METHOD

TECHNICAL FIELD

The present disclosure relates to prenatal screening and diagnostic systems that are operable to process maternal blood in order to determine fetal (foetal) characteristics. Moreover, the present disclosure concerns methods of (for) using aforementioned prenatal screening systems, for example for processing maternal blood in order to determine fetal (foetal) characteristics. Additionally, the present disclosure is concerned with computer program products comprising a non-transitory computer-readable storage medium having computer-readable instructions stored thereon, the computer-readable instructions being executable by a computerized device comprising processing hardware to execute the aforesaid methods.

BACKGROUND

Zygote formation and associated subsequent fetal (foetal) development is a complex biological process that does not always occur without defects arising. It is of great societal benefit that such defects are detected reliably, for example as early as possible, during fetal growth.

Antenatal or prenatal screening is provided to pregnant women to prevent or treat potential health problems that may occur during their pregnancy. Such problems may affect both a given mother and/or a fetus of the given mother. Moreover, the problems may be influenced by factors such as lifestyle, environment or genetics. However, of particular importance are fetal (foetal) abnormalities that are genetic in origin. These abnormalities may be caused by mutations inherited from one or both parents (namely, of paternal and/or maternal origin), or may arise "de novo" (namely, stochastically or spontaneously arising). The mutations can range extensively from changes in single nucleotides to a presence of additional whole chromosomes; for example, the human genome usually includes 46 chromosomes (two pairs of 23 chromosomes), but abnormalities can result in a total of for example, 45 or 47 chromosomes arising. Of particular clinical significance are chromosomal disorders known as ^{^} aneuploidies' that occur when there are an abnormal number of chromosomes (for example, as occurs in Down's syndrome). Many chromosomal disorders are incompatible with life or result in multiple congenital anomalies for a given new born child. Prenatal screening for risk of fetal (foetal) chromosomal abnormalities during pregnancy is contemporarily available through public and private healthcare providers. This prenatal screening is normally carried around the first trimester of pregnancy (normally between 8 and 14 weeks gestation) and typically involves obtaining a maternal blood sample from a given mother combined with performing an ultrasound scan of a fetus of the given mother; such a procedure is known as a "Combined Test". When undertaking the "Combined Test", concentrations (namely, 'levels') of human chorionic gonadotrophin (hCG) and pregnancy-associated plasma protein (PAPP-A) are measured, together with executing a nuchal translucency (NT) scan; once other medical factors (for example, maternal age) have been taken into account, a risk-score is provided, namely computed, at a conclusion of the "Combined Test".

If a given mother's pregnancy is categorised as being of a high-risk following the combined test, an invasive diagnostic procedure (for example, chorionic villus sampling, an amniocentesis, a cordocentesis) is offered to the given mother to confirm or rule out Down's syndrome (trisomy chromosome 21 - T21), Edwards's syndrome (trisomy chromosome 18 - T18) and Patau syndrome (trisomy chromosome 13 - T13). Pregnant women are also offered a second ultrasound scan at 18 to 21 weeks (after conception) to check for structural fetal anomalies such as cardiac malformations, brain malformations and skeletal abnormalities. This second ultrasound scan can be used to direct antenatal treatments, identify anomalies that require early intervention following delivery of a given child or enable follow-on diagnostic testing and pregnancy management. Invasive tests such as chorionic villus sampling, amniocentesis and cordocentesis carry a 1% chance of miscarriage.

During recent years, non-invasive techniques (without an associated increased risk of miscarriage) have been developed for diagnosing fetal chromosomal anomalies that rely on a presence of circulating cell free fetal DNA (cffDNA) in the mother's blood. The testing of cell-free fetal DNA (cffDNA) is now available for clinical practice for non-invasive prenatal testing (NIPT) for aneuploidy (associated with chromosomes T21, T18, T13) and has a broad application as a replacement, or contingent test for the aforementioned ^{^} Combined Test'. The anomalies that can be tested by NIPT are increasing as methods are developed for identifying sub-chromosomal rearrangements such as 22ql l.2/DiGeorge syndrome and other nucleic acid based microdeletion syndromes. However, the false positive rate for these sub-chromosomal anomalies is considered to be too high to offer such testing on a screening basis, and it is recommended that it is only offered if there is an accompanying clinical indication, such as a congenital heart defect. NIPT is classified as ^{^} testing' rather than ^{^} diagnosis', as the cffDNA that is measured is derived from a placenta of a given mother rather than a fetus of the given mother, meaning that false positives can occur due to confined placental mosaicism. For this reason, it is recommended that positive NIPT results are confirmed by performing an invasive amniocentesis (often referred to colloquially as an ^{^} amnio'). Non-invasive prenatal diagnosis (NIPD), namely a form of test, is classified as being a diagnostic assay with no need for performing a subsequent invasive assay to confirm results provided by the diagnostic assay. The use of NIPD is more limited than NIPT and is used for investigating fetuses at risk of single gene disorders (namely, affected by inherited and de novo mutations) or those that present with a suspicion of a monogenic disorder when performing a fetal ultrasound investigation.

