greek warrior helmet' appearance of the nose, high forehead, prominent glabella, hypertelorism, high-arched eyebrows, protruding eyes, epicanthal folds, short philtrum, distinct mouth with downturned corners, and micrognathia), and a seizure disorder.

[00419] Partial deletion of chromosome 5, also known as 5p- or 5p minus, and named Cris du Chat syndrome (OMIN#123450), is caused by a deletion of the short arm (p arm) of chromosome 5 (5pl5.3-pl5.2). Infants with this condition often have a high-pitched cry that sounds like that of a cat. The disorder is characterized by intellectual disability and delayed development, small head size (microcephaly), low birth weight, and weak muscle tone (hypotonia) in infancy, distinctive facial features and possibly heart defects.

[00420] Williams-Beuren Syndrome also known as chromosome 7ql 1.23 deletion syndrome (OMIN 194050) is a contiguous gene deletion syndrome resulting in a multisystem disorder caused by hemizygous deletion of 1.5 to 1.8 Mb on chromosome 7ql 1.23, which contains approximately 28 genes. [00421] Jacobsen Syndrome, also known as l lq deletion disorder, is a rare congenital disorder resulting from deletion of a terminal region of chromosome 11 that includes band l lq24.1. It can cause intellectual disabilities, a distinctive facial appearance, and a variety of physical problems including heart defects and a bleeding disorder. [00422] Partial monosomy of chromosome 18, known as monosomy 18p is a rare chromosomal disorder in which all or part of the short arm (p) of chromosome 18 is deleted (monosomic). The disorder is typically characterized by short stature, variable degrees of mental retardation, speech delays, malformations of the skull and facial (craniofacial) region, and/or additional physical abnormalities. Associated craniofacial defects may vary greatly in range and severity from case to case.

[00423] Conditions caused by changes in the structure or number of copies of chromosome 15 include Angelman Syndrome and Prader-Willi Syndrome, which involve a loss of gene activity in the same part of chromosome 15, the 15ql l-ql3 region. It will be appreciated that several translocations and microdeletions can be asymptomatic in the carrier parent, yet can cause a major genetic disease in the offspring. For example, a healthy mother who carries the 15ql l-ql3 microdeletion can give birth to a child with Angelman syndrome, a severe neurodegenerative disorder. Thus, the methods, apparatus and systems described herein can be used to identify such a partial deletion and other deletions in the fetus.

[00424] Partial monosomy 13q is a rare chromosomal disorder that results when a piece of the long arm (q) of chromosome 13 is missing (monosomic). Infants born with partial monosomy 13q may exhibit low birth weight, malformations of the head and face (craniofacial region), skeletal abnormalities (especially of the hands and feet), and other physical abnormalities. Mental retardation is characteristic of this condition. The mortality rate during infancy is high among individuals born with this disorder. Almost all cases of partial monosomy 13q occur randomly for no apparent reason (sporadic).

[00425] Smith-Magenis syndrome (SMS - OMIM #182290) is caused by a deletion, or loss of genetic material, on one copy of chromosome 17. This well- known syndrome is associated with developmental delay, mental retardation, congenital anomalies such as heart and kidney defects, and neurobehavioral abnormalities such as severe sleep disturbances and self-injurious behavior. Smith- Magenis syndrome (SMS) is caused in most cases (90%) by a 3.7-Mb interstitial deletion in chromosome 17pl 1.2.

[00426] 22ql l .2 deletion syndrome, also known as DiGeorge syndrome, is a syndrome caused by the deletion of a small piece of chromosome 22. The deletion (22 ql l .2) occurs near the middle of the chromosome on the long arm of one of the pair of chromosome. The features of this syndrome vary widely, even among members of the same family, and affect many parts of the body. Characteristic signs and symptoms may include birth defects such as congenital heart disease, defects in the palate, most commonly related to neuromuscular problems with closure (velo- pharyngeal insufficiency), learning disabilities, mild differences in facial features, and recurrent infections. Microdeletions in chromosomal region 22ql l .2 are associated with a 20 to 30-fold increased risk of schizophrenia.

[00427] Deletions on the short arm of chromosome 10 are associated with a

DiGeorge Syndrome like phenotype. Partial monosomy of chromosome lOp is rare but has been observed in a portion of patients showing features of the DiGeorge Syndrome. [00428] In one embodiment, the methods, apparatus, and systems described herein is used to determine partial monosomies including but not limited to partial monosomy of chromosomes 1, 4, 5, 7, 11, 18, 15, 13, 17, 22 and 10, e.g., partial monosomy 1 q21.11, partial monosomy 4pl6.3, partial monosomy 5pl5.3-pl5.2, partial monosomy 7ql 1.23, partial monosomy l lq24.1, partial monosomy 18p, partial monosomy of chromosome 15 (15ql l-ql3), partial monosomy 13q, partial monosomy 17pl l .2, partial monosomy of chromosome 22 (22ql l .2), and partial monosomy lOp can also be determined using the method.

[00429] Other partial monosomies that can be determined according to the methods described herein include unbalanced translocation t(8; l l)(p23.2;pl5.5); l lq23 microdeletion; 17pl 1.2 deletion; 22ql3.3 deletion; Xp22.3 microdeletion; 10pl4 deletion; 20p microdeletion, [del(22)(ql 1.2ql 1.23)], 7ql l .23 and 7q36 deletions; lp36 deletion; 2p microdeletion; neurofibromatosis type 1 (17ql 1.2 microdeletion), Yq deletion ; 4pl6.3 microdeletion; lp36.2 microdeletion; l lql4 deletion; 19ql3.2 microdeletion; Rubinstein-Taybi (16 pi 3.3 microdeletion); 7p21 microdeletion; Miller-Dieker syndrome (17pl3.3); and 2q37 microdeletion. Partial deletions can be small deletions of part of a chromosome, or they can be microdeletions of a chromosome where the deletion of a single gene can occur.

[00430] Several duplication syndromes caused by the duplication of part of chromosome arms have been identified (see OMIN [Online Mendelian Inheritance in Man viewed online at ncbi.nlm.nih.gov/omim]). In one embodiment, the present method can be used to determine the presence or absence of duplications and/or multiplications of segments of any one of chromosomes 1-22, X and Y. Non-limiting examples of duplications syndromes that can be determined according to the present method include duplications of part of chromosomes 8, 15, 12, and 17, which are described in the following.

[00431] 8p23.1 duplication syndrome is a rare genetic disorder caused by a duplication of a region from human chromosome 8. This duplication syndrome has an estimated prevalence of 1 in 64,000 births and is the reciprocal of the 8p23.1 deletion syndrome. The 8p23.1 duplication is associated with a variable phenotype including one or more of speech delay, developmental delay, mild dysmorphism, with prominent forehead and arched eyebrows, and congenital heart disease (CHD). [00432] Chromosome 15q Duplication Syndrome (Dupl5q) is a clinically identifiable syndrome which results from duplications of chromosome 15ql 1-13.1 Babies with Dupl5q usually have hypotonia (poor muscle tone), growth retardation; they may be born with a cleft lip and/or palate or malformations of the heart, kidneys or other organs; they show some degree of cognitive delay/disability (mental retardation), speech and language delays, and sensory processing disorders.

[00433] Pallister Killian syndrome is a result of extra #12 chromosome material. There is usually a mixture of cells (mosaicism), some with extra #12 material, and some that are normal (46 chromosomes without the extra #12 material). Babies with this syndrome have many problems including severe mental retardation, poor muscle tone, "coarse" facial features, and a prominent forehead. They tend to have a very thin upper lip with a thicker lower lip and a short nose. Other health problems include seizures, poor feeding, stiff joints, cataracts in adulthood, hearing loss, and heart defects. Persons with Pallister Killian have a shortened lifespan. [00434] Individuals with the genetic condition designated as dup(17)(pl l .2pl l .2) or dup 17p carry extra genetic information (known as a duplication) on the short arm of chromosome 17. Duplication of chromosome 17pl l .2 underlies Potocki-Lupski syndrome (PTLS), which is a newly recognized genetic condition with only a few dozen cases reported in the medical literature. Patients who have this duplication often have low muscle tone, poor feeding, and failure to thrive during infancy, and also present with delayed development of motor and verbal milestones. Many individuals who have PTLS have difficulty with articulation and language processing. In addition, patients may have behavioral characteristics similar to those seen in persons with autism or autism-spectrum disorders. Individuals with PTLS may have heart defects and sleep apnea. . A duplication of a large region in chromosome 17pl2 that includes the gene PMP22 is known to cause Charcot-Marie Tooth disease.

[00435] CNV have been associated with stillbirths. However, due to inherent limitations of conventional cytogenetics, the contribution of CNV to stillbirth is thought to be underrepresented (Harris et al., Prenatal Diagn 31 :932-944 [2011]). As is shown in the examples and described elsewhere herein, the present method is capable of determining the presence of partial aneuploidies, e.g., deletions and multiplications of chromosome segments, and can be used to identify and determine the presence or absence of CNV that are associated with stillbirths.

Determination of CNV of clinical disorders

[00436] In addition to the early determination of birth defects, the methods described herein can be applied to the determination of any abnormality in the representation of genetic sequences within the genome. A number of abnormalities in the representation of genetic sequences within the genome have been associated with various pathologies. Such pathologies include, but are not limited to cancer, infectious and autoimmune diseases, diseases of the nervous system, metabolic and/or cardiovascular diseases, and the like.

[00437] Accordingly in various embodiments use of the methods described herein in the diagnosis, and/or monitoring, and or treating such pathologies is contemplated. For example, the methods can be applied to determining the presence or absence of a disease, to monitoring the progression of a disease and/or the efficacy of a treatment regimen, to determining the presence or absence of nucleic acids of a pathogen e.g. virus; to determining chromosomal abnormalities associated with graft versus host disease (GVHD), and to determining the contribution of individuals in forensic analyses.

CNVs in Cancer [00438] It has been shown that blood plasma and serum DNA from cancer patients contains measurable quantities of tumor DNA, that can be recovered and used as surrogate source of tumor DNA, and tumors are characterized by aneuploidy, or inappropriate numbers of gene sequences or even entire chromosomes. The determination of a difference in the amount of a given sequence i.e. a sequence of interest, in a sample from an individual can thus be used in the prognosis or diagnosis of a medical condition. In some embodiments, the present method can be used to determine the presence or absence of a chromosomal aneuploidy in a patient suspected or known to be suffering from cancer.

[00439] Some implementations herein provide methods for detecting cancer, tracking therapeutic response and minimal residual disease based on circulating cfDNA samples using shallow sequencing of the samples with paired-end methodology and using fragment size information available from paired-end reads to identify presence of differentially-methylated apoptotic DNA from cancer cells in the background of normal cells. It has been shown that tumor-derived cfDNA are shorter than non-tumor-derived cfDNA in some cancers. Therefore the size-based method described herein can be used to determine CNV including aneuploidies associated with these cancers, enabling (a) detection of tumor present in a screening or diagnostic setting; (b) monitoring response to therapy; (c) monitoring minimal residual disease.

[00440] In certain embodiments the aneuploidy is characteristic of the genome of the subject and results in a generally increased predisposition to a cancer. In certain embodiments the aneuploidy is characteristic of particular cells (e.g., tumor cells, proto-tumor neoplastic cells, etc.) that are or have an increased predisposition to neoplasia. Particular aneuploidies are associated with particular cancers or predispositions to particular cancers as described below. In some embodiments, a very shallow paired-end sequencing approach can be used to detect / monitor cancer presence in a cost-effective way.

[00441] Accordingly, various embodiments of the methods described herein provide a determination of copy number variation of sequence(s) of interest e.g. clinically-relevant sequence(s), in a test sample from a subject where certain variations in copy number provide an indicator of the presence and/or a predisposition to a cancer. In certain embodiments the sample comprises a mixture of nucleic acids is derived from two or more types of cells. In one embodiment, the mixture of nucleic acids is derived from normal and cancerous cells derived from a subject suffering from a medical condition e.g. cancer. [00442] The development of cancer is often accompanied by an alteration in number of whole chromosomes i.e. complete chromosomal aneuploidy, and/or an alteration in the number of segments of chromosomes i.e. partial aneuploidy, caused by a process known as chromosome instability (CIN) (Thoma et al, Swiss Med Weekly 2011 : 141 :wl3170). It is believed that many solid tumors, such as breast cancer, progress from initiation to metastasis through the accumulation of several genetic aberrations. [Sato et al, Cancer Res., 50: 7184-7189 [1990]; Jongsma et al, J Clin Pathol: Mol Path 55:305-309 [2002])]. Such genetic aberrations, as they accumulate, may confer proliferative advantages, genetic instability and the attendant ability to evolve drug resistance rapidly, and enhanced angiogenesis, proteolysis and metastasis. The genetic aberrations may affect either recessive "tumor suppressor genes" or dominantly acting oncogenes. Deletions and recombination leading to loss of heterozygosity (LOH) are believed to play a major role in tumor progression by uncovering mutated tumor suppressor alleles.

[00443] cfDNA has been found in the circulation of patients diagnosed with malignancies including but not limited to lung cancer (Pathak et al. Clin Chem 52: 1833-1842 [2006]), prostate cancer (Schwartzenbach et al. Clin Cancer Res 15: 1032-8 [2009]), and breast cancer (Schwartzenbach et al. available online at breast-cancer-research. com/content/l l/5/R71 [2009]). Identification of genomic instabilities associated with cancers that can be determined in the circulating cfDNA in cancer patients is a potential diagnostic and prognostic tool. In one embodiment, methods described herein are used to determine CNV of one or more sequence(s) of interest in a sample, e.g., a sample comprising a mixture of nucleic acids derived from a subject that is suspected or is known to have cancer e.g. carcinoma, sarcoma, lymphoma, leukemia, germ cell tumors and blastoma. In one embodiment, the sample is a plasma sample derived (processed) from peripheral blood that may comprise a mixture of cfDNA derived from normal and cancerous cells. In another embodiment, the biological sample that is needed to determine whether a CNV is present is derived from a cells that, if a cancer is present, comprise a mixture of cancerous and noncancerous cells from other biological tissues including, but not limited to biological fluids such as serum, sweat, tears, sputum, urine, sputum, ear flow, lymph, saliva, cerebrospinal fluid, ravages, bone marrow suspension, vaginal flow, transcervical lavage, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, and leukophoresis samples, or in tissue biopsies, swabs, or smears. In other embodiments, the biological sample is a stool (fecal) sample.

[00444] The methods described herein are not limited to the analysis of cfDNA. It will be recognized that similar analyses can be performed on cellular DNA samples.

[00445] In various embodiments the sequence(s) of interest comprise nucleic acid sequence(s) known or is suspected to play a role in the development and/or progression of the cancer. Examples of a sequence of interest include nucleic acids sequences e.g. complete chromosomes and/or segments of chromosomes, that are amplified or deleted in cancerous cells as described below. Total CNV number and risk for cancer.