Cell-free fetal DNA (cffDNA) circulates in maternal blood at approximately 10% of the total cell free component. Coupled with low concentrations of total cell free DNA, next generation sequencing library preparation methods of (for) analysing this cell-free fetal DNA (cffDNA) material require Polymerase Chain Reaction (PCR) amplification to be employed. PCR amplification generally introduces errors, which can be at a rate that is higher than a rate of a fetal fraction; thus, a determination of a true variation in a given fetal genome may be obscured, or false positives obtained, as a result of such introduced errors (namely, stochastic noise). Even using PCR-free approaches, a final sequencing step employed requires copies of a given original DNA molecule to be made, which can also introduce errors. Such an introduction of errors is particularly relevant when trying to identify de novo variants which have occurred in a given fetus.

To address erroneous artefacts that are PCR duplicates, analysis protocols typically remove duplicate reads based upon an assumption that two reads with a same given start and a same given end position have arisen from the PCR process, as opposed to being unique DNA molecules; such an assumption is essentially a form of correlation with a purpose of reducing stochastic noise when making measurements. The number of PCR duplicates required tends to increase with lower (namely, smaller) starting amounts of DNA (as is the case with cfDNA). However, it has been determined that unique molecules of cfDNA and cffDNA can have a same start and a same end point, due to preferences of where DNA is sheared, based upon open chromatin regions. This means that by applying a PCR duplicate removal step, 14% of genuine DNA fragments are being discarded (Chan et al., 2016). Thus, such a ^{^} correlation' approach is not without its own problems and inaccuracies.

A technical problem that the present disclosure seeks to address is how to identify unique DNA molecules, wherein the DNA molecules have a mutually same start position and a mutually same end position.

A solution that exists to identify unique DNA molecules is molecular barcoding (MBC); also known as Unique Molecular Indices (UMI). UMI's enable reads to be identified that have arisen as a result of sequencing error. This means PCR artefacts can be removed and real variants kept; for example, use of UMIs means a genuine mosaic variant may be discarded due to a low allele frequency being encountered. Molecular barcoding of individual DNA molecules can be used to increase a confidence in a given variant calling, when an expected frequency of mutant reads is at or below an error rate threshold of a DNA nucleic acid base sequencing method. Moreover, each original DNA fragment in a given sample, when implementing the method, is attached to a unique barcode, or unique molecular index (UMI). This UMI is typically a string of random nucleotides, degenerate nucleotides or defined nucleotides. Reads which contain a sequencing error can be removed from downstream analysis while processing various DNA fragment reads. Such a barcoding approach can account for PCR and DNA sequencing errors, and may potentially improve a detection of low allele frequency variants. Based upon this sequencing method using barcodes, the method is potentially susceptible to being used to identify which DNA fragments with mutually identical start and end points are genuine, and which DNA fragments are biological duplicates, and therefore which can be retained for use in further analysis.

Known types of molecular barcoding include incorporation into sequencing adapters during library construction (duplex sequencing) (for example, Peng, Vijaya Satya, Lewis, Randad, & Wang, 2015); and smMIP (single molecule molecular inversion probes), wherein a method includes employing single- molecule tagging combined with multiplex targeted capture. Specifically, Hiatt, Pritchard, Salipante, O'Roak, & Shendure, (2013) first described this method, wherein 1312 smMIP oligos targeting coding sequences of 33 genes (approx. 125 kb) were designed. Furthermore, publications describing smMIP include :

(i) a published US patent application US2016/0055293A describing such a method, systems implementing the method, and algorithms and software for MIP design associated with the method ; there is also described a BRCA kit that is available that uses the method;

(ii) a published US patent application US2016/0055293A describing such a method, systems implementing the method, and algorithms and software for MIP design associated with the method .

Additionally, smMIP for non-invasive prenatal diagnosis (NIPD) is being developed at Maastricht University and Radbound UMC. Such an approach appears presently to be on a single gene basis, rather than a panel of genes. Furthermore, it has been suggested that such an approach is a most favoured option for developments such as combined barcoding and enrichment, wherein there is focus upon a scalability of target regions.

Known commercially-available customizable methods of (for) providing molecular barcodes include Agilent HaloPlex ^HS ; Agilent whitepaper on molecular barcoding; QiaSeq Targeted DNA Panel® and ArcherDX® Archer MBC Adapters; these names include trade marks (US: trademarks) ® TM.

Molecules are labelled with a unique sequence prior to performing PCR amplification. There is employed an adapter that contains a sample-specific index of pre-defined sequences and a random 8-mer molecular barcode (or UMI). This random 8-mer molecular barcode is ligated to fragmented gDNA before amplification. The random 8-mer, along with a random start site generated during the enzymatic shearing, is used to identify duplicates. The cfDNA samples that are of interest, in respect of technology described in the present disclosure, is not subjected to experimental enzymatic fragmentation, but by natural enzymatic processes.

Contemporary aforementioned methods that are currently available for molecular barcoding are generally restricted to a relatively small number of regions of interest in a DNA molecule via PCR amplicon approaches, meaning that associated DNA analysis has to be very targeted in order to achieve useful DNA sequence readout results.

Therefore, in light of the foregoing discussion, there exist problems associated with conventional pre-natal screening systems.

SUMMARY

The present disclosure seeks to provide an improved prenatal screening and diagnostic system that is capable of testing for an extended number of genetic conditions, with a lower occurrence of false-positives and false-negatives, when the screening system is employed for providing a prenatal screening service. Moreover, the present disclosure seeks to provide an improved method of (for) using a prenatal screening and diagnostic system that is capable of testing for an extended number of genetic conditions, with a lower occurrence of false- positives and false-negatives, when the screening system is employed for providing a prenatal screening service.

In a first aspect, embodiments of the present disclosure provide a prenatal screening and diagnostic system, wherein the prenatal screening and diagnostic system includes a wet-laboratory arrangement for processing a blood sample to determine cell-free DNA readout data from the blood sample, and a data processing arrangement for processing the cell-free DNA readout data with reference to information stored in a database arrangement to generate a risk score indicative of whether or not there are genetic abnormalities in the blood sample that are indicative of fetal abnormalities, characterized in that the prenatal screening and diagnostic system ligates in operation nucleic acid base molecular barcodes to fragments of the cell-free DNA present in the blood sample prior to amplifying the molecular barcode- ligated DNA fragments for sequencing the amplified molecular barcode-ligated fragments to generate the cell-free DNA readout data.

The present disclosure is of advantage in that it provides an improved personalized non-invasive system and method of (for) identifying genetic abnormalities in a fetus.

"To generate a risk score" is be construed to mean, for example, to compute a risk score.

Moreover, the system disclosed herein is advantageous because it provides an improved method of (for) identifying genetic abnormalities in a fetus, without an associated increased risk of miscarriage, as well as providing a higher accuracy with less risk of false negative and false positive results, for example in the risk score.

Embodiments of the disclosure are advantageous in terms of providing a rapid, simple, patient specific and highly efficient method and system of screening that can efficiently decrease an error that may arise during amplification of DNA sequences. Furthermore, the present disclosure provides a method of identifying unique DNA molecules, wherein the DNA molecules have a mutually same start position and a mutually same end position.

Optionally, the prenatal screening and diagnostic system ligates in operation both the fragments of the cell free DNA with adaptors including the nucleic acid base molecular barcodes to the fragments of the cell-free DNA. By such an approach, fragments can be effectively labelled and traced in an early stage prior to PCR amplification and subsequent sequence readout, thereby potentially reducing a risk of read error and improving measurement accuracy of the system through improved traceability of DNA fragments through the system.

Optionally, the prenatal screening system implements in operation the molecular barcode (UMI) as an n-mer, wherein n is in a range of 3 to 100. More optionally, the n is in a range of 4 to 20. Moreover optionally, the n is 10.

Optionally, the molecular barcode (UMI) includes a random sequence of nucleic acid bases.

Optionally, the wet-laboratory arrangement incorporates in operation the molecular barcode (UMI) to a cell-free DNA library containing a fetal component, and uses the cell-free DNA library thereby obtained in hybridisation-based enrichment for identifying de novo variants when computing the risk score. Optionally, the prenatal screening system generates in operation with ligation of nucleic acid base molecular barcodes to the cell free DNA fragments to generate corresponding barcoded fragments, and performs enrichment by hybridization using baits targeted at genes that are susceptible to causing fetal illnesses.