[00446] Common cancer S Ps - and by analogy common cancer CNVs may each confer only a minor increase in disease risk. However, collectively they may cause a substantially elevated risk for cancers. In this regard it is noted that germline gains and losses of large DNA segments have been reported as factors predisposing individuals to neuroblastoma, prostate and colorectal cancer, breast cancer, and BRCA1 -associated ovarian cancer {see, e.g., Krepischi et al. Breast Cancer Res., 14: R24 [2012]; Diskin et al. Nature 2009, 459:987-991; Liu et al. Cancer Res 2009, 69: 2176-2179; Lucito et al. Cancer Biol Ther 2007, 6: 1592-1599; Thean et al. Genes Chromosomes Cancer 2010, 49:99-106; Venkatachalam et al. Int J Cancer 2011, 129: 1635-1642; and Yoshihara et al. Genes Chromosomes Cancer 2011, 50: 167-177). It is noted that CNVs frequently found in the healthy population (common CNVs) are believed to have a role in cancer etiology {see, e.g., Shlien and Malkin (2009) Genome Medicine, 1(6): 62). In one study testing the hypothesis that common CNVs are associated with malignancy (Shlien et al. Proc Natl Acad Sci USA 2008, 105: 11264-11269) a map of every known CNV whose locus coincides with that of bona fide cancer-related genes (as catalogued by Higgins et al. Nucleic Acids Res 2007, 35:D721-726) was created. These were termed "cancer CNVs". In an initial analysis (Shlien et al. Proc Natl Acad Sci USA 2008, 105: 11264-11269), 770 healthy genomes were evaluated using the Affymetrix 500K array set, which has an average inter-probe distance of 5.8 kb. As CNVs are generally thought to be depleted in gene regions (Redon et al. (2006) Nature 2006, 444:444-454), it was surprising to find 49 cancer genes that were directly encompassed or overlapped by a CNV in more than one person in a large reference population. In the top ten genes, cancer CNVs could be found in four or more people.

[00447] It is thus believed that CNV frequency can be used as a measure of risk for cancer (see, e.g., U.S. Patent Publication No: 2010/0261183 Al). The CNV frequency can be determined simply by the constitutive genome of the organism or it can represent a fraction derived from one or more tumors (neoplastic cells) if such are present.

[00448] In certain embodiments a number of CNVs in a test sample {e.g., a sample comprising a constitutional (germline) nucleic acid) or a mixture of nucleic acids {e.g., a germline nucleic acid and nucleic acid(s) derived from neoplastic cells) is determined using the methods described herein for copy number variations. Identification of an increased number of CNVs in the test sample, e.g., in comparison to a reference value is indicative of a risk of or pre-disposition for cancer in the subject. It will be appreciated that the reference value may vary with a given population. It will also be appreciated that the absolute value of the increase in CNV frequency will vary depending on the resolution of the method utilized to determine CNV frequency and other parameters. Typically, an increase in CNV frequency of at least about 1.2 times the reference value been determined to indicative of risk for cancer (see, e.g., U.S. Patent Publication No: 2010/0261183 Al), for example an increase in CNV frequency of at least or about 1.5 times the reference value or greater, such as 2-4 times the reference value is an indicator of an increased risk of cancer (e.g., as compared to the normal healthy reference population).

[00449] A determination of structural variation in the genome of a mammal in comparison to a reference value is also believed to be indicative of risk of cancer. In this context, in one embodiment, the term "structural variation" is can be defined as the CNV frequency in a mammal multiplied by the average CNV size (in bp) in the mammal. Thus, high structural variation scores will result due to increased CNV frequency and/or due to the occurrence of large genomic nucleic acid deletions or duplications. Accordingly, in certain embodiments a number of CNVs in a test sample (e.g., a sample comprising a constitutional (germline) nucleic acid) is determined using the methods described herein to determine size and number of copy number variations. In certain embodiments a total structural variation score within genomic DNA of greater than about 1 megabase, or greater than about 1.1 megabases, or greater than about 1.2 megabases, or greater than about 1.3 megabases, or greater than about 1.4 megabases, or greater than about 1.5 megabases, or greater than about 1.8 megabases, or greater than about 2 megabases of DNA is indicative of risk of cancer.

[00450] It is believed these methods provide a measure of the risk of any cancer including but not limited to, acute and chronic leukemias, lymphomas, numerous solid tumors of mesenchymal or epithelial tissue, brain, breast, liver, stomach, colon cancer, B cell lymphoma, lung cancer, a bronchus cancer, a colorectal cancer, a prostate cancer, a breast cancer, a pancreas cancer, a stomach cancer, an ovarian cancer, a urinary bladder cancer, a brain or central nervous system cancer, a peripheral nervous system cancer, an esophageal cancer, a cervical cancer, a melanoma, a uterine or endometrial cancer, a cancer of the oral cavity or pharynx, a liver cancer, a kidney cancer, a biliary tract cancer, a small bowel or appendix cancer, a salivary gland cancer, a thyroid gland cancer, a adrenal gland cancer, an osteosarcoma, a chondrosarcoma, a liposarcoma, a testes cancer, and a malignant fibrous histiocytoma, and other cancers.

Full chromosome aneuploidies.

[00451] As indicated above, there exists a high frequency of aneuploidy in cancer. In certain studies examining the prevalence of somatic copy number alterations (SCNAs) in cancer, it has been discovered that one-quarter of the genome of a typical cancer cell is affected either by whole-arm SCNAs or by the whole- chromosome SCNAs of aneuploidy {see, e.g., Beroukhim et al. Nature 463 : 899-905 [2010]). Whole-chromosome alterations are recurrently observed in several cancer types. For example, the gain of chromosome 8 is seen in 10-20% of cases of acute myeloid leukaemia (AML), as well as some solid tumours, including Ewing's Sarcoma and desmoid tumours {see, e.g., Barnard et al. Leukemia 10: 5-12 [1996]; Maurici et al. Cancer Genet. Cytogenet. 100: 106-110 [1998]; Qi et al. Cancer Genet. Cytogenet. 92: 147-149 [1996]; Barnard, D. R. et al. Blood 100: 427-434 [2002]; and the like. Illustrative, but non-limiting list of chromosome gains and losses in human cancers are shown in Table 2.

TABLE 2. Illustrative specific, recurrent chromosome gains and losses in human cancer (see, g.g., Gordon et al. (2012) Nature Rev. Genetics. 13: 189-203).

leukaemia

8 Acute myeloid leukaemia Adenocarcinoma (kidney)

Chronic myeloid leukaemia

Ewing's sarcoma

9 Multiple myeloma

Polycythaemia vera

10 Acute lymphoblastic leukaemia Astrocytoma

Adenocarcinoma (uterus) Multiple myeloma

11 Multiple myeloma

12 Chronic lymphocytic leukaemia Multiple myeloma

Wilms' tumor

13 Acute myeloid leukaemia Multiple myeloma

Wilms' tumor

14 Acute lymphoblastic leukaemia Adenocarcinoma (kidney)

Meningioma

15 Multiple myeloma

16 Adenocarcinoma (kidney) Multiple myeloma

17 Adenocarcinoma (kidney)

Acute lymphoblastic leukaemia

18 Acute lymphoblastic leukaemia Adenocarcinoma (kidney)

Wilms' tumour

19 Multiple myeloma Adenocarcinoma (Breast)

Chronic myeloid leukaemia Meningioma

20 Hepatoblastoma

Adenocarcinoma (kidney)

21 Acute lymphoblastic leukaemia

Acute megakaryoblastic leukaemia

22 Acute lymphoblastic leukaemia Meningioma

X Acute lymphoblastic leukaemia

Follicular lymphoma

Y

[00452] In various embodiments, the methods described herein can be used to detect and/or quantify whole chromosome aneuploidies that are associated with cancer generally, and/or that are associated with particular cancers. Thus, for example, in certain embodiments, detection and/or quantification of whole chromosome aneuploidies characterized by the gains or losses shown in Table 2 are contemplated.

Arm level chromosomal segment copy number variations.

[00453] Multiple studies have reported patterns of arm-level copy number variations across large numbers of cancer specimens (Lin et al. Cancer Res 68, 664- 673 (2008); George et al. PLoS ONE 2, e255 (2007); Demichelis et al. Genes Chromosomes Cancer 48: 366-380 (2009); Beroukhim et al. Nature. 463(7283): 899- 905 [2010]). It has additionally been observed that the frequency of arm-level copy number variations decreases with the length of chromosome arms. Adjusted for this trend, the majority of chromosome arms exhibit strong evidence of preferential gain or loss, but rarely both, across multiple cancer lineages (see, e.g., Beroukhim et al. Nature. 463(7283): 899-905 [2010]).

[00454] Accordingly, in one embodiment, methods described herein are used to determine arm level CNVs (CNVs comprising one chromosomal arm or substantially one chromosomal arm) in a sample. The CNVs can be determined in a CNVs in a test sample comprising a constitutional (germline) nucleic acid and the arm level CNVs can be identified in those constitutional nucleic acids. In certain embodiments arm level CNVs are identified (if present) in a sample comprising a mixture of nucleic acids (e.g., nucleic acids derived from normal and nucleic acids derived from neoplastic cells). In certain embodiments the sample is derived from a subject that is suspected or is known to have cancer e.g. carcinoma, sarcoma, lymphoma, leukemia, germ cell tumors, blastoma, and the like. In one embodiment, the sample is a plasma sample derived (processed) from peripheral blood that may comprise a mixture of cfDNA derived from normal and cancerous cells. In another embodiment, the biological sample that is used to determine whether a CNV is present is derived from a cells that, if a cancer is present, comprise a mixture of cancerous and non-cancerous cells from other biological tissues including, but not limited to biological fluids such as serum, sweat, tears, sputum, urine, sputum, ear flow, lymph, saliva, cerebrospinal fluid, ravages, bone marrow suspension, vaginal flow, transcervical lavage, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, and leukophoresis samples, or in tissue biopsies, swabs, or smears. In other embodiments, the biological sample is a stool (fecal) sample.

[00455] In various embodiments the CNVs identified as indicative of the presence of a cancer or an increased risk for a cancer include, but are not limited to the arm level CNVs listed in Table 3. As illustrated in Table 3 certain CNVs that comprise a substantial arm-level gain are indicative of the presence of a cancer or an increased risk for a certain cancers. Thus, for example, a gain in lq is indicative of the presence or increased risk for acute lymphoblastic leukemia (ALL), breast cancer, GIST, HCC, lung NSC, medulloblastoma, melanoma, MPD, ovarian cancer, and/or prostate cancer. A gain in 3q is indicative of the presence or increased risk for Esophageal Squamous cancer, Lung SC, and/or MPD. A gain in 7q is indicative of the presence or increased risk for colorectal cancer, glioma, HCC, lung NSC, medulloblastoma, melanoma, prostate cancer, and/or renal cancer. A gain in 7p is indicative of the presence or increased risk for breast cancer, colorectal cancer, esophageal adenocarcinoma, glioma, HCC, Lung NSC, medulloblastoma, melanoma, and/or renal cancer. A gain in 20q is indicative of the presence or increased risk for breast cancer, colorectal cancer, dedifferentiated liposarcoma, esophageal adenocarcinoma, esophageal squamous, glioma cancer, HCC, lung NSC, melanoma, ovarian cancer, and/or renal cancer, and so forth.

[00456] Similarly as illustrated in Table 3 certain CNVs that comprise a substantial arm-level loss are indicative of the presence of and/or an increased risk for certain cancers. Thus, for example, a loss in lp is indicative of the presence or increased risk for gastrointestinal stromal tumor. A loss in 4q is indicative of the presence or increased risk for colorectal cancer, esophageal adenocarcinoma, lung sc, melanoma, ovarian cancer, and/or renal cancer, a loss in 17p is indicative of the presence or increased risk for breast cancer, colorectal cancer, esophageal adenocarcinoma, HCC, lung NSC, lung SC, and/or ovarian cancer, and the like.

TABLE 3. Significant arm-level chromosomal segment copy number alterations in each of 16 cancer subtypes (breast, colorectal, dedifferentiated liposarcoma, esophageal adenocarcinoma, esophageal squamous, GIST (gastrointestinal stromal tumor), glioma, HCC (hepatocellular carcinoma), lung NSC, lung SC, medulloblastoma, melanoma, MPD (myeloproliferative disease), ovarian, prostate, acute lymphoblastic leukemia (ALL), and renal) (see, e.g., Beroukhim et ah Nature (2010) 463(7283): 899-905).

p ALL Breast, Esophageal

Adenocarcinoma, Renal

q ALL Colorectal, Esophageal

Adenocarcinoma, Lung

SC, Melanoma, Ovarian,

Renal

5p Esophageal Squamous, TERT HCC, Lung NSC, Lung

SC, Renal

5q HCC, Renal Esophageal ARC

Adenocarcinoma, Lung

NSC

6p ALL, HCC, Lung NSC, —

Melanoma

6q ALL Melanoma, Renal

7p Breast, Colorectal, EGFR Esophageal

Adenocarcinoma, Glioma,

HCC, Lung NSC,

Medulloblastoma,

Melanoma, Renal

7q Colorectal, Glioma, HCC, BRAF, MET Lung NSC,

Medulloblastoma,

Melanoma, Prostate, Renal

8p ALL, MPD Breast, HCC, Lung NSC,

Medulloblastoma,

Prostate, Renal

8q ALL, Breast, Colorectal, Medulloblastoma MYC Esophageal

Adenocarcinoma,

Esophageal Squamous,

HCC, Lung NSC, MPD,

Ovarian, Prostate

9p MPD ALL, Breast, Esophageal CDKN2A/B

Adenocarcinoma, Lung

NSC, Melanoma, Ovarian,

Renal

9q ALL, MPD Lung NSC, Melanoma,

Ovarian, Renal

lOp ALL Glioma, Lung SC,

Melanoma

lOq ALL Glioma, Lung SC, PTEN

Medulloblastoma,

Melanoma

l ip — Medulloblastoma WT1 l lq Dedifferentiated ATM

Liposarcoma,

Medulloblastoma,

Lung NSC, Lung SC,

Ovarian, Prostate

[00457] The examples of associations between arm level copy number variations are intended to be illustrative and not limiting. Other arm level copy number variations and their cancer associations are known to those of skill in the art.

Smaller, e.g., focal, copy number variations. [00458] As indicated above, in certain embodiments, the methods described herein can be used to determine the presence or absence of a chromosomal amplification. In some embodiments, the chromosomal amplification is the gain of one or more entire chromosomes. In other embodiments, the chromosomal amplification is the gain of one or more segments of a chromosome. In yet other embodiments, the chromosomal amplification is the gain of two or more segments of two or more chromosomes. In various embodiments, the chromosomal amplification can involve the gain of one or more oncogenes.

[00459] Dominantly acting genes associated with human solid tumors typically exert their effect by overexpression or altered expression. Gene amplification is a common mechanism leading to upregulation of gene expression. Evidence from cytogenetic studies indicates that significant amplification occurs in over 50% of human breast cancers. Most notably, the amplification of the proto-oncogene human epidermal growth factor receptor 2 (HER2) located on chromosome 17 (17(17q21- q22)), results in overexpression of HER2 receptors on the cell surface leading to excessive and dysregulated signaling in breast cancer and other malignancies (Park et al, Clinical Breast Cancer 8:392-401 [2008]). A variety of oncogenes have been found to be amplified in other human malignancies. Examples of the amplification of cellular oncogenes in human tumors include amplifications of: c-myc in promyelocytic leukemia cell line HL60, and in small-cell lung carcinoma cell lines, N-myc in primary neuroblastomas (stages III and IV), neuroblastoma cell lines, retinoblastoma cell line and primary tumors, and small-cell lung carcinoma lines and tumors, L-myc in small-cell lung carcinoma cell lines and tumors, c-myb in acute myeloid leukemia and in colon carcinoma cell lines, c-erbb in epidermoid carcinoma cell, and primary gliomas, c-K-ras-2 in primary carcinomas of lung, colon, bladder, and rectum, N-ras in mammary carcinoma cell line (Varmus H., Ann Rev Genetics 18: 553-612 (1984) [cited in Watson et al, Molecular Biology of the Gene (4th ed.; Benjamin/Cummings Publishing Co. 1987)].

[00460] Duplications of oncogenes are a common cause of many types of cancer, as is the case with P70-S6 Kinase 1 amplification and breast cancer. In such cases the genetic duplication occurs in a somatic cell and affects only the genome of the cancer cells themselves, not the entire organism, much less any subsequent offspring. Other examples of oncogenes that are amplified in human cancers include MYC, ERBB2 (EFGR), CCNDl (Cyclin Dl), FGFR1 and FGFR2 in breast cancer, MYC and ERBB2 in cervical cancer, HRAS, KRAS, and MYB in colorectal cancer, MYC, CCNDl and MDM2 in esophageal cancer, CCNE, KRAS and MET in gastric cancer, ERBB 1, and CDK4 in glioblastoma, CCNDl, ERBB1, and MYC in head and neck cancer, CCNDl in hepatocellular cancer, MYCB in neuroblastoma, MYC, ERBB2 and AKT2 in ovarian cancer, MDM2 and CDK4 in sarcoma, and MYC in small cell lung cancer. In one embodiment, the present method can be used to determine the presence or absence of amplification of an oncogene associated with a cancer. In some embodiments, the amplified oncogene is associated with breast cancer, cervical cancer, colorectal cancer, esophageal cancer, gastric cancer, glioblastoma, head and neck cancer, hepatocellular cancer, neuroblastoma, ovarian cancer, sarcoma, and small cell lung cancer. [00461] In one embodiment, the present method can be used to determine the presence or absence of a chromosomal deletion. In some embodiments, the chromosomal deletion is the loss of one or more entire chromosomes. In other embodiments, the chromosomal deletion is the loss of one or more segments of a chromosome. In yet other embodiments, the chromosomal deletion is the loss of two or more segments of two or more chromosomes. The chromosomal deletion can involve the loss of one or more tumor suppressor genes.

[00462] Chromosomal deletions involving tumor suppressor genes are believed to play an important role in the development and progression of solid tumors. The retinoblastoma tumor suppressor gene (Rb-1), located in chromosome 13ql4, is the most extensively characterized tumor suppressor gene. The Rb-1 gene product, a 105 kDa nuclear phosphoprotein, apparently plays an important role in cell cycle regulation (Howe et al, Proc Natl Acad Sci (USA) 87:5883-5887 [1990]). Altered or lost expression of the Rb protein is caused by inactivation of both gene alleles either through a point mutation or a chromosomal deletion. Rb-i gene alterations have been found to be present not only in retinoblastomas but also in other malignancies such as osteosarcomas, small cell lung cancer (Rygaard et al, Cancer Res 50: 5312-5317 [1990)]) and breast cancer. Restriction fragment length polymorphism (RFLP) studies have indicated that such tumor types have frequently lost heterozygosity at 13q suggesting that one of the Rb-1 gene alleles has been lost due to a gross chromosomal deletion (Bowcock et al, Am J Hum Genet, 46: 12 [1990]). Chromosome 1 abnormalities including duplications, deletions and unbalanced translocations involving chromosome 6 and other partner chromosomes indicate that regions of chromosome 1, in particular Iq21-lq32 and lpl l-13, might harbor oncogenes or tumor suppressor genes that are pathogenetically relevant to both chronic and advanced phases of myeloproliferative neoplasms (Caramazza et al, Eur J Hematol 84: 191-200 [2010]). Myeloproliferative neoplasms are also associated with deletions of chromosome 5. Complete loss or interstitial deletions of chromosome 5 are the most common karyotypic abnormality in myelodysplastic syndromes (MDSs). Isolated del(5q)/5q- MDS patients have a more favorable prognosis than those with additional karyotypic defects, who tend to develop myeloproliferative neoplasms (MPNs) and acute myeloid leukemia. The frequency of unbalanced chromosome 5 deletions has led to the idea that 5q harbors one or more tumor-suppressor genes that have fundamental roles in the growth control of hematopoietic stem/progenitor cells (HSCs/HPCs). Cytogenetic mapping of commonly deleted regions (CDRs) centered on 5q31 and 5q32 identified candidate tumor-suppressor genes, including the ribosomal subunit RPS14, the transcription factor Egrl/Krox20 and the cytoskeletal remodeling protein, alpha-catenin (Eisenmann et al, Oncogene 28:3429-3441 [2009]). Cytogenetic and allelotyping studies of fresh tumors and tumor cell lines have shown that allelic loss from several distinct regions on chromosome 3p, including 3p25, 3p21-22, 3p21.3, 3pl2— 13 and 3pl4, are the earliest and most frequent genomic abnormalities involved in a wide spectrum of major epithelial cancers of lung, breast, kidney, head and neck, ovary, cervix, colon, pancreas, esophagus, bladder and other organs. Several tumor suppressor genes have been mapped to the chromosome 3p region, and are thought that interstitial deletions or promoter hypermethylation precede the loss of the 3p or the entire chromosome 3 in the development of carcinomas (Angeloni D., Briefings Functional Genomics 6: 19-39 [2007]). [00463] Newborns and children with Down syndrome (DS) often present with congenital transient leukemia and have an increased risk of acute myeloid leukemia and acute lymphoblastic leukemia. Chromosome 21, harboring about 300 genes, may be involved in numerous structural aberrations, e.g., translocations, deletions, and amplifications, in leukemias, lymphomas, and solid tumors. Moreover, genes located on chromosome 21 have been identified that play an important role in tumorigenesis. Somatic numerical as well as structural chromosome 21 aberrations are associated with leukemias, and specific genes including RUNX1, TMPRSS2, and TFF, which are located in 21q, play a role in tumorigenesis (Fonatsch C Gene Chromosomes Cancer 49:497-508 [2010]).

[00464] In view of the foregoing, in various embodiments the methods described herein can be used to determine the segment CNVs that are known to comprise one or more oncogenes or tumor suppressor genes, and/or that are known to be associated with a cancer or an increased risk of cancer. In certain embodiments, the CNVs can be determined in a test sample comprising a constitutional (germline) nucleic acid and the segment can be identified in those constitutional nucleic acids. In certain embodiments segment CNVs are identified (if present) in a sample comprising a mixture of nucleic acids (e.g., nucleic acids derived from normal and nucleic acids derived from neoplastic cells). In certain embodiments the sample is derived from a subject that is suspected or is known to have cancer e.g. carcinoma, sarcoma, lymphoma, leukemia, germ cell tumors, blastoma, and the like. In one embodiment, the sample is a plasma sample derived (processed) from peripheral blood that may comprise a mixture of cfDNA derived from normal and cancerous cells. In another embodiment, the biological sample that is used to determine whether a CNV is present is derived from a cells that, if a cancer is present, comprises a mixture of cancerous and non-cancerous cells from other biological tissues including, but not limited to biological fluids such as serum, sweat, tears, sputum, urine, sputum, ear flow, lymph, saliva, cerebrospinal fluid, ravages, bone marrow suspension, vaginal flow, transcervical lavage, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, and leukophoresis samples, or in tissue biopsies, swabs, or smears. In other embodiments, the biological sample is a stool (fecal) sample. [00465] The CNVs used to determine presence of a cancer and/or increased risk for a cancer can comprise amplification or deletions.

[00466] In various embodiments the CNVs identified as indicative of the presence of a cancer or an increased risk for a cancer include one or more of the amplifications shown in Table 4.

TABLE 4. Illustrative, but non-limiting chromosomal segments characterized by amplifications that are associated with cancers. Cancer types listed are those identified in Beroukhim et al. Nature 18: 463: 899-905.

chr6:43556800- 0.72 Esophageal adenocarcinoma,

44361368 Hepatocellular, Ovarian

chr6:63255006- 1.988 Esophageal adenocarcinoma, Lung NSC 65243766

chr7: 115981465- 0.69 Esophageal adenocarcinoma, Lung NSC, 116676953 Melanoma, Ovarian

chr7:54899301- 0.363 Esophageal adenocarcinoma, Esophageal 55275419 squamous

chr7:89924533- 9.068 Breast, Esophageal adenocarcinoma, 98997268 Esophageal squamous, Ovarian chr8: 101163387- 2.516 Lung NSC, Melanoma, Ovarian

103693879

chr8: 116186189- 4.4 Breast, Hepatocellular, Lung NSC, 120600761 Ovarian

chr8: 128774432- 0.009 Esophageal adenocarcinoma, Esophageal 128849112 squamous, Hepatocellular, Lung SC,

Medulloblastoma, Myeloproliferative disorder, Ovarian

chr8: 140458177- 5.784 Lung NSC, Medulloblastoma, Melanoma, 146274826 Ovarian

chr8:38252951- 0.167 Colorectal, Esophageal adenocarcinoma, 38460772 Esophageal squamous

chr8:42006632- 0.257 Esophageal adenocarcinoma, Lung NSC, 42404492 Lung SC, Ovarian, Prostate

chr8:81242335- 0.717 Breast, Melanoma

81979194

chr9: 137859478- 2.29 Colorectal, Dedifferentiated liposarcoma 140273252

chrl0:74560456- 7.455 Breast, Ovarian, Prostate

82020637

chrl 1 : 101433436- 0.683 Lung NSC, Lung SC

102134907

chrl 1 :32027116- 5.744 Breast, Dedifferentiated liposarcoma, 37799354 Lung NSC, Lung SC

chrl 1 :69098089- 0.161 Dedifferentiated liposarcoma, Esophageal 69278404 adenocarcinoma, Hepatocellular, Lung

SC, Ovarian

chrl 1 :76699529- 1.286 Dedifferentiated liposarcoma, Esophageal 78005085 adenocarcinoma, Lung SC, Ovarian chrl2: l-1311104 1.271 Lung NSC

chrl2:25189655- 0.112 Acute lymphoblastic leukemia,

25352305 Esophageal adenocarcinoma, Esophageal squamous, Ovarian

chrl2:30999223- 1.577 Acute lymphoblastic leukemia,

32594050 Colorectal, Esophageal adenocarcinoma,

Esophageal squamous, Lung NSC, Lung SC

chrl2:38788913- 3.779 Breast, Colorectal, Dedifferentiated 42596599 liposarcoma, Esophageal squamous, Lung chrl7:55144989- 0.31 Lung NSC, Medulloblastoma, Melanoma,

55540417 Ovarian

chrl7:62318152- 1.519 Breast, Lung NSC, Melanoma, Ovarian

63890591

chrl7:70767943- 0.537 Breast, Lung NSC, Melanoma, Ovarian

71305641

chrl 8: 17749667- 5.029 Colorectal, Esophageal adenocarcinoma,

22797232 Ovarian

chrl9:34975531- 0.096 Breast, Esophageal adenocarcinoma,

35098303 Esophageal squamous

chrl9:43177306- 2.17 Lung NSC, Ovarian

45393020

chrl9:59066340- 0.321 Breast, Lung NSC, Ovarian

59471027

chr2: 15977811- 0.056 Lung SC

16073001

chr20:29526118- 0.246 Ovarian

29834552

chr20: 51603033- 0.371 Hepatocellular, Lung NSC, Ovarian

51989829

chr20:61329497- 0.935 Hepatocellular, Lung NSC

62435964

chr22: 19172385- 0.487 Colorectal, Melanoma, Ovarian

19746441

chrX: 152729030- 1.748 Breast, Lung NSC, Renal

154913754

chrX:66436234- 0.267 Ovarian, Prostate

67090514

[00467] In certain embodiments in combination with the amplifications described above (herein), or separately, the CNVs identified as indicative of the presence of a cancer or an increased risk for a cancer include one or more of the deletions shown in Table 5.

TABLE 5. Illustrative, but non-limiting chromosomal segments characterized by deletions that are associated with cancers. Cancer types listed are those identified in Beroukhim et al. Nature 18: 463: 899-905.

disorder, Ovarian, Prostate

chrl :3756302- lp36.31 Acute lymphoblastic leukemia, Breast, 6867390 Esophageal squamous, Hepatocellular,

Lung NSC, Lung SC, Medulloblastoma, Myeloproliferative disorder, Ovarian, Prostate, Renal

chrl :71284749- lp31.1 Breast, Esophageal adenocarcinoma,

74440273 Glioma, Hepatocellular, Lung NSC, Lung

SC, Melanoma, Ovarian, Renal chr2: 1-15244284 2p25.3 Lung NSC, Ovarian

chr2: 138479322- 2q22.1 Breast, Colorectal, Esophageal

143365272 adenocarcinoma, Esophageal squamous,

Hepatocellular, Lung NSC, Ovarian, Prostate, Renal

chr2:204533830- 2q33.2 Esophageal adenocarcinoma,

206266883 Hepatocellular, Lung NSC,

Medulloblastoma, Renal

chr2:241477619- 2q37.3 Breast, Dedifferentiated liposarcoma, 242951149 Esophageal adenocarcinoma, Esophageal squamous, Hepatocellular, Lung NSC, Lung SC, Medulloblastoma, Melanoma, Ovarian, Renal

chr3 : 116900556- 3ql3.31 Dedifferentiated liposarcoma, Esophageal 120107320 adenocarcinoma, Hepatocellular, Lung

NSC, Melanoma, Myeloproliferative disorder, Prostate

chr3 : l-2121282 3p26.3 Colorectal, Dedifferentiated liposarcoma,

Esophageal adenocarcinoma, Lung NSC, Melanoma, Myeloproliferative disorder chr3 : 175446835- 3q26.31 Acute lymphoblastic leukemia,

178263192 Dedifferentiated liposarcoma, Esophageal adenocarcinoma, Lung NSC, Melanoma, Myeloproliferative disorder, Prostate chr3 : 58626894- 3pl4.2 Breast, Colorectal, Dedifferentiated

61524607 liposarcoma, Esophageal adenocarcinoma,

Esophageal squamous, Hepatocellular, Lung NSC, Lung SC, Medulloblastoma, Melanoma, Myeloproliferative disorder, Ovarian, Prostate, Renal

chr4: 1-435793 4pl6.3 Myeloproliferative disorder

chr4: 186684565- 4q35.2 Breast, Esophageal adenocarcinoma,

191273063 Esophageal squamous, Lung NSC,

Medulloblastoma, Melanoma, Prostate, Renal

chr4:91089383- 4q22.1 Acute lymphoblastic leukemia, Esophageal 93486891 adenocarcinoma, Hepatocellular, Lung

NSC, Renal

chr5: 177541057- 5q35.3 Breast, Lung NSC, Myeloproliferative 180857866 disorder, Ovarian chr5: 57754754- 5ql l .2 Breast, Colorectal, Dedifferentiated 59053198 liposarcoma, Esophageal adenocarcinoma,

Esophageal squamous, Lung SC,

Melanoma, Myeloproliferative disorder, Ovarian, Prostate

chr5:85837489- 5q21.1 Colorectal, Dedifferentiated liposarcoma, 133480433 Lung NSC, Lung SC, Myeloproliferative disorder, Ovarian

chr6: 101000242- 6q22.1 Colorectal, Lung NSC, Lung SC

121511318

chr6: 1543157- 6p25.3 Colorectal, Dedifferentiated liposarcoma, 2570302 Esophageal adenocarcinoma, Lung NSC,

Lung SC, Ovarian, Prostate

chr6: 161612277- 6q26 Colorectal, Esophageal adenocarcinoma, 163134099 Esophageal squamous, Lung NSC, Lung

SC, Ovarian, Prostate

chr6: 76630464- 6ql6.1 Colorectal, Hepatocellular, Lung NSC 105342994

chr7: 141592807- 7q34 Breast, Colorectal, Esophageal

142264966 adenocarcinoma, Esophageal squamous,

Hepatocellular, Lung NSC, Ovarian, Prostate, Renal chr7: 144118814- 7q35 Breast, Esophageal adenocarcinoma, 148066271 Esophageal squamous, Lung NSC,