Optionally, the prenatal screening and diagnostic system utilizes in operation the molecular barcoded adaptor-ligated cell-free DNA fragments to perform enrichment by hybridization using baits targeted at genes, or primers targeted at genes that are susceptible to causing one or more diseases; for example, by employing such hybridization, it is feasible to for detecting not only prenatal genetic defects, but also other diseases such as cancer.

Optionally, the prenatal screening system performs in operation non-invasive molecular diagnosis of a fetus which on ultrasound investigation presents with at least one abnormality, wherein the abnormality is for example, a skeletal abnormality or a cardiac abnormality. More optionally, the skeletal abnormality and/or the cardiac abnormality is caused by a de novo mutation.

In a second aspect, embodiments of the present disclosure provide a method of (for) using a prenatal screening system, wherein the prenatal screening system includes a wet-laboratory arrangement for processing a blood sample to determine cell-free DNA readout data from the blood sample, and a data processing arrangement for processing the cell-free DNA readout data with reference to information stored in a database arrangement to generate a risk score indicative of whether or not there are genetic abnormalities in the blood sample that are indicative of fetal abnormalities, characterized in that the method includes:

(i) ligating nucleic acid base molecular barcodes to fragments of the cell- free DNA present in the blood sample;

(ii) amplifying the molecular barcode-ligated fragments; and (iii) sequencing the amplified molecular barcode-ligated fragments to generate the cell-free DNA readout data.

Optionally, the method includes operating the prenatal screening and diagnostic system to implement the molecular barcode as an n-mer, wherein n is in a range 3 to 100.

Optionally, the method includes arranging for the molecular barcode to include a random sequence of nucleic acid bases.

Optionally, the method includes operating the wet-laboratory arrangement to incorporate the molecular barcode to a cell-free DNA library containing a fetal component, and to use the cell-free DNA library thereby obtained in hybridisation-based enrichment for identifying de novo variants when computing the risk score.

Optionally, the method includes operating the prenatal screening system to ligate nucleic acid base molecular barcodes to the fragments to generate corresponding barcoded fragments, and to perform enrichment by hybridization using baits targeted at genes which for one or more diseases that are susceptible to causing fetal illnesses.

Optionally, the method includes operating the prenatal screening system to perform non-invasive molecular diagnosis of a fetus which on ultrasound presents with at least one abnormality, wherein the abnormality is, for example, a skeletal abnormality and/or a cardiac abnormality. More optionally, the skeletal abnormality and/or the cardiac abnormality is caused by a de novo mutation.

In a third aspect, embodiments of the present disclosure provide a computer program product comprising a non-transitory computer-readable storage medium having computer-readable instructions stored thereon, the computer- readable instructions being executable by a computerized device comprising processing hardware to execute the aforementioned method.

Additional aspects, advantages, features and objects of the present disclosure would be made apparent from the drawings and the detailed description of the illustrative embodiments construed in conjunction with the appended claims that follow.

It will be appreciated that features of the present disclosure are susceptible to being combined in various combinations without departing from the scope of the present disclosure as defined by the appended claims.

A better understanding of the present invention may be obtained through the following examples which are set forth to illustrate, but are not to be construed as limiting the present invention.

BRIEF DESCRIPTION OF DRAWINGS

Embodiments of the present disclosure will be more fully understood from examples described hereinafter and the accompanying drawings, which are given by way of illustration only, and are thus not limitative of the present invention, and wherein:

FIG. 1 is a block diagram of a prenatal screening and diagnostic system, in accordance with an embodiment of the present disclosure;

FIG. 2 is an illustration of a Kalman filter equivalent representation of the prenatal screening and diagnostic system of FIG. 1, in accordance with an embodiment of the present disclosure;

FIG. 3 is an illustration of molecular barcode-ligated DNA fragments, in accordance with an embodiment of the present disclosure; FIG. 4 is an illustration of amplified molecular barcode-ligated fragment, in accordance with an embodiment of the present disclosure; and

FIG. 5 is an illustration of steps of a method of using the prenatal screening and diagnostic system of FIG. 1, in accordance with an embodiment of the present disclosure.

In the accompanying diagrams, an underlined number is employed to represent an item over which the underlined number is positioned or an item to which the underlined number is adjacent. A non-underlined number relates to an item identified by a line linking the non-underlined number to the item. When a number is non-underlined and accompanied by an associated arrow, the non-underlined number is used to identify a general item at which the arrow is pointing.