Melanoma, Myeloproliferative disorder, Ovarian

chr7: 156893473- 7q36.3 Breast, Esophageal adenocarcinoma, 158821424 Esophageal squamous, Lung NSC,

Melanoma, Myeloproliferative disorder, Ovarian, Prostate

chr7: 3046420- 7p22.2 Melanoma, Myeloproliferative disorder, 4279470 Ovarian

chr7:65877239- 7q21.11 Breast, Medulloblastoma, Melanoma, 79629882 Myeloproliferative disorder, Ovarian chr8: 1-392555 8p23.3 Acute lymphoblastic leukemia, Breast,

Myeloproliferative disorder

chr8:2053441- 8p23.2 Acute lymphoblastic leukemia,

6259545 Dedifferentiated liposarcoma, Esophageal adenocarcinoma, Esophageal squamous, Hepatocellular, Lung NSC,

Myeloproliferative disorder

chr8:22125332- 8p21.2 Acute lymphoblastic leukemia,

30139123 Dedifferentiated liposarcoma,

Hepatocellular, Myeloproliferative disorder, Ovarian, Renal

chr8:39008109- 8p 11.22 Acute lymphoblastic leukemia, Breast, 41238710 Dedifferentiated liposarcoma, Esophageal squamous, Hepatocellular, Lung NSC, Myeloproliferative disorder, Renal chr8:42971602- 8ql l .22 Breast, Dedifferentiated liposarcoma, 72924037 Esophageal squamous, Hepatocellular,

Lung NSC, Myeloproliferative disorder, Renal

chr9: 1-708871 9p24.3 Acute lymphoblastic leukemia, Breast,

Lung NSC, Myeloproliferative disorder, Ovarian, Prostate

chr9:21489625- 9p21.3 Colorectal, Esophageal adenocarcinoma, 22474701 Esophageal squamous, Myeloproliferative disorder, Ovarian

chr9:36365710- 9pl3.2 Myeloproliferative disorder

37139941

chr9:7161607- 9p24.1 Acute lymphoblastic leukemia, Breast, 12713130 Colorectal, Esophageal adenocarcinoma,

Hepatocellular, Lung SC,

Medulloblastoma, Melanoma,

Myeloproliferative disorder, Ovarian, Prostate, Renal chrlO: 1-1042949 10pl5.3 Colorectal, Lung NSC, Lung SC, Ovarian,

Prostate, Renal

chrlO: 129812260- 10q26.3 Breast, Colorectal, Glioma, Lung NSC, 135374737 Lung SC, Melanoma, Ovarian, Renal chrl0:52313829- 10ql l .23 Colorectal, Lung NSC, Lung SC, Ovarian, 53768264 Renal

chrl0:89467202- 10q23.31 Breast, Lung SC, Ovarian, Renal

90419015

chrl 1 : 107086196- l lq23.1 Esophageal adenocarcinoma,

116175885 Medulloblastoma, Renal

chrl l : l-1391954 l lpl5.5 Breast, Dedifferentiated liposarcoma,

Esophageal adenocarcinoma, Lung NSC, Medulloblastoma, Ovarian

chrl 1 : 130280899- l lq25 Esophageal adenocarcinoma, Esophageal 134452384 squamous, Hepatocellular, Lung NSC,

Medulloblastoma, Renal

chrl 1 :82612034- l lql4.1 Melanoma, Renal

85091467

chrl2: 11410696- 12pl3.2 Breast, Hepatocellular, Myeloproliferative 12118386 disorder, Prostate

chrl2: 131913408- 12q24.33 Dedifferentiated liposarcoma, Lung NSC, 132349534 Myeloproliferative disorder

chrl2:97551177- 12q23.1 Breast, Colorectal, Esophageal squamous, 99047626 Lung NSC, Myeloproliferative disorder chrl3 : 111767404- 13q34 Breast, Hepatocellular, Lung NSC

114142980

chrl3 : l-23902184 13q l2.11 Breast, Lung SC, Ovarian

chrl3 :46362859- 13ql4.2 Hepatocellular, Lung SC,

48209064 Myeloproliferative disorder, Prostate chrl3 :92308911- 13q31.3 Breast, Hepatocellular, Lung NSC, Renal 94031607

chrl4: 1-29140968 14ql l .2 Acute lymphoblastic leukemia, Esophageal adenocarcinoma, Myeloproliferative disorder

chrl4:65275722- 14q23.3 Dedifferentiated liposarcoma,

67085224 Myeloproliferative disorder

chrl4:80741860- 14q32.12 Acute lymphoblastic leukemia,

106368585 Dedifferentiated liposarcoma, Melanoma,

Myeloproliferative disorder

chrl 5: 1-24740084 15ql 1.2 Acute lymphoblastic leukemia, Breast,

Esophageal adenocarcinoma, Lung NSC, Myeloproliferative disorder, Ovarian chrl5:35140533- 15ql5.1 Esophageal adenocarcinoma, Lung NSC, 43473382 Myeloproliferative disorder chrl6: 1-359092 16pl3.3 Esophageal adenocarcinoma,

Hepatocellular, Lung NSC, Renal chrl6:31854743- 16ql l .2 Breast, Hepatocellular, Lung NSC, 53525739 Melanoma, Renal

chrl6:5062786- 16pl3.3 Hepatocellular, Lung NSC,

7709383 Medulloblastoma, Melanoma,

Myeloproliferative disorder, Ovarian, Renal

chrl6:76685816- 16q23.1 Breast, Colorectal, Esophageal

78205652 adenocarcinoma, Hepatocellular, Lung

NSC, Lung SC, Medulloblastoma, Renal chrl6:80759878- 16q23.3 Colorectal, Hepatocellular, Renal

82408573

chrl6:88436931- 16q24.3 Colorectal, Hepatocellular, Lung NSC, 88827254 Prostate, Renal

chrl7: 10675416- 17pl2 Lung NSC, Lung SC, Myeloproliferative 12635879 disorder

chrl7:26185485- 17ql l .2 Breast, Colorectal, Dedifferentiated 27216066 liposarcoma, Lung NSC, Lung SC,

Melanoma, Myeloproliferative disorder, Ovarian

chrl7:37319013- 17q21.2 Breast, Colorectal, Dedifferentiated 37988602 liposarcoma, Lung SC, Melanoma,

Myeloproliferative disorder, Ovarian chrl7:7471230- 17pl3.1 Lung SC, Myeloproliferative disorder 7717938

chrl7:78087533- 17q25.3 Colorectal, Myeloproliferative disorder 78774742

chrl8: l-587750 18pl l .32 Myeloproliferative disorder

chrl 8:46172638- 18q21.2 Esophageal adenocarcinoma, Lung NSC 49935241

chrl8:75796373- 18q23 Colorectal, Esophageal adenocarcinoma, 76117153 Esophageal squamous, Ovarian, Prostate chrl9: 1-526082 19pl3.3 Hepatocellular, Lung NSC, Renal

[00468] The anuploidies identified as characteristic of various cancers (e.g., the anuploidies identified in Tables 4 and 5) may contain genes known to be implicated in cancer etiologies (e.g., tumor suppressors, oncogenes, etc.). These aneuploidies can also be probed to identifiy relevant but previously unknown genes. [00469] For example Beroukhim et al. supra, assessed potential cancer-causing genes in the copy number alterations using GRAIL (Gene Relationships Among Implicated L0C120), an algorithm that searches for functional relationships among genomic regions. GRAIL scores each gene in a collection of genomic regions for its 'relatedness' to genes in other regions based on textual similarity between published abstracts for all papers citing the genes, on the notion that some target genes will function in common pathways. These methods permit identification/characterization of genes previously not associated with the particular cancers at issue. Table 6 illustrates target genes known to be within the identified amplified segment and predicted genes, and Table 7 illustrates target genes known to be within the identified deleted segment and predicted genes. TABLE 6. Illustrative, but non-limiting chromosomal segments and genes known or predicted to be present in regions characterized by amplification in various cancers (see, e.g., Beroukhim et al. supra.).

17q21.33 chrl7:44673157- 4 NGFR, PHB 45060263

p24.3 chr2: 15977811- 1 MYCN MYCN

16073001

7q21.3 chr7:89924533- 62 CDK6 CDK6

98997268

13q34 chrl3 : 108477140- 4 IRS2

110084607

l lql4.1 chrl 1 :76699529- 14 GAB2

78005085

0ql3.33 chr20:61329497- 38 BIRC7

62435964

17q23.1 chrl7:55144989- 5 RPS6KB1

55540417

lpl2 chrl : 119996566- 5 REG4

120303234

8q21.13 chr8:81242335- 3 ZNF704,

81979194 ZBTB10

6p21.1 chr6:43556800- 18 VEGFA

44361368

5pl l chr5:45312870- 0

49697231

0ql l .21 chr20:29526118- 5 BCL2L1 BCL2L1, ID1

29834552

6q23.3 chr6: 135561194- 1 MYB hsa-mir-548a- 135665525 2

lq44 chrl :241364021- 71 AKT3

247249719

5q35.3 chr5: 174477192- 92 FLT4

180857866

7q31.2 chr7: 115981465- 3 MET MET

116676953

18ql 1.2 chrl 8: 17749667- 21 CABLES!

22797232

17q25.1 chrl7:70767943- 13 GRB2, ITGB4

71305641

lp32.1 chrl :58658784- 7 JUN JUN

60221344

17ql l .2 chrl7:24112056- 5 DHRS13,

24310787 FLOT2,

ERALl, PHF12

17pl l .2 chrl7: 18837023- 12 MAPK7

19933105

8q24.11 chr8: 116186189- 13 NOV

120600761

12ql5 chrl2:66458200- 0

66543552 19ql3.2 chrl9:43177306- 60 LGALS7, 45393020 DYRKIB l lq22.2 chrl 1 : 101433436- 8 BIRC2, BIRC2

102134907 YAPl

4ql2 chr4 : 54471680- 7 PDGFRA, KDR, KIT

55980061 KIT

12pl 1.21 chrl2:30999223- 9 DDX11,

32594050 FAM60A

3q28 chr3 : 178149984- 143 PIK3CA PIK3CA

199501827

lp36.33 chrl : 1-5160566 77 TP 73

17q24.2 chrl7:62318152- 12 BPTF

63890591

lq23.3 chrl : 158317017- 52 PEA15

159953843

lq24.3 chrl : 169549478- 6 BAT2D1,

170484405 MYOC

8q22.3 chr8: 101163387- 14 RRM2B

103693879

13q31.3 chrl3 :89500014- 3 GPC5

93206506

12q21.1 chrl2:70849987- 0

70966467

12pl3.33 chrl2: l-1311104 10 WNK1

12q21.2 chrl2:76852527- 0

77064746

lq32.1 chrl :201678483- 21 MDM4 MDM4

203358272

19ql3.42 chrl9:59066340- 19 PRKCG,

59471027 TSEN34

12ql2 chrl2:38788913- 12 ADAMTS20

42596599

12q23.1 chrl2:95089777- 2 ELK3

95350380

12q21.32 chrl2:85072329- 0

85674601

10q22.3 chrl0:74560456- 46 SFTPA1B

82020637

3pl l . l chr3 :86250885- 8 POU1F1

95164178

17ql l . l chrl7:22479313- 1 WSB1

22877776

8q24.3 chr8: 140458177- 97 PTP4A3,

146274826 MAFA,

PARPIO

Xql2 chrX:66436234- 1 AR AR

67090514

6ql2 chr6:63255006- 3 PTP4A1 65243766

14q l l .2 chrl4: l-23145193 95 BCL2L2

9q34.3 chr9: 137859478- 76 NRARP,

140273252 MRPL41,

TRAF2, LHX3

6p24.1 chr6: 1-23628840 95 E2F3

13q l2.2 chrl3 : 1-40829685 110 FOXOl

12q21.1 chrl2:72596017- 0

73080626

14q32.33 chrl4: 106074644- 0

106368585

l lpl3 chrl 1 :32027116- 35 WT1

37799354

TABLE 7. Illustrative, but non-limiting chromosomal segments and genes known or predicted to be present in regions charactierzed by amplification in various cancers (see, e.g., Beroukhim et al. supra.).

37139941

17pl3.1 chrl7:7471230- 10 TP53 ATP1B2

7717938

12q24.33 chrl2: 131913408- 7 CHFR

132349534

7q36.3 chr7: 156893473- 7 PTPRN2 NCAPG2

158821424

6ql6.1 chr6: 76630464- 76 FUT9,

105342994 C6orfl65,

C6orfl62, GJA10

5q21.1 chr5:85837489- 142 APC APC

133480433

8pl l .22 chr8:39008109- 7 C8orf4,

41238710 ZMAT4

19ql3.32 chrl9:52031294- 25 BBC3

53331283

10pl5.3 chrlO: 1-1042949 4 TUBB8 lp31.1 chrl :71284749- 4 NEGRI NEGRI

74440273

13q31.3 chrl3 :92308911- 2 GPC6 GPC6,

94031607 DCT

16ql l .2 chrl6:31854743- 37 RBL2

53525739

0pl3 chr20: 1-325978 10 SOX12

5q35.3 chr5: 177541057- 43 SCGB3A1

180857866

lq43 chrl :223876038- 173 RYR2 FH,

247249719 ZNF678

16pl3.3 chrl6: 1-359092 16 HBZ

17q21.2 chrl7:37319013- 22 CNP

37988602

p25.3 chr2: 1-15244284 51 MYT1L

3ql3.31 chr3 : 116900556- 1 LSAMP

120107320

7q21.11 chr7:65877239- 73 MAGI 2 CLDN4

79629882

7q35 chr7: 144118814- 3 CNTNAP CNTNAP2

148066271 2

14q32.12 chrl4:80741860- 154 PRIMAl

106368585

16q24.3 chrl6:88436931- 9 C16orf3

88827254

3q26.31 chr3 : 175446835- 1 NAALAD NAALADL

178263192 L2 2

17q25.3 chrl7:78087533- 8 ZNF750

78774742

19pl2 chrl9:21788507- 12 ZNF492, 34401877 ZNF99

12q23.1 chrl2:97551177- 3 ANKS1B ANKS1B

99047626

4pl6.3 chr4: 1-435793 4 ZNF141

18pl l .32 chrl8: l-587750 4 COLEC12

2q33.2 chr2:204533830- 1 PARD3B PARD3B

206266883

8p21.2 chr8:22125332- 63 DPYSL2,

30139123 STMN4

8ql l .22 chr8:42971602- 86 SNTG1 FLJ23356,

72924037 ST18,

RBICCI

16q23.3 chrl6:80759878- 2 CDH13 CDH13

82408573

l lql4.1 chrl 1 :82612034- 6 DLG2 CCDC89,

85091467 CCDC90B,

TMEM126 A

14q23.3 chrl4:65275722- 7 GPHN,

67085224 MPP5

7p22.2 chr7: 3046420- 1 SDK1 SDK1

4279470

13q34 chrl3 : 111767404- 25 TUBGCP3

114142980

17pl2 chrl7: 10675416- 5 MAP2K4 MAP2K4,

12635879 ZNF18

21q22.2 chr21 :38584860- 19 DSCAM, DSCAM

42033506 TMPRSS

2/ERG

18q21.2 chrl 8:46172638- 7 SMAD4, DCC

49935241 DCC

6q22.1 chr6: 101000242- 87 GTF3C6,

121511318 TUBE],

ROSl

14ql l .2 chrl4: 1-29140968 140 ZNF219,

NDRG2

[00470] In various embodiments, it is contemplated to use the methods identified herein to identify CNVs of segments comprising the amplified regions or genes identified in Table 6 and/or to use the methods identified herein to identify CNVs of segments comprising the deleted regions or genes identified in 7. [00471] In one embodiment, the methods described herein provide a means to assess the association between gene amplification and the extent of tumor evolution. Correlation between amplification and/or deletion and stage or grade of a cancer may be prognostically important because such information may contribute to the definition of a genetically based tumor grade that would better predict the future course of disease with more advanced tumors having the worst prognosis. In addition, information about early amplification and/or deletion events may be useful in associating those events as predictors of subsequent disease progression. [00472] Gene amplification and deletions as identified by the method can be associated with other known parameters such as tumor grade, histology, Brd/Urd labeling index, hormonal status, nodal involvement, tumor size, survival duration and other tumor properties available from epidemiological and biostatistical studies. For example, tumor DNA to be tested by the method could include atypical hyperplasia, ductal carcinoma in situ, stage I-III cancer and metastatic lymph nodes in order to permit the identification of associations between amplifications and deletions and stage. The associations made may make possible effective therapeutic intervention. For example, consistently amplified regions may contain an overexpressed gene, the product of which may be able to be attacked therapeutically (for example, the growth factor receptor tyrosine kinase, pl85 ^HER2 ).