LIST OF ABBREVIATIONS Abbreviation Meaning

PCR Polymerase Chain Reaction cfDNA Cell-Free DNA

UMI Unique Molecular Identifier

DEFINITIONS

As used herein, the following terms shall have the following meanings:

As used herein, the term 'data processing arrangement' refers to a process and/or system that can be embodied in software that determines, when in operation, the biological significance of acquired data (i.e., the ultimate results of an assay). For example, a data processing arrangement can determine the amount of each nucleotide sequence species based upon the data collected. A data processing arrangement may also control an instrument and/or a data collection system based upon results determined. A data processing and a data collection arrangement often are integrated and provide feedback to operate data acquisition by the instrument, and hence provide assay-based judging methods provided herein.

As used herein, the term ^{^} database arrangement' refers to a nucleic acid database known in the art including, for example, GenBank®, dbEST®, dbSTS®, EMBL® (European Molecular Biology Laboratory), ClinVar, gnomAD and DDBJ® (DNA Databank of Japan). BLAST® or similar tools can be used to search the identified sequences against a sequence database.

As used herein, the term ^{^} genetic information' refers to information related to nucleic acids, altered nucleotide sequence, chromosomes, segments of chromosomes, polymorphic regions, translocated regions, the like or combinations of the foregoing. Furthermore, the nucleic acids may include, but are not limited to, DNA, cfDNA, cDNA, RNA, mRNA, t RNA and rRNA. Moreover, the genetic information may include information related to mutations, copy number variations, transversions, translocations, inversion, deletions, aneuploidy, partial aneuploidy, polyploidy, chromosomal instability, chromosomal structure alterations, gene fusions, chromosome fusions, gene truncations, gene amplification, gene duplications, chromosomal lesions, DNA lesions, abnormal changes in nucleic acid chemical modifications, abnormal changes in epigenetic patterns, abnormal changes in nucleic acid methylation infection or cancer.

As used herein, the term ^{^} cell-free DNA' refers to DNA that is not within a cell. In one embodiment, cell free DNA includes DNA circulating in blood. In another embodiment, cell free DNA includes DNA existing outside a cell. In yet another embodiment, cell free DNA includes DNA existing outside a cell as well as DNA present in a blood sample after such a blood sample has undergone partial or gentle cell lysing.

As used herein, the terms ' biological sample' or ' maternal sample' or ' maternal blood sample' or ^{^} blood sample' refers to a sample obtained from a female who is pregnant, wherein the sample may include, but is not limited to, plasma, serum, peripheral blood and urine. Typically, the sample is a maternal plasma sample, although other tissue sources that contain both maternal and fetal DNA are optionally used. Maternal plasma can be obtained from a peripheral whole blood sample from a pregnant woman and the plasma can be obtained by standard methods, for example by employing centrifuging processes. A volume in a range of 3 ml to 5 ml of plasma is typically sufficient to provide a suitable quantity of DNA material for analysis. The cell free DNA can be extracted from the sample using standard techniques, wherein non- limiting examples of which include a QIASymphony® protocol (Qiagen) suitable for free fetal DNA isolation, or any other automated or manual extraction method suitable for cell free DNA isolation.

As used herein, the term ^{^} biological characteristics' refers to genetic variations, abnormalities, irregularities or mutations which range extensively from changes in single nucleotides to a presence of additional whole chromosomes or abnormal number of chromosomes. Such a chromosomal abnormality is a structural abnormality, including, but not limited to, copy number changes including microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures.

As used herein, the term ¹ wet-laboratory arrangement' refers to a facility, clinic and/or a setup of: instruments, equipment and/or devices used for extraction, collection, processing and/or analysis of body fluid samples; instruments, equipment and/or devices used for extraction, collection, processing and/or analysis of genetic material ; instruments, equipment and/or devices used for amplification, enrichment and/or processing of genetic material received from the body fluid samples; instruments, equipment and/or devices used for extraction and/or analysis of the genetic information received from the amplified genetic material. Herein the instruments, equipment and/or devices may include but not limited to centrifuge, ELISA®, spectrophotometer, PCR, RT- PCR, High-Throughput-Screening (HTS) system, Microarray system, ultrasound (scanning), genetic analyser, deoxyribonucleic acid (DNA) sequencer and SNP analyser. The wet-laboratory arrangement is operable to monitor and/or scan a given fetus. Herein, the wet-laboratory arrangement may include equipment, instruments and/or devices for scanning the fetus; such examples include an ultrasound scan, presymptomatic genetic testing and/or combined tests.

As used herein, ^{^} polymerase chain reaction (PCR)' is a technique used in molecular biology to amplify a single copy, or a few copies, of a segment of DNA by several orders of magnitude, thereby generating potentially thousands of millions of copies of a particular given DNA sequence.