[00473] In various embodiments, the methods described herein can be used to identify amplification and/or deletion events that are associated with drug resistance by determining the copy number variation of nucleic acid sequences from primary cancers to those of cells that have metastasized to other sites. If gene amplification and/or deletion is a manifestation of karyotypic instability that allows rapid development of drug resistance, more amplification and/or deletion in primary tumors from chemoresistant patients than in tumors in chemosensitive patients would be expected. For example, if amplification of specific genes is responsible for the development of drug resistance, regions surrounding those genes would be expected to be amplified consistently in tumor cells from pleural effusions of chemoresistant patients but not in the primary tumors. Discovery of associations between gene amplification and/or deletion and the development of drug resistance may allow the identification of patients that will or will not benefit from adjuvant therapy.

[00474] In a manner similar to that described for determining the presence or absence of complete and/or partial fetal chromosomal aneuploidies in a maternal sample, methods, apparatus, and systems described herein can be used to determine the presence or absence of complete and/or partial chromosomal aneuploidies in any patient sample comprising nucleic acids e.g. DNA or cfDNA (including patient samples that are not maternal samples). The patient sample can be any biological sample type as described elsewhere herein. Preferably, the sample is obtained by non-invasive procedures. For example, the sample can be a blood sample, or the serum and plasma fractions thereof. Alternatively, the sample can be a urine sample or a fecal sample. In yet other embodiments, the sample is a tissue biopsy sample. In all cases, the sample comprises nucleic acids e.g. cfDNA or genomic DNA, which is purified, and sequenced using any of the NGS sequencing methods described previously.

[00475] Both complete and partial chromosomal aneuploidies associated with the formation, and progression of cancer can be determined according to the present method.

[00476] In various embodiments, when using the methods described herein to determine the presence and/or increased risk of cancer normalization of the data can be made with respect to the chromosome(s) for which the CNV is determined. In certain embodiments normalization of the data can be made with respect to the chromosome arm(s) for which the CNV is determined. In certain embodiments, normalization of the data can be made with respect to the particular segment(s) for which the CNV is determined.

[00477] In addition to the role of CNV in cancer, CNVs have been associated with a growing number of common complex disease, including human immunodeficiency virus (HIV), autoimmune diseases and a spectrum of neuropsychiatric disorders.

CNVs in infectious and autoimmune disease

[00478] To date a number of studies have reported association between CNV in genes involved in inflammation and the immune response and HIV, asthma, Crohn's disease and other autoimmune disorders (Fanciulli et al, Clin Genet 77:201-213 [2010]). For example, CNV in CCL3L1, has been implicated in HIV/AIDS susceptibility (CCL3L1, 17ql l .2 deletion), rheumatoid arthritis (CCL3L1, 17ql l .2 deletion), and Kawasaki disease (CCL3L1, 17ql l .2 duplication); CNV HBD-2, has been reported to predispose to colonic Crohn's disease (HDB-2, 8p23.1 deletion) and psoriasis (HDB-2, 8p23.1 deletion); C ⁷ in FCGR3B, was shown to predispose to glomerulonephritis in systemic lupus erthematosous (FCGR3B, lq23 deletion, lq23 duplication), anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculatis (FCGR3B, lq23 deletion), and increase the risk of developing rheumatoid arthritis. There are at least two inflammatory or autoimmune diseases that have been shown to be associated with CNV at different gene loci. For example, Crohn's disease is associated with low copy number at HDB-2, but also with a common deletion polymorphism upstream of the IGRM gene that encodes a member of the p47 immunity-related GTPase family. In addition to the association with FCGR3B copy number, SLE susceptibility has also been reported to be significantly increased among subjects with a lower number of copies of complement component C4. [00479] Associations between genomic deletions at the GSTM1 (GSTM1, lq23deletion) and GSTT1 (GSTT1, 22ql l .2 deletion) loci and increased risk of atopic asthma have been reported in a number of independent studies. In some embodiments, the methods described herein can be used to determine the presence or absence of a CNV associated with inflammation and/or autoimmune diseases. For example, the methods can be used to determine the presence of a CNV in a patient suspected to be suffering from HIV, asthma, or Crohn's disease. Examples of CNV associated with such diseases include without limitation deletions at 17ql 1.2, 8p23.1, lq23, and 22ql l .2, and duplications at 17ql 1.2, and lq23. In some embodiments, the present method can be used to determine the presence of CNV in genes including but not limited to CCL3L1, HBD-2, FCGR3B, GSTM, GSTT1, C4, and IRGM.

CNV diseases of the nervous system

[00480] Associations between de novo and inherited CNV and several common neurological and psychiatric diseases have been reported in autism, schizophrenia and epilepsy, and some cases of neurodegenerative diseases such as Parkinson's disease, amyotrophic lateral sclerosis (ALS) and autosomal dominant Alzheimer's disease (Fanciulli et al, Clin Genet 77:201-213 [2010]). Cytogenetic abnormalities have been observed in patients with autism and autism spectrum disorders (ASDs) with duplications at 15ql l-ql3. According to the Autism Genome project Consortium, 154 CNV including several recurrent CNVs, either on chromosome 15ql l-ql3 or at new genomic locations including chromosome 2pl6, lq21 and at 17pl2 in a region associated with Smith-Magenis syndrome that overlaps with ASD. Recurrent microdeletions or microduplications on chromosome 16pl 1.2 have highlighted the observation that de novo CNVs are detected at loci for genes such as SHANK3 (22ql3.3 deletion), neurexin 1 (NRXN1, 2pl6.3 deletion) and the neuroglins (NLGN4, Xp22.33 deletion) that are known to regulate synaptic differentiation and regulate glutaminergic neurotransmitter release. Schizophrenia has also been associated with multiple de novo CNVs. Microdeletions and microduplications associated with schizophrenia contain an overrepresentation of genes belonging to neurodevelopmental and glutaminergic pathways, suggesting that multiple CNVs affecting these genes may contribute directly to the pathogenesis of schizophrenia e.g. ERBB4, 2q34 deletion, SLCJA3, 5pl3.3 deletion; RAPEGF4, 2q31.1 deletion; CIT, 12.24 deletion; and multiple genes with de novo CNV. CNVs have also been associated with other neurological disorders including epilepsy (CHRNA 7, 15ql3.3 deletion), Parkinson's disease (SNCA 4q22 duplication) and ALS {SMN1, 5ql2.2.-ql3.3 deletion; and SMN2 deletion). In some embodiments, the methods described herein can be used to determine the presence or absence of a CNV associated with diseases of the nervous system. For example, the methods can be used to determine the presence of a CNV in a patient suspected to be suffering from autisim, schizophrenia, epilepsy, neurodegenerative diseases such as Parkinson's disease, amyotrophic lateral sclerosis (ALS) or autosomal dominant Alzheimer's disease. The methods can be used to determine CNV of genes associated with diseases of the nervous system including without limitation any of the Autism Spectrum Disorders (ASD), schizophrenia, and epilepsy, and CNV of genes associated with neurodegenerative disorders such as Parkinson's disease. Examples of CNV associated with such diseases include without limitation duplications at 15ql l-ql3, 2pl6, lq21, 17pl2, 16pl 1.2, and 4q22, and deletions at 22ql3.3, 2pl6.3, Xp22.33, 2q34, 5pl3.3, 2q31.1, 12.24, 15ql3.3, and 5ql2.2. In some embodiments, the methods can be used to determine the presence of CNV in genes including but not limited to SHANK3, NLGN4, NRXN1, ERBB4, SLC1A3, RAPGEF4, CIT, CHRNA 7, SNCA, SMNl,and MN2.

CNV and metabolic or cardiovascular diseases [00481] The association between metabolic and cardiovascular traits, such as familial hypercholesterolemia (FH), atherosclerosis and coronary artery disease, and CNVs has been reported in a number of studies (Fanciulli et al, Clin Genet 77:201- 213 [2010]). For example, germline rearrangements, mainly deletions, have been observed at the LDLR gene (LDLR, 19pl3.2 deletion/duplication) in some FH patients who carry no other LDLR mutations. Another example is the LP A gene that encodes apolipoprotein(a) (apo(a)) whose plasma concentration is associated with risk of coronary artery disease, myocardial infarction (MI) and stroke. Plasma concentrations of the apo(a) containing lipoprotein Lp(a) vary over 1000-fold between individuals and 90% of this variability is genetically determined at the LP A locus, with plasma concentration and Lp(a) isoform size being proportional to a highly variable number of 'kringle 4' repeat sequences (range 5-50). These data indicate that CNV in at least two genes can be associated with cardiovascular risk. The methods described herein can be used in large studies to search specifically for CNV associations with cardiovascular disorders. In some embodiments, the present method can be used to determine the presence or absence of a CNV associated with metabolic or cardiovascular disease. For example, the present method can be used to determine the presence of a CNV in a patient suspected to be suffering from familial hypercholesterolemia. The methods described herein can be used to determine CNV of genes associated with metabolic or cardiovascular disease e.g. hypercholesterolemia. Examples of CNV associated with such diseases include without limitation 19pl3.2 deletion/duplication of the LDLR gene, and multiplications in the LPA gene. Apparatus and systems for determining CNV

[00482] Analysis of the sequencing data and the diagnosis derived therefrom are typically performed using various computer executed algorithms and programs. Therefore, certain embodiments employ processes involving data stored in or transferred through one or more computer systems or other processing systems. Embodiments disclosed herein also relate to apparatus for performing these operations. This apparatus may be specially constructed for the required purposes, or it may be a general-purpose computer (or a group of computers) selectively activated or reconfigured by a computer program and/or data structure stored in the computer. In some embodiments, a group of processors performs some or all of the recited analytical operations collaboratively (e.g., via a network or cloud computing) and/or in parallel. A processor or group of processors for performing the methods described herein may be of various types including microcontrollers and microprocessors such as programmable devices (e.g., CPLDs and FPGAs) and non-programmable devices such as gate array ASICs or general purpose microprocessors.

[00483] In addition, certain embodiments relate to tangible and/or non- transitory computer readable media or computer program products that include program instructions and/or data (including data structures) for performing various computer-implemented operations. Examples of computer-readable media include, but are not limited to, semiconductor memory devices, magnetic media such as disk drives, magnetic tape, optical media such as CDs, magneto-optical media, and hardware devices that are specially configured to store and perform program instructions, such as read-only memory devices (ROM) and random access memory (RAM). The computer readable media may be directly controlled by an end user or the media may be indirectly controlled by the end user. Examples of directly controlled media include the media located at a user facility and/or media that are not shared with other entities. Examples of indirectly controlled media include media that is indirectly accessible to the user via an external network and/or via a service providing shared resources such as the "cloud." Examples of program instructions include both machine code, such as produced by a compiler, and files containing higher level code that may be executed by the computer using an interpreter.

[00484] In various embodiments, the data or information employed in the disclosed methods and apparatus is provided in an electronic format. Such data or information may include reads and tags derived from a nucleic acid sample, counts or densities of such tags that align with particular regions of a reference sequence (e.g., that align to a chromosome or chromosome segment), reference sequences (including reference sequences providing solely or primarily polymorphisms), chromosome and segment doses, calls such as aneuploidy calls, normalized chromosome and segment values, pairs of chromosomes or segments and corresponding normalizing chromosomes or segments, counseling recommendations, diagnoses, and the like. As used herein, data or other information provided in electronic format is available for storage on a machine and transmission between machines. Conventionally, data in electronic format is provided digitally and may be stored as bits and/or bytes in various data structures, lists, databases, etc. The data may be embodied electronically, optically, etc. [00485] One embodiment provides a computer program product for generating an output indicating the presence or absence of an aneuploidy, e.g., a fetal aneuploidy or cancer, in a test sample. The computer product may contain instructions for performing any one or more of the above-described methods for determining a chromosomal anomaly. As explained, the computer product may include a non- transitory and/or tangible computer readable medium having a computer executable or compilable logic (e.g., instructions) recorded thereon for enabling a processor to determine chromosome doses and, in some cases, whether a fetal aneuploidy is present or absent. In one example, the computer product comprises a computer readable medium having a computer executable or compilable logic (e.g., instructions) recorded thereon for enabling a processor to diagnose a fetal aneuploidy comprising: a receiving procedure for receiving sequencing data from at least a portion of nucleic acid molecules from a maternal biological sample, wherein said sequencing data comprises a calculated chromosome and/or segment dose; computer assisted logic for analyzing a fetal aneuploidy from said received data; and an output procedure for generating an output indicating the presence, absence or kind of said fetal aneuploidy.

[00486] The sequence information from the sample under consideration may be mapped to chromosome reference sequences to identify a number of sequence tags for each of any one or more chromosomes of interest and to identify a number of sequence tags for a normalizing segment sequence for each of said any one or more chromosomes of interest. In various embodiments, the reference sequences are stored in a database such as a relational or object database, for example.

[00487] It should be understood that it is not practical, or even possible in most cases, for an unaided human being to perform the computational operations of the methods disclosed herein. For example, mapping a single 30 bp read from a sample to any one of the human chromosomes might require years of effort without the assistance of a computational apparatus. Of course, the problem is compounded because reliable aneuploidy calls generally require mapping thousands (e.g., at least about 10,000) or even millions of reads to one or more chromosomes.

[00488] The methods disclosed herein can be performed using a system for evaluation of copy number of a genetic sequence of interest in a test sample. The system comprising: (a) a sequencer for receiving nucleic acids from the test sample providing nucleic acid sequence information from the sample; (b) a processor; and (c) one or more computer-readable storage media having stored thereon instructions for execution on said processor to carry out a method for identifying any CNV, e.g., chromosomal or partial aneuploidies.

In some embodiments, the methods are instructed by a computer-readable medium having stored thereon computer-readable instructions for carrying out a method for identifying any CNV, e.g., chromosomal or partial aneuploidies. Thus one embodiment provides a computer program product comprising one or more computer- readable non-transitory storage media having stored thereon computer-executable instructions that, when executed by one or more processors of a computer system, cause the computer system to implement a method for evaluation of copy number of a sequence of interest in a test sample comprising fetal and maternal cell-free nucleic acids. The method includes: (a) receiving sequence reads obtained by sequencing the cell-free nucleic acid fragments in the test sample; (b) aligning the sequence reads of the cell-free nucleic acid fragments to a reference genome comprising the sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins; (c) determining sizes of the cell-free nucleic acid fragments existing in the test sample; (d) weighting the test sequence tags based on the sizes of cell-free nucleic acid fragments from which the tags are obtained; (e) calculating coverages for the bins based on the weighted tags of (d); and (f) identifying a copy number variation in the sequence of interest from the calculated coverages. In some implementations, weighting the test sequence tags involves biasing the coverages toward test sequence tags obtained from cell-free nucleic acid fragments of a size or a size range characteristic of one genome in the test sample. In some implementations, weighting the test sequence tags involves assigning a value of 1 to tags obtained from cell-free nucleic acid fragments of the size or the size range, and assigning a value of 0 to other tags. In some implementations, the method further involves determining, in bins of the reference genome, including the sequence of interest, values of a fragment size parameter including a quantity of the cell-free nucleic acid fragments in the test sample having fragment sizes shorter or longer than a threshold value. Here, identifying the copy number variation in the sequence of interest involves using the values of the fragment size parameter as well as the coverages calculated in (e). In some implementations, the system is configured to evaluate copy number in the test sample using the various methods and processes discussed above.