As used herein, 'bridge amplification' or ¹ amplification' is employed in massively parallel sequencing for DNA sequencing purposes using a concept of massively parallel processing, wherein use is made of miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 nucleic acid bases each) per instrument run.

As used herein, the term ^{^} baits' refers to a bioactive molecule which is used to detect other bioactive molecules such as genes of interest or target genes. This bait design, or primer design, will be in combination with the targeting of genes which are relevant to monogenic clinical disorders and for the enrichment of fetal DNA from cell free DNA derived from a maternal plasma sample. The baits for example or primers are, prepared beforehand, and are optionally selected from a library of prepared baits or primers.

Target enrichment is used to isolate specific fragments of genomic DNA for sequencing. A library of complementary oligonucleotide "baits" is used to retrieve fragments of interest (namely, target DNA). The target DNA hybridizes well with the baits, but other DNA does not, which forms a basis of a powerful selection method for genomic regions of interest.

Such baits, when designed, will be employed in combination with the targeting of genes which are relevant to monogenic clinical disorders and for the enrichment of fetal DNA from cell-free DNA from a maternal plasma sample. The baits are, for example, prepared beforehand, and are optionally selected from a library of prepared baits. Libraries of such baits are provided by commercial organizations, for example based in the USA. Moreover, such libraries include up to, for example, 100000 different types of baits. Beneficially, the baits correspond to active synthesizing parts of the human genome, wherein DNA sequence variation can give rise to illnesses to be detected using systems and methods of the present disclosure.

The baits include a portion of DNA bases (for example 120 bases in sequence, although other numbers of bases are possible, for example in a range of 20 to 200 bases) with a biotin group attached to end of the portion.

When processing a sample of maternal blood, the baits are added to the cfDNA derived from blood plasma, so the baits (with their biotin groups) bind to corresponding fragments of cfDNA in, attracted baits and associated cfDNA fragments attached are enriched and cfDNA fragments amplified.

The baits are commercially available (for example, from Agilent Biosystems, USA), wherein the baits are available in large libraries that provide a choice of many tens of thousands of different types of baits, for example as aforementioned. Agilent Biosystems, for example, provides a target enrichment library that is, for example, used in embodiments of the present disclosure, to provide a final product containing a set of biotinylated oligonucleotides. However, when the library is created in eArray® (by Agilent®), the bait sequences are specified in terms of DNA bases (A, C, G, T). The baits are designed to have DNA sequences corresponding to specific groups of DNA bases in the human genome, wherein the specific groups can give rise to various types of illnesses that have fetal health consequences.

Alternatively, non-commercially available baits may be preferred. These baits may be specifically designed and may be formed of any number of DNA bases, preferably 20 to 300 bases, for example 50 to 200 bases, preferably 100 to 150 bases.

As used herein, the term "barcode" refers to a unique oligonucleotide sequence that allows a unique nucleic acid fragment to be identified. This unique oligonucleotide sequence may be termed a unique molecular identifier (UMI) or a molecular barcode. In certain aspects, the nucleic acid base and/or nucleic acid sequence is located at a specific position on a larger polynucleotide sequence (for example, a covalently attached polynucleotide to a bead). Oligonucleotides are often short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Moreover, such oligonucleotides are commonly made in a laboratory by solid-phase chemical synthesis; these small bits of nucleic acids can be manufactured as single-stranded molecules with potentially any user- specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (for example, microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

As used herein, the term "adaptor" refers to a molecule which is used to link the ends of two other genetic materials. The adaptor may include but not limited to chemically synthesized molecules which may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid . Conventionally, adapter is used to join a DNA insert cut with one Restriction enzyme. Alternatively, adaptors may be used to link the ends of two DNA molecules that have different sequences at their ends.

The adaptor may include a bioactive molecule which is used to ligate with a fragment of cell free DNA (cfDNA) and the barcode. The adaptor comprises a first strand and a second strand having complementary region therebetween that comprises a fragment pf cell free DNA (cfDNA) or a unique barcode.

In an embodiment, the adaptor may be Y-shaped, and in some cases they may be commercially obtained. In certain embodiments, adaptors that are ligated to the fetal DNA fragments are not from the same population of adaptors that are ligated to parental DNA fragments.

As used herein, the term ^{^} variants' refers to an abnormality, a suspected abnormality or a mutation. The variant may be a single point mutation, insertion, deletion, inversion, transversion, and so forth. The variants may be associated with at least one of a physical abnormality, a mental abnormality, an intellectual abnormality, a structural abnormality, or a combination thereof. Optionally, the variants for the fetal DNA includes, but is not limited to, one or more de novo variants, paternally inherited, maternally inherited, inherited from both parents, and so on. The variants for the fetal DNA may arise if the biological age of the father may be 45 years or greater and/or the biological age of the mother is 35 or more. In an example, the variant may be associated with a monogenic Mendelian disorder, an aneuploidy, and so forth.

As used herein, the term "inherited variants" or "inherited mutations" refers to variations, such as a single point mutation, insertion, deletion, inversion, transversion and so on, passed on to an offspring by at least one parent. Specifically, inherited variants comprise various alleles of a gene that differentiates an organism from another within and among populations. More specifically, inherited variants result from germline mutations. In an example, DNA of a given biological father may include a known variant associated with a disorder, and a same disorder is diagnosed in the fetal DNA. In such a case, the inherited variant is associated with the paternally-inherited variant. For example, autism is a paternally inherited variant of cis-regulatory elements (CRE-SVs). Moreover, pathogenic variants may also be paternally inherited, such as COL1A1, COL1A2, FGFR3, NIPBL, PTPN 11 and RIT1. As used herein, the term 'fetal illness' refers to disorders or diseases resulting from altered genetic or chromosomal information which could include single- gene or monogenic abnormalities, autosomal recessive and dominant abnormalities and X-linked conditions. In an embodiment, fetal illness may result from aforesaid variants.

DETAILED DESCRIPTION

Practical implementation of the embodiments of the present disclosure are described in further detail below; these embodiments are operable to employ (namely, employ when in operation), unless otherwise indicated, conventional methods of diagnostics, molecular biology, cell biology, biochemistry and immunology within the skill of the art. Such techniques are explained fully in the literature, for example contemporary academic research literature pertaining to pregnancy and genetic material processing. However, it will be appreciated that new combinations of known methods of diagnostics can give rise to new inventions.

It will be appreciated that certain features of the present invention, which are for clarity described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely various features of the invention, which are for brevity, described in the context of a single embodiment, may also be provided separately and/or in any suitable sub ^¬ combination.

The following detailed description illustrates embodiments of the present disclosure and ways in which they can be implemented . Although some modes of carrying out the present disclosure have been described, those skilled in the art would recognize that other embodiments for carrying out or practicing the present disclosure are also possible.

Referring to FIG. 1, there is shown a block diagram of a prenatal screening and diagnostic system 100, in accordance with an embodiment of the present disclosure. The prenatal screening and diagnostic system 100 includes a wet- laboratory arrangement 102, wherein the wet-laboratory arrangement 102 includes apparatus such as blood sample collection apparatus, centrifuges, PCR rapid gene sequencing apparatus and similar apparatuses. For example, the wet-laboratory arrangement 102 includes apparatus manufactured by Illumina® Inc. for performing gene sequencing tasks. Furthermore, the prenatal screening and diagnostic system 100 processes, when in operation, a blood sample in the wet-laboratory arrangement 102 to obtain cell-free DNA readout data therefrom.

In an embodiment, the prenatal screening and diagnostic system 100 performs, when in operation, non-invasive molecular diagnosis of a fetus which, on ultrasound testing (for example, ultrasound scanning), presents with (but not limited to) a skeletal abnormality and/or a cardiac abnormality. Optionally, the wet-laboratory arrangement 102 performs, when in operation, non-invasive molecular diagnosis of a fetus, such as ultrasound testing, to detect fetal abnormalities, such as a skeletal abnormality and/or a cardiac abnormality. Furthermore, the prenatal screening and diagnostic system 100, optionally, the wet-laboratory arrangement 102, generates, when in operation, an ultrasonic image or video of the fetus, to deduce a possibility, or probability of, of a fetal abnormality identified from the ultrasonic test.

In an example embodiment, the prenatal screening and diagnostic system 100 may ligate both ends of the molecular barcodes and the fragments of the cell free DNA with adaptors prior to ligating the nucleic acid base molecular barcodes to the fragments of the cell-free DNA.

In operation, the fetal cell-free DNA (cfDNA) is fragmented, and ends of the fragmented fetal cell-free DNA (cfDNA) are prepared such that adaptors can be ligated thereto. Optionally, the ends of the fragmented fetal cell-free DNA (cfDNA) may be polished using a polymerase, such as a Taq polymerase, and a single nucleotide is added to the ends of the fragmented fetal cell-free DNA (cfDNA) to facilitate ligation of the adaptors thereto. Adaptors are ligated to the fetal cell-free DNA (cfDNA) such that the fetal cell-free DNA (cfDNA) is individually and uniquely labelled. Optionally, labeling is achieved by utilizing a molecular barcode. More optionally, each fragment of the fetal cell-free DNA (cfDNA) is labeled with a given molecular barcode on each end of the fetal cell-free DNA (cfDNA) fragment. Furthermore, optionally, the molecular barcodes may comprise a certain number of random bases, such as 5 or more random bases.