[00489] In some embodiments, the instructions may further include automatically recording information pertinent to the method such as chromosome doses and the presence or absence of a fetal chromosomal aneuploidy in a patient medical record for a human subject providing the maternal test sample. The patient medical record may be maintained by, for example, a laboratory, physician's office, a hospital, a health maintenance organization, an insurance company, or a personal medical record website. Further, based on the results of the processor-implemented analysis, the method may further involve prescribing, initiating, and/or altering treatment of a human subject from whom the maternal test sample was taken. This may involve performing one or more additional tests or analyses on additional samples taken from the subject. [00490] Disclosed methods can also be performed using a computer processing system which is adapted or configured to perform a method for identifying any CNV, e.g., chromosomal or partial aneuploidies. One embodiment provides a computer processing system which is adapted or configured to perform a method as described herein. In one embodiment, the apparatus comprises a sequencing device adapted or configured for sequencing at least a portion of the nucleic acid molecules in a sample to obtain the type of sequence information described elsewhere herein. The apparatus may also include components for processing the sample. Such components are described elsewhere herein.

[00491] Sequence or other data, can be input into a computer or stored on a computer readable medium either directly or indirectly. In one embodiment, a computer system is directly coupled to a sequencing device that reads and/or analyzes sequences of nucleic acids from samples. Sequences or other information from such tools are provided via interface in the computer system. Alternatively, the sequences processed by system are provided from a sequence storage source such as a database or other repository. Once available to the processing apparatus, a memory device or mass storage device buffers or stores, at least temporarily, sequences of the nucleic acids. In addition, the memory device may store tag counts for various chromosomes or genomes, etc. The memory may also store various routines and/or programs for analyzing the presenting the sequence or mapped data. Such programs/routines may include programs for performing statistical analyses, etc.

[00492] In one example, a user provides a sample into a sequencing apparatus. Data is collected and/or analyzed by the sequencing apparatus which is connected to a computer. Software on the computer allows for data collection and/or analysis. Data can be stored, displayed (via a monitor or other similar device), and/or sent to another location. The computer may be connected to the internet which is used to transmit data to a handheld device utilized by a remote user (e.g., a physician, scientist or analyst). It is understood that the data can be stored and/or analyzed prior to transmittal. In some embodiments, raw data is collected and sent to a remote user or apparatus that will analyze and/or store the data. Transmittal can occur via the internet, but can also occur via satellite or other connection. Alternately, data can be stored on a computer-readable medium and the medium can be shipped to an end user (e.g., via mail). The remote user can be in the same or a different geographical location including, but not limited to a building, city, state, country or continent.

[00493] In some embodiments, the methods also include collecting data regarding a plurality of polynucleotide sequences (e.g., reads, tags and/or reference chromosome sequences) and sending the data to a computer or other computational system. For example, the computer can be connected to laboratory equipment, e.g., a sample collection apparatus, a nucleotide amplification apparatus, a nucleotide sequencing apparatus, or a hybridization apparatus. The computer can then collect applicable data gathered by the laboratory device. The data can be stored on a computer at any step, e.g., while collected in real time, prior to the sending, during or in conjunction with the sending, or following the sending. The data can be stored on a computer-readable medium that can be extracted from the computer. The data collected or stored can be transmitted from the computer to a remote location, e.g., via a local network or a wide area network such as the internet. At the remote location various operations can be performed on the transmitted data as described below.

[00494] Among the types of electronically formatted data that may be stored, transmitted, analyzed, and/or manipulated in systems, apparatus, and methods disclosed herein are the following:

Reads obtained by sequencing nucleic acids in a test sample Tags obtained by aligning reads to a reference genome or other reference sequence or sequences

The reference genome or sequence

Sequence tag density - Counts or numbers of tags for each of two or more regions (typically chromosomes or chromosome segments) of a reference genome or other reference sequences

Identities of normalizing chromosomes or chromosome segments for particular chromosomes or chromosome segments of interest

Doses for chromosomes or chromosome segments (or other regions) obtained from chromosomes or segments of interest and corresponding normalizing chromosomes or segments

Thresholds for calling chromosome doses as either affected, non-affected, or no call

The actual calls of chromosome doses

Diagnoses (clinical condition associated with the calls)

Recommendations for further tests derived from the calls and/or diagnoses Treatment and/or monitoring plans derived from the calls and/or diagnoses

[00495] These various types of data may be obtained, stored transmitted, analyzed, and/or manipulated at one or more locations using distinct apparatus. The processing options span a wide spectrum. At one end of the spectrum, all or much of this information is stored and used at the location where the test sample is processed, e.g., a doctor's office or other clinical setting. In other extreme, the sample is obtained at one location, it is processed and optionally sequenced at a different location, reads are aligned and calls are made at one or more different locations, and diagnoses, recommendations, and/or plans are prepared at still another location (which may be a location where the sample was obtained).

[00496] In various embodiments, the reads are generated with the sequencing apparatus and then transmitted to a remote site where they are processed to produce aneuploidy calls. At this remote location, as an example, the reads are aligned to a reference sequence to produce tags, which are counted and assigned to chromosomes or segments of interest. Also at the remote location, the counts are converted to doses using associated normalizing chromosomes or segments. Still further, at the remote location, the doses are used to generate aneuploidy calls. [00497] Among the processing operations that may be employed at distinct locations are the following:

Sample collection

Sample processing preliminary to sequencing

Sequencing

Analyzing sequence data and deriving aneuploidy calls

Diagnosis

Reporting a diagnosis and/or a call to patient or health care provider Developing a plan for further treatment, testing, and/or monitoring Executing the plan

Counseling

[00498] Any one or more of these operations may be automated as described elsewhere herein. Typically, the sequencing and the analyzing of sequence data and deriving aneuploidy calls will be performed computationally. The other operations may be performed manually or automatically.

[00499] Examples of locations where sample collection may be performed include health practitioners' offices, clinics, patients' homes (where a sample collection tool or kit is provided), and mobile health care vehicles. Examples of locations where sample processing prior to sequencing may be performed include health practitioners' offices, clinics, patients' homes (where a sample processing apparatus or kit is provided), mobile health care vehicles, and facilities of aneuploidy analysis providers. Examples of locations where sequencing may be performed include health practitioners' offices, clinics, health practitioners' offices, clinics, patients' homes (where a sample sequencing apparatus and/or kit is provided), mobile health care vehicles, and facilities of aneuploidy analysis providers. The location where the sequencing takes place may be provided with a dedicated network connection for transmitting sequence data (typically reads) in an electronic format. Such connection may be wired or wireless and have and may be configured to send the data to a site where the data can be processed and/or aggregated prior to transmission to a processing site. Data aggregators can be maintained by health organizations such as Health Maintenance Organizations (HMOs). [00500] The analyzing and/or deriving operations may be performed at any of the foregoing locations or alternatively at a further remote site dedicated to computation and/or the service of analyzing nucleic acid sequence data. Such locations include for example, clusters such as general purpose server farms, the facilities of an aneuploidy analysis service business, and the like. In some embodiments, the computational apparatus employed to perform the analysis is leased or rented. The computational resources may be part of an internet accessible collection of processors such as processing resources colloquially known as the cloud. In some cases, the computations are performed by a parallel or massively parallel group of processors that are affiliated or unaffiliated with one another. The processing may be accomplished using distributed processing such as cluster computing, grid computing, and the like. In such embodiments, a cluster or grid of computational resources collective form a super virtual computer composed of multiple processors or computers acting together to perform the analysis and/or derivation described herein. These technologies as well as more conventional supercomputers may be employed to process sequence data as described herein. Each is a form of parallel computing that relies on processors or computers. In the case of grid computing these processors (often whole computers) are connected by a network (private, public, or the Internet) by a conventional network protocol such as Ethernet. By contrast, a supercomputer has many processors connected by a local high-speed computer bus.

[00501] In certain embodiments, the diagnosis (e.g., the fetus has Downs syndrome or the patient has a particular type of cancer) is generated at the same location as the analyzing operation. In other embodiments, it is performed at a different location. In some examples, reporting the diagnosis is performed at the location where the sample was taken, although this need not be the case. Examples of locations where the diagnosis can be generated or reported and/or where developing a plan is performed include health practitioners' offices, clinics, internet sites accessible by computers, and handheld devices such as cell phones, tablets, smart phones, etc. having a wired or wireless connection to a network. Examples of locations where counseling is performed include health practitioners' offices, clinics, internet sites accessible by computers, handheld devices, etc. [00502] In some embodiments, the sample collection, sample processing, and sequencing operations are performed at a first location and the analyzing and deriving operation is performed at a second location. However, in some cases, the sample collection is collected at one location (e.g., a health practitioner's office or clinic) and the sample processing and sequencing is performed at a different location that is optionally the same location where the analyzing and deriving take place.

[00503] In various embodiments, a sequence of the above-listed operations may be triggered by a user or entity initiating sample collection, sample processing and/or sequencing. After one or more these operations have begun execution the other operations may naturally follow. For example, the sequencing operation may cause reads to be automatically collected and sent to a processing apparatus which then conducts, often automatically and possibly without further user intervention, the sequence analysis and derivation of aneuploidy operation. In some implementations, the result of this processing operation is then automatically delivered, possibly with reformatting as a diagnosis, to a system component or entity that processes reports the information to a health professional and/or patient. As explained such information can also be automatically processed to produce a treatment, testing, and/or monitoring plan, possibly along with counseling information. Thus, initiating an early stage operation can trigger an end to end sequence in which the health professional, patient or other concerned party is provided with a diagnosis, a plan, counseling and/or other information useful for acting on a physical condition. This is accomplished even though parts of the overall system are physically separated and possibly remote from the location of, e.g., the sample and sequence apparatus.

[00504] Figure 5 shows one implementation of a dispersed system for producing a call or diagnosis from a test sample. A sample collection location 01 is used for obtaining a test sample from a patient such as a pregnant female or a putative cancer patient. The samples then provided to a processing and sequencing location 03 where the test sample may be processed and sequenced as described above. Location 03 includes apparatus for processing the sample as well as apparatus for sequencing the processed sample. The result of the sequencing, as described elsewhere herein, is a collection of reads which are typically provided in an electronic format and provided to a network such as the Internet, which is indicated by reference number 05 in Figure 5. [00505] The sequence data is provided to a remote location 07 where analysis and call generation are performed. This location may include one or more powerful computational devices such as computers or processors. After the computational resources at location 07 have completed their analysis and generated a call from the sequence information received, the call is relayed back to the network 05. In some implementations, not only is a call generated at location 07 but an associated diagnosis is also generated. The call and or diagnosis are then transmitted across the network and back to the sample collection location 01 as illustrated in Figure 5. As explained, this is simply one of many variations on how the various operations associated with generating a call or diagnosis may be divided among various locations. One common variant involves providing sample collection and processing and sequencing in a single location. Another variation involves providing processing and sequencing at the same location as analysis and call generation.

[00506] Figure 6 elaborates on the options for performing various operations at distinct locations. In the most granular sense depicted in Figure 6, each of the following operations is performed at a separate location: sample collection, sample processing, sequencing, read alignment, calling, diagnosis, and reporting and/or plan development.

[00507] In one embodiment that aggregates some of these operations, sample processing and sequencing are performed in one location and read alignment, calling, and diagnosis are performed at a separate location. See the portion of Figure 6 identified by reference character A. In another implementation, which is identified by character B in Figure 6, sample collection, sample processing, and sequencing are all performed at the same location. In this implementation, read alignment and calling are performed in a second location. Finally, diagnosis and reporting and/or plan development are performed in a third location. In the implementation depicted by character C in Figure 6, sample collection is performed at a first location, sample processing, sequencing, read alignment, calling,, and diagnosis are all performed together at a second location, and reporting and/or plan development are performed at a third location. Finally, in the implementation labeled D in Figure 6, sample collection is performed at a first location, sample processing, sequencing, read alignment, and calling are all performed at a second location, and diagnosis and reporting and/or plan management are performed at a third location. [00508] One embodiment provides a system for use in determining the presence or absence of any one or more different complete fetal chromosomal aneuploidies in a maternal test sample comprising fetal and maternal nucleic acids, the system including a sequencer for receiving a nucleic acid sample and providing fetal and maternal nucleic acid sequence information from the sample; a processor; and a machine readable storage medium comprising instructions for execution on said processor, the instructions comprising:

(a) code for obtaining sequence information for said fetal and maternal nucleic acids in the sample;

(b) code for using said sequence information to computationally identify a number of sequence tags from the fetal and maternal nucleic acids for each of any one or more chromosomes of interest selected from chromosomes 1-22, X, and Y and to identify a number of sequence tags for at least one normalizing chromosome sequence or normalizing chromosome segment sequence for each of said any one or more chromosomes of interest;

(c) code for using said number of sequence tags identified for each of said any one or more chromosomes of interest and said number of sequence tags identified for each normalizing chromosome sequence or normalizing chromosome segment sequence to calculate a single chromosome dose for each of the any one or more chromosomes of interest; and

(d) code for comparing each of the single chromosome doses for each of the any one or more chromosomes of interest to a corresponding threshold value for each of the one or more chromosomes of interest, and thereby determining the presence or absence of any one or more complete different fetal chromosomal aneuploidies in the sample.

[00509] In some embodiments, the code for calculating a single chromosome dose for each of the any one or more chromosomes of interest comprises code for calculating a chromosome dose for a selected one of the chromosomes of interest as the ratio of the number of sequence tags identified for the selected chromosome of interest and the number of sequence tags identified for a corresponding at least one normalizing chromosome sequence or normalizing chromosome segment sequence for the selected chromosome of interest. [00510] In some embodiments, the system further comprises code for repeating the calculating of a chromosome dose for each of any remaining chromosome segments of the any one or more segments of any one or more chromosomes of interest. [00511] In some embodiments, the one or more chromosomes of interest selected from chromosomes 1-22, X, and Y comprise at least twenty chromosomes selected from chromosomes 1-22, X, and Y, and wherein the instructions comprise instructions for determining the presence or absence of at least twenty different complete fetal chromosomal aneuploidies is determined. [00512] In some embodiments, the at least one normalizing chromosome sequence is a group of chromosomes selected from chromosomes 1-22, X, and Y. In other embodiments, the at least one normalizing chromosome sequence is a single chromosome selected from chromosomes 1-22, X, and Y.

[00513] Another embodiment provides a system for use in determining the presence or absence of any one or more different partial fetal chromosomal aneuploidies in a maternal test sample comprising fetal and maternal nucleic acids, the system comprising: a sequencer for receiving a nucleic acid sample and providing fetal and maternal nucleic acid sequence information from the sample; a processor; and a machine readable storage medium comprising instructions for execution on said processor, the instructions comprising:

(a) code for obtaining sequence information for said fetal and maternal nucleic acids in said sample;

(b) code for using said sequence information to computationally identify a number of sequence tags from the fetal and maternal nucleic acids for each of any one or more segments of any one or more chromosomes of interest selected from chromosomes 1- 22, X, and Y and to identify a number of sequence tags for at least one normalizing segment sequence for each of said any one or more segments of any one or more chromosomes of interest;

(c) code using said number of sequence tags identified for each of said any one or more segments of any one or more chromosomes of interest and said number of sequence tags identified for said normalizing segment sequence to calculate a single chromosome segment dose for each of said any one or more segments of any one or more chromosomes of interest; and

(d) code for comparing each of said single chromosome segment doses for each of said any one or more segments of any one or more chromosomes of interest to a corresponding threshold value for each of said any one or more chromosome segments of any one or more chromosome of interest, and thereby determining the presence or absence of one or more different partial fetal chromosomal aneuploidies in said sample.

[00514] In some embodiments, the code for calculating a single chromosome segment dose comprises code for calculating a chromosome segment dose for a selected one of the chromosome segments as the ratio of the number of sequence tags identified for the selected chromosome segment and the number of sequence tags identified for a corresponding normalizing segment sequence for the selected chromosome segment. [00515] In some embodiments, the system further comprises code for repeating the calculating of a chromosome segment dose for each of any remaining chromosome segments of the any one or more segments of any one or more chromosomes of interest.

[00516] In some embodiments, the system further comprises (i) code for repeating (a)-(d) for test samples from different maternal subjects, and (ii) code for determining the presence or absence of any one or more different partial fetal chromosomal aneuploidies in each of said samples.

[00517] In other embodiments of any of the systems provided herein, the code further comprises code for automatically recording the presence or absence of a fetal chromosomal aneuploidy as determined in (d) in a patient medical record for a human subject providing the maternal test sample, wherein the recording is performed using the processor.

[00518] In some embodiments of any of the systems provided herein, the sequencer is configured to perform next generation sequencing (NGS). In some embodiments, the sequencer is configured to perform massively parallel sequencing using sequencing-by-synthesis with reversible dye terminators. In other embodiments, the sequencer is configured to perform sequencing-by-ligation. In yet other embodiments, the sequencer is configured to perform single molecule sequencing.

EXPERIMENTAL

Example 1

Preparation and sequencing of primary and enriched sequencing libraries a. Preparation of sequencing libraries— abbreviated protocol

(ABB)

[00519] All sequencing libraries, i.e., primary and enriched libraries, were prepared from approximately 2 ng of purified cfDNA that was extracted from maternal plasma. Library preparation was performed using reagents of the NEBNext™ DNA Sample Prep DNA Reagent Set 1 (Part No. E6000L; New England Biolabs, Ipswich, MA), for Illumina® as follows. Because cell-free plasma DNA is fragmented in nature, no further fragmentation by nebulization or sonication was done on the plasma DNA samples. The overhangs of approximately 2 ng purified cfDNA fragments contained in 40 μΐ were converted into phosphorylated blunt ends according to the NEBNext® End Repair Module by incubating in a 1.5 ml microfuge tube the cfDNA with 5μ1 10X phosphorylation buffer, 2 μΐ deoxynucleotide solution mix (10 mM each dNTP), Ι μΐ of a 1 :5 dilution of DNA Polymerase I, 1 μΐ T4 DNA Polymerase and 1 μΐ T4 Polynucleotide Kinase provided in the NEBNext™ DNA Sample Prep DNA Reagent Set 1 for 15 minutes at 20°C. The enzymes were then heat inactivated by incubating the reaction mixture at 75°C for 5 minutes. The mixture was cooled to 4°C, and dA tailing of the blunt-ended DNA was accomplished using ΙΟμΙ of the dA-tailing master mix containing the Klenow fragment (3' to 5' exo minus) (NEBNext™ DNA Sample Prep DNA Reagent Set 1), and incubating for 15 minutes at 37°C. Subsequently, the Klenow fragment was heat inactivated by incubating the reaction mixture at 75°C for 5 minutes. Following the inactivation of the Klenow fragment, 1 μΐ of a 1 :5 dilution of Illumina Genomic Adaptor Oligo Mix (Part No. 1000521; Illumina Inc., Hayward, CA) was used to ligate the Illumina adaptors (Non-Index Y-Adaptors) to the dA-tailed DNA using 4 μΐ of the T4 DNA ligase provided in the NEBNext™ DNA Sample Prep DNA Reagent Set 1, by incubating the reaction mixture for 15 minutes at 25°C. The mixture was cooled to 4°C, and the adaptor-ligated cfDNA was purified from unligated adaptors, adaptor dimers, and other reagents using magnetic beads provided in the Agencourt AMPure XP PCR purification system (Part No. A63881; Beckman Coulter Genomics, Danvers, MA). Eighteen cycles of PCR were performed to selectively enrich adaptor- ligated cfDNA (25 μΐ) using Phusion ® High-Fidelity Master Mix (25 μΐ; Finnzymes, Woburn, MA) and Illumina's PCR primers (0.5 μΜ each) complementary to the adaptors (Part No. 1000537 and 1000537). The adaptor-ligated DNA was subjected to PCR (98°C for 30 seconds; 18 cycles of 98°C for 10 seconds, 65°C for 30 seconds, and 72°C for 30; final extension at 72°C for 5 minutes, and hold at 4°C) using Illumina Genomic PCR Primers (Part Nos. 100537 and 1000538) and the Phusion HF PCR Master Mix provided in the NEBNext™ DNA Sample Prep DNA Reagent Set 1 , according to the manufacturer's instructions. The amplified product was purified using the Agencourt AMPure XP PCR purification system (Agencourt Bioscience Corporation, Beverly, MA) according to the manufacturer's instructions available at www.beckmangenomics.com/products/AMPureXPProtocol_000387v001 .pdf. The purified amplified product was eluted in 40 μΐ of Qiagen EB Buffer, and the concentration and size distribution of the amplified libraries was analyzed using the Agilent DNA 1000 Kit for the 2100 Bioanalyzer (Agilent technologies Inc., Santa Clara, CA). b. Preparation of sequencing libraries—full-length protocol [00520] The full-length protocol described here is essentially the standard protocol provided by Illumina, and only differs from the Illumina protocol in the purification of the amplified library. The Illumina protocol instructs that the amplified library be purified using gel electrophoresis, while the protocol described herein uses magnetic beads for the same purification step. Approximately 2 ng of purified cfDNA extracted from maternal plasma was used to prepare a primary sequencing library using NEBNext™ DNA Sample Prep DNA Reagent Set 1 (Part No. E6000L; New England Biolabs, Ipswich, MA) for Illumina® essentially according to the manufacturer's instructions. All steps except for the final purification of the adaptor-ligated products, which was performed using Agencourt magnetic beads and reagents instead of the purification column, were performed according to the protocol accompanying the NEBNext™ Reagents for Sample Preparation for a genomic DNA library that is sequenced using the Illumina® GAIL The NEBNext™ protocol essentially follows that provided by Illumina, which is available at grcf.jhml.edu/hts/protocols/11257047_ChIP_Sample_Prep.pdf.

[00521] The overhangs of approximately 2 ng purified cfDNA fragments contained in 40 μΐ were converted into phosphorylated blunt ends according to the NEBNext® End Repair Module by incubating the 40μ1 cfDNA with 5μ1 10X phosphorylation buffer, 2 μΐ deoxynucleotide solution mix (10 mM each dNTP), 1 μΐ of a 1 :5 dilution of DNA Polymerase I, 1 μΐ T4 DNA Polymerase and 1 μΐ T4 Polynucleotide Kinase provided in the NEBNext™ DNA Sample Prep DNA Reagent Set 1 in a 200 μΐ microfuge tube in a thermal cycler for 30 minutes at 20°C. The sample was cooled to 4°C, and purified using a QIAQuick column provided in the QIAQuick PCR Purification Kit (QIAGEN Inc., Valencia, CA) as follows. The 50 μΐ reaction was transferred to 1.5 ml microfuge tube, and 250 μΐ of Qiagen Buffer PB were added. The resulting 300 μΐ were transferred to a QIAquick column, which was centrifuged at 13,000 RPM for 1 minute in a microfuge. The column was washed with 750 μΐ Qiagen Buffer PE, and re-centrifuged. Residual ethanol was removed by an additional centrifugation for 5 minutes at 13,000 RPM. The DNA was eluted in 39 μΐ Qiagen Buffer EB by centrifugation. dA tailing of 34 μΐ of the blunt-ended DNA was accomplished using 16 μΐ of the dA-tailing master mix containing the Klenow fragment (3' to 5' exo minus) (NEBNext™ DNA Sample Prep DNA Reagent Set 1), and incubating for 30 minutes at 37°C according to the manufacturer's NEBNext® dA-Tailing Module. The sample was cooled to 4°C, and purified using a column provided in the MinElute PCR Purification Kit (QIAGEN Inc., Valencia, CA) as follows. The 50 μΐ reaction was transferred to 1.5 ml microfuge tube, and 250 μΐ of Qiagen Buffer PB were added. The 300 μΐ were transferred to the MinElute column, which was centrifuged at 13,000RPM for 1 minute in a microfuge. The column was washed with 750 μΐ Qiagen Buffer PE, and re-centrifuged. Residual ethanol was removed by an additional centrifugation for 5 minutes at 13,000 RPM. The DNA was eluted in 15 μΐ Qiagen Buffer EB by centrifugation. Ten microliters of the DNA eluate were incubated with 1 μΐ of a 1 :5 dilution of the Illumina Genomic Adapter Oligo Mix (Part No. 1000521), 15 μΐ of 2X Quick Ligation Reaction Buffer, and 4 μΐ Quick T4 DNA Ligase, for 15 minutes at 25°C according to the NEBNext® Quick Ligation Module. The sample was cooled to 4°C, and purified using a MinElute column as follows. One hundred and fifty microliters of Qiagen Buffer PE were added to the 30 μΐ reaction, and the entire volume was transferred to a MinElute column were transferred to a MinElute column, which was centrifuged at 13,000RPM for 1 minute in a microfuge. The column was washed with 750 μΐ Qiagen Buffer PE, and re-centrifuged. Residual ethanol was removed by an additional centrifugation for 5 minutes at 13,000 RPM. The DNA was eluted in 28 μΐ Qiagen Buffer EB by centrifugation. Twenty three microliters of the adaptor-ligated DNA eluate were subjected to 18 cycles of PCR (98°C for 30 seconds; 18 cycles of 98°C for 10 seconds, 65°C for 30 seconds, and 72°C for 30; final extension at 72°C for 5 minutes, and hold at 4°C) using Illumina Genomic PCR Primers (Part Nos. 100537 and 1000538) and the Phusion HF PCR Master Mix provided in the NEBNext™ DNA Sample Prep DNA Reagent Set 1, according to the manufacturer's instructions. The amplified product was purified using the Agencourt AMPure XP PCR purification system (Agencourt Bioscience Corporation, Beverly, MA) according to the manufacturer's instructions available at www.beckmangenomics.com/products/AMPureXPProtocol_000387v001 .pdf. The Agencourt AMPure XP PCR purification system removes unincorporated dNTPs, primers, primer dimers, salts and other contaminates, and recovers amplicons greater than 100 bp. The purified amplified product was eluted from the Agencourt beads in 40 μΐ of Qiagen EB Buffer and the size distribution of the libraries was analyzed using the Agilent DNA 1000 Kit for the 2100 Bioanalyzer (Agilent technologies Inc., Santa Clara, CA).

_ Analysis of sequencing libraries prepared according to the abbreviated (a) and the full-length (b) protocols

[00522] The electropherograms generated by the Bioanalyzer are shown in Figures 7A and 7B. Figure 7A shows the electropherogram of library DNA prepared from cfDNA purified from plasma sample M24228 using the full-length protocol described in (a), and Figure 7B shows the electropherogram of library DNA prepared from cfDNA purified from plasma sample M24228 using the full-length protocol described in (b). In both figures, peaks 1 and 4 represent the 15 bp Lower Marker, and the 1,500 Upper Marker, respectively; the numbers above the peaks indicate the migration times for the library fragments; and the horizontal lines indicate the set threshold for integration. The electropherogram in Figure 7A shows a minor peak of fragments of 187 bp and a major peak of fragments of 263 bp, while the electropherogram in Figure 7B shows only one peak at 265 bp. Integration of the peak areas resulted in a calculated concentration of 0.40 ng/μΐ for the DNA of the 187 bp peak in Figure 7A, a concentration of 7.34 ng/μΐ for the DNA of the 263bp peak in Figure 7A, and a concentration of 14.72 ng/μΐ for the DNA of the 265 bp peak in Figure 7B. The Illumina adaptors that were ligated to the cfDNA are known to be 92 bp, which when subtracted from the 265 bp, indicate that the peak size of the cfDNA is 173 bp. It is possible that the minor peak at 187 bp represents fragments of two primers that were ligated end-to-end. The linear two-primer fragments are eliminated from the final library product when the abbreviated protocol is used. The abbreviated protocol also eliminates other smaller fragments of less than 187 bp. In this example, the concentration of purified adaptor-ligated cfDNA is double that of the adaptor- ligated cfDNA produced using the full-length protocol. It has been noted that the concentration of the adaptor-ligated cfDNA fragments was always greater than that obtained using the full-length protocol (data not shown).

[00523] Thus, an advantage of preparing the sequencing library using the abbreviated protocol is that the library obtained consistently comprises only one major peak in the 262-267 bp range while the quality of the library prepared using the full-length protocol varies as reflected by the number and mobility of peaks other than that representing the cfDNA. Non-cfDNA products would occupy space on the flow cell and diminish the quality of the cluster amplification and subsequent imaging of the sequencing reactions, which underlies the overall assignment of the aneuploidy status. The abbreviated protocol was shown not to affect the sequencing of the library.

[00524] Another advantage of preparing the sequencing library using the abbreviated protocol is that the three enzymatic steps of blunt-ending, d-A tailing, and adaptor-ligation, take less than an hour to complete to support the validation and implementation of a rapid aneuploid diagnostic service.

[00525] Another advantage is that the three enzymatic steps of blunt-ending, d-

A tailing, and adaptor ligation, are performed in the same reaction tube, thus avoiding multiple sample transfers that would potentially lead to loss of material, and more importantly to possible sample mix-up and sample contamination. Example 2

Non-Invasive Prenatal Testing Using Fragment Size Introduction

[00526] Since its commercial introduction in late 2011 and early 2012, non- invasive prenatal testing (NIPT) of cell free DNA (cfDNA) in maternal plasma has rapidly become the method of choice to screen pregnant women at high risk for fetal aneuploidies. The methods are based primarily on isolating and sequencing cfDNA in the plasma of pregnant women, and counting the number of cfDNA fragments that align to particular regions of the reference human genome (references: Fan et al., Lo et al.). These DNA sequencing and molecular counting methods allow a high precision determination of the relative copy numbers for each of the chromosomes across the genome. High sensitivities and specificities for the detection of trisomies 21, 18 and 13 have been reproducibly achieved in multiple clinical studies (refs, cite Gil/Nicolaides meta-analysis). [00527] More recently, additional clinical studies have shown that this approach can be extended to the general obstetric population. There are no detectable differences in the fetal fractions between the high- and average-risk populations (refs). Clinical study results demonstrate that NIPT using molecular counting by cfDNA sequencing performs equivalently in both populations. A statistically significant improvement in the positive predictive value (PPV) over standard serum screening has been demonstrated (refs). Lower false positive test results, as compared with serum biochemistry and nuchal translucency measurement, have significantly reduced the need for invasive diagnostic procedures (see Larion et al. references from Abuhamad's group). [00528] Given the good NIPT performance in the general obstetric population, workflow simplicity and costs have now become a main consideration for the implementation of cfDNA sequencing for whole chromosome aneuploidy detection in the general obstetric population (reference: ISPD Debate 1, Brisbane). Most NIPT laboratory methods utilize a polymerase chain reaction (PCR) amplification step after the library preparation and single end sequencing that requires 10-20 million unique cfDNA fragments to achieve reasonable sensitivity to detect aneuploidy. The complexity of the PCR based workflow and deeper sequencing requirements have limited the potential of the NIPT assay and have resulted in increased costs.

[00529] Here it is demonstrated that high analytical sensitivities and specificities can be achieved with a simple library preparation using very low cfDNA input that does not require PCR amplification. The PCR free method simplifies the workflow, improves the turnaround time and eliminates biases that are inherent with PCR methods. The amplification free workflow can be coupled with paired end sequencing to allow determination of fragment length for each tag and the total fetal fraction in each sample. Since the fetal cfDNA fragments are shorter than maternal fragments [ref Quake 2010, should also cite Lo's Science Clin Translation article], the detection of fetal aneuploidy from maternal plasma can be made much more robust and efficient, requiring fewer unique cfDNA fragments. In combination, improved analytical sensitivity and specificity is achieved with a very fast turnaround time at a significantly lower number of cfDNA fragments. This potentially allows NIPT to be carried out at significantly lower costs to facilitate application in the general obstetric population.

Methods

[00530] Peripheral blood samples were drawn into BCT tubes (Streck, Omaha, NE, USA) and shipped to the Illumina CLIA laboratory in Redwood City for commercial NIPT testing. Signed patient consent forms permitted second plasma aliquots to be de-identified and utilized for clinical research, with the exception of patient samples sent from the state of New York. Plasma samples for this work were selected to include both unaffected and aneuploid fetuses with a range of cfDNA concentrations and fetal fractions. Simplification of Library Processing

[00531] cfDNA was extracted from 900μΙ. of maternal plasma using the

NucleoSpin 96-well blood purification kit (Macherey-Nagel, Diiren, Germany) with minor modifications to accommodate a larger lysate input. The isolated cfDNA was put directly into the sequencing library process without any normalization of the cfDNA input. Sequencing libraries were prepared with a TruSeq PCR Free DNA library kit (Illumina, San Diego, CA, USA) with dual indexes for barcoding the cfDNA fragments for sample identification. The following modifications to the library protocol were used to improve the compatibility of the library preparation with the low concentration of input cfDNA. Template input volume was increased, while the end repair, A-tailing and ligation master mix and adapter concentrations were decreased. Additionally, after end repair, a heat kill step was introduced to deactivate enzymes, the post end repair SPRI (vendor) bead purification step was removed, and elution during the post ligation SPRI bead purification step utilized HT1 buffer (Illumina).

[00532] A single MICROLAB® STAR (Hamilton, Reno, NV, USA) liquid handler, configured with a 96 channel head and 8 1-mL pipetting channels, was used to batch process 96 plasma samples at a time. The liquid handler processed each individual plasma sample through DNA extraction, sequencing library preparation and quantitation. Individual sample libraries were quantified with AccuClear (Biotium, Hayward, CA, USA) and pools of 48 samples were prepared with normalized inputs resulting in a final concentration of 32 pM for sequencing.

Paired End Sequencing

[00533] DNA sequencing was carried out with an Illumina NextSeq 500 instrument utilizing 2x36 bp paired end sequencing, plus an additional 16 cycles for sequencing the sample barcodes. A total of 364 samples were run across 8 independent sequencing batches.

[00534] Paired DNA sequences were de-multiplexed using bcl2fastq (Illumina) and mapped to the reference human genome (hgl9) using bowtie2 aligner algorithm [ref. Landmead]. Paired reads had to match forward and reverse strands to be counted. All counted mapped pairs exceeding mapping quality scores of 10 (Ruan et al.) with globally unique first reads were assigned to non-overlapping consecutive fixed-width genomic bins of 100 kb in size. Approximately 2% of the genome showed highly variable coverage across an independent set of NIPT samples and was excluded from further analysis.

[00535] Using genomic location information and fragment size available from mapped locations of each of the two ends of the sequenced cfDNA fragments, two variables were derived for each 100 kb window: (a) total counts of short fragments below 150 base pairs in length, and (b) fraction of fragments between 80 and 150 base pairs within the set of all fragments below 250 base pairs. Limiting the size of fragments to less than 150 base pairs enriches for fragments originating from the placenta, which is a proxy for fetal DNA. The fraction of short fragments characterizes the relative fetal cfDNA amounts in the plasma mixture. CfDNA from a trisomic fetus would be expected to have a higher fraction of short reads mapping to the trisomic chromosome compared to a euploid fetus that is disomic for that chromosome.

[00536] The counts and fractions of short fragments were independently normalized to remove systematic assay biases and sample-specific variations attributable to genomic guanine cytosine (GC) content utilizing the process shown in Figure 2D. Normalized values were trimmed by removing bins deviating from the whole chromosome median by more than 3 robust measures of standard deviation. Finally, for each of the two variables, trimmed normalized values associated with the target chromosome were compared to those on normalizing reference chromosomes to construct a t-statistic.

[00537] Data from each paired end sequencing run followed four steps for analysis: 1) read conversion, 2) feature binning at lOOkb resolution, 3) normalization of each feature (counts and fraction) at lOOkb resolution and 4) combining features and scoring for aneuploidy detection. In step 1, sample data is de-multiplexed from the individual barcodes, aligned to the genome and filtered for sequence quality. Step 2 total counts of short fragments below 150 base pairs in length, and fraction of fragments between 80 and 150 base pairs within the set of all fragments below 250 base pairs are determined for each bin. Assay bias and sample specific variations are removed in step 3. Finally, enrichment over a reference is determined and scored using a t-test for each of the counts and fraction, and combined for final score for aneuploidy detection.

Detection of Fetal Whole Chromosome Aneuploidy

[00538] We tested whether the counts and fraction data could be combined to enhance the ability to detect fetal trisomy 21. Sixteen plasma samples from pregnant women carrying fetuses with karyotype-confirmed trisomy 21 and 294 samples from unaffected pregnancies were randomly distributed across processing batches, resulting in nine flow cells for sequencing. Each algorithm step was examined separately to determine the ability of each step and combination of steps to detect aneuploidy. The final score for fetal aneuploidy detection in the combined case was defined as the square root of the sum of squares of the two individual t-statistics, and a single threshold was applied to generate a call of "aneuploidy detected" versus "aneuploidy not detected".

Calculation of Fetal Fraction

[00539] For each sample, fetal fraction was estimated using a ratio of the total number of fragments of size [111,136 bp] to the total number of fragments of size [165,175 bp] within a subset of the genomic 100 kb bins. Using samples from women carrying known male fetuses, the top 10% of genomic bins that had the highest correlation with fetal fraction derived from the number of copies of the X chromosome [ref Rava] were determined. The correlation between fragment size- based fetal fraction estimates and those derived from the X chromosome in known male fetuses was computed using a leave-one-out cross validation [REF] analysis that included both bin selection and regression model parameter estimation. The estimated fetal fraction was then derived using a linear regression model from the fragment size ratios.

Results

Simplification of Library Processing

[00540] Figure 8 shows the overall workflow and timeline for this new version of NIPT compared to the standard laboratory workflow. The entire 96-sample preparation workflow for plasma isolation, cfDNA extraction, library construction, quantitation, and pooling was able to process samples in less than 6 hours total preparation time on a single Hamilton STAR. This compares to 9 hours and two Hamilton STARs with the PCR based methods used in the CLIA laboratory. The amount of cfDNA extracted per sample averaged 60 pg/μΐ _^ , and the yield of the sequencing library output was linearly correlated (R ² =0.94) with cfDNA input as shown in Figure 9. The average recovery was greater than 70% (add range), indicating a highly efficient recovery of the cfDNA after the SPRI bead purification. Each sequencing run used normalized amounts of 48 samples multiplexed and took approximately 14 hours to complete. The median number of uniquely mapped paired reads was XXX M with 95% of samples above YYY.

Paired End Sequencing

[00541] The total sequencing time per 48-sample batch was less than 14 hours on the NextSeq 500. This compares to a 40 hours (1 flow cell, 96 samples) or 50 hours (2 flow cells, 192 samples) for the laboratory process on a HiSeq 2500. The mapped genomic locations of both ends of cfDNA fragments provided cfDNA fragment size information. Figure 10 shows the cfDNA fragment size distribution as measured from 324 samples from pregnancies with a male fetus. The size of fragments that mapped to autosomal chromosomes known to be euploid and primarily represent the maternal chromosomes is represented by the thin curve. The average size of the inserts was 175 bp with XX% of fragments measuring between lOObp and 200bp. The thick curve represents the fragment size that exclusively arises from the Y-chromosome representing only fetal cfDNA fragments. The size distribution from the Y-chromosome specific sequences was smaller, averaging 167 bp with a 10 base periodicity at shorter fragment sizes.

[00542] Since the shorter fragments of cfDNA are enriched for fetal DNA, selective analysis using only shorter fragments would be expected to increase the relative fetal representation due to preferential selection of fetal reads. Figure 11 shows the relative fetal fraction from the total counts of mapped paired end reads compared to the counts from paired end reads that are less than 150 bp. Overall, the median fetal fraction increases by a factor of 2 compared to the total counts albeit with some increase in the variance. The size cutoff of 150 bp was found to provide an optimum tradeoff for counts with an increase in fetal representation versus variance in the counts.

Detection of Fetal Whole Chromosome Aneuploidy

[00543] Each of the available metrics, total counts, counts less than 150 bp, fraction of counts enriched for fetal cfDNA (counts between 80 and 150 bp/counts <250bp) and the combination of the shorter fragment counts with fraction, were tested for the ability to differentiate trisomy 21 samples from those euploid in chromosome 21. Figure 12 shows the results for each of these metrics. The total counts have a median of XX counts while the counts less than 150 bp has a median of YY counts. Yet, as can be seen in Fig 4A and 4B, the smaller counts show better separation between trisomy 21 and euploid primarily because this metric is enriched for the fetal cfDNA. The fraction alone is nearly as effective as the total counts for differentiating aneuploidy (Fig. 4C), but when used in combination with the short fragment counts (Fig. 4D) provides improved differentiation over short fragment counts alone. This indicates that the fraction is providing independent information that enhances the detection of trisomy 21. When compared to the current CLIA laboratory workflow using library prep with PCR amplification and a median of 16 M counts/sample, the PCR free, paired end sequencing workflow shows equivalent performance with significantly fewer counts/sample (e.g., 6 M counts/sample or fewer) and a simpler, shorter sample preparation workflow.

Calculation of Fetal Fraction

[00544] Using the X chromosome results from pregnancies with male fetuses, normalized chromosome values can be utilized to determine fetal fractions for the counts (ClinChem ref) and compared for different cfDNA fragment sizes. Fetal fractions derived from the X chromosome were used to calibrate the ratios for a set of 140 samples and estimate performance using a leave-one-out cross-validation. Figure 13 shows the results of cross-validated fetal fraction predictions and demonstrates the correlation between the two data sets, indicating that fetal fraction estimates can be obtained from any samples, including ones from women carrying female fetuses once a calibration set has been measured.

Discussion

[00545] It has been demonstrated that high analytical sensitivity and specificity for fetal aneuploidy detection from cfDNA in maternal plasma can be achieved with a PCR free library preparation coupled with paired end DNA sequencing. The method simplifies workflow, improves turnaround time (Figure 8) and should eliminate some biases inherent with PCR methods. Paired end sequencing allows determination of fragment length sizes and fetal fraction that can be further utilized to enhance detection of aneuploidy at significantly lower tag counts compared to currently implemented commercial methods. Performance of the PCR free paired end implementation appears to be similar to single end sequencing methods that utilize up to three times the number of tags. Simplification of Library Processing

[00546] The PCR free workflow has several advantages for the clinical laboratory. Because of the high yield and linear behavior of the library preparation, normalized pools of samples for sequencing can be made directly from the individual sample library concentrations. Biases inherent in the PCR amplification of the library preparation process are thereby eliminated. In addition, there is no need to isolate separate liquid handlers for pre- and post-PCR activities; this reduces the capital burden for the laboratory. This simplified workflow allows batches of samples to be prepared within a single shift of the clinical laboratory, and then sequenced and analyzed overnight. Overall, the reduced capital expenditure, reduced "hands on" time and rapid turnaround allow for potentially significant reductions in the cost and overall robustness of NIPT.

Paired End Sequencing

[00547] Using paired end sequencing on the NextSeq 500 system has several advantages for the counting of cfDNA fragments. First, with dual index barcodes, samples can be multiplexed at a high level allowing normalization and correction of run-to-run variation with high statistical confidence. In addition, because 48 samples are being multiplexed per run, and the amount needed on the flow cell for clustering is limited, the input requirement per sample is significantly reduced, allowing the PCR free library workflow to be utilized. With their typical cfDNA yield of approximately 5 ng per sample, researchers were able to get 2-3 sequencing runs per sample even without PCR amplification. This is in contrast to other approaches that require significant amounts of plasma input from multiple blood tubes to yield enough cfDNA for aneuploidy determination (REF). Finally, paired end sequencing allows the determination of cfDNA fragment size and analytical enrichment for fetal cfDNA.

Detection of Fetal Whole Chromosome Aneuploidy

[00548] Our results demonstrate that counts of cfDNA fragments below 150 bp are able to better differentiate aneuploidy from euploid chromosomes than the total counts. This observation is in contrast to the results of Fan et al., who suggested that the accuracy of the counting statistics would be decreased using shorter fragments (Fan et al.) because of the reduction the number of available counts. The fraction of short fragments also provides some differentiation for trisomy 21 detection as implied by Yu et al., albeit with less dynamic range than the counts. However, combining the counting and fraction metrics results in the best separation of the trisomy 21 samples from euploid, and implies that these two metrics are complementary measurements for chromosome representation. Other biological metrics, e.g. methylation, might also provide orthogonal information that could enhance the signal-to-noise ratio for aneuploidy detection.

Calculation of Fetal Fraction

[00549] The methods presented here also allow an estimation of the fetal fraction in each sample without creating additional laboratory work. With many samples on each flow cell, approximately half of which are male, an accurate fetal fraction estimate can be obtained for all samples by calibrating fetal fraction measurement from fragment size information with that determined from the male samples. In the commercial setting, researchers' clinical experience has shown that standard counting methods using a larger number of single end tags has led to very low false negative rates even in the absence of specific fetal fraction measurements (REF). Given the similar limit of detection observed here, equivalent test performance is expected.

Conclusion

[00550] It has been demonstrated that high analytical sensitivity and specificity for fetal aneuploidy detection from cfDNA in maternal plasma can be achieved with a PCR free library preparation coupled with paired end DNA sequencing. This simplified workflow has a very fast turnaround time, potentially allowing NIPT to be carried out at significantly lower cost for use in the general obstetric population. In addition, the paired end sequencing techniques have the potential to measure other biological phenomena, as well as providing other clinical applications. For example, size information from methylated specific regions of the genome or CpG islands could provide another orthogonal metric for enhancing the detection of copy number variants across the genome.

[00551] The present disclosure may be embodied in other specific forms without departing from its spirit or essential characteristics. The described embodiments are to be considered in all respects only as illustrative and not restrictive. The scope of the disclosure is, therefore, indicated by the appended claims rather than by the foregoing description. All changes which come within the meaning and range of equivalency of the claims are to be embraced within their scope