Optionally, the wet-laboratory arrangement 102 may perform, when in operation, a combined test for prenatal screening of fetal chromosomal abnormalities. More optionally, the combined test may include, but is not limited to, a maternal blood test and an ultrasound scan of a fetus. Furthermore, the wet-laboratory arrangement 102 provides, when in operation, information representative of the combined test of the fetus.

In operation, the sample is obtained from a person, for example a blood sample from a pregnant mother; however, it will be appreciated that tissue sample are optionally additionally or alternatively employ relative to a blood sample. Optionally, with regard to the pregnant mother, the blood sample is a non-invasive sample, wherein collection of sample does not have an associated risk of miscarriage therewith. Furthermore, the blood sample includes plasma that includes, as a component part thereof, a mixture of cell- free DNA (cfDNA). Specifically, the cell-free DNA (cfDNA) may comprise a portion derived from the pregnant mother, from the placenta of the pregnant mother and/or from a fetus of the pregnant mother.

In an embodiment, a genetic abnormality may include genetic diseases that are present in the DNA sequences of a given mother. Specifically, such genetic diseases may or may not be inherited by a fetus of the given mother. Additionally, a fetal abnormality may include diseases that may be paternally inherited or that may arise de novo in the fetus. Furthermore, the DNA of the biological father may include a known variant associated with a disorder, such as autism spectrum disorder (ASD). In this case, due to a germline mutation, the fetus is susceptible to autism.

Moreover, the prenatal screening and diagnostic system 100 further includes a data processing arrangement 104, including a database arrangement 106, for receiving cell-free DNA readout data from the wet-laboratory arrangement 102. Optionally, the data processing arrangement 104 provides feedback data to the wet-laboratory arrangement 102 for controlling various tests performed thereat. Furthermore, the database arrangement 106 stores information comprising genomic mapping data and research data analysing structure, location and sequencing of human genes, and clinical effects of mutations and their co-relation with biological sequences and structures. Furthermore, the wet-laboratory arrangement 102 may be amplify, when in operation, the fragments of DNA to provide amplified DNA for nucleic acid base sequencing or readout to generate the cell-free DNA readout data. In this exemplary embodiment, the wet-laboratory arrangement 102 may include a PCR or RT-PCR for amplifying the free fetal DNA fragments for providing a plurality of copies of the free fetal DNA to the data processing arrangement 104 for accessing genetic information in the database arrangement 106. Additionally, the data processing arrangement 104 also includes data communication connections to networks such as the Internet®, for example for accessing various external databases associated with university research departments and hospitals.

Furthermore, the data processing arrangement 104 processes, when in operation, the cell-free DNA readout data with reference to information stored in a database arrangement 106 to generate, namely to compute, a risk score indicative of whether or not there are genetic abnormalities in the blood sample that are indicative, for example, of fetal abnormalities. Specifically, a risk score may be associated with a given fetus, wherein a higher risk score is indicative a higher possibility of a genetic abnormality. Furthermore, the risk score is generated, namely computed, after processing of cell-free DNA readout data with reference to information stored in the database arrangement 106. Specifically, the cell-free DNA readout data may correspond to a given genomic information in the database arrangement 106. Furthermore, such genomic information may be linked with a risk of a given genetic abnormality, as aforementioned. In an exemplary embodiment, the cell-free DNA readout data may comprise a sequential arrangement of ^Λ Α-Τ- G-C-A-T-G-C DNA base pairs with an anomaly 'A-G-T-C'. In such an embodiment, the data processing arrangement 102 may compare the anomaly against sequential arrangements of DNA stored in the database arrangement 106. Subsequently in the embodiment, the data processing arrangement 104 may assess if the anomaly may or may not cause a genetic disorder. Additionally, the data processing arrangement 104 may compare and provide the risk score representative of a risk to the fetus of inheriting or acquiring the genetic disorder. It will be appreciated that the DNA base pairs A, T, G, C represent DNA base pairs adenine, thymine, guanine and cytosine for illustrative purposes only and do not represent the actual arrangement of the DNA base pairs which may be responsible for a specific disease.

In an embodiment, fragments of cell-free DNA are generated in the prenatal screening and diagnostic system 100 by employing enzymic digestion. Specifically, cell-free DNA may undergo natural enzymic digestion. More specifically, strands of DNA may be fragmented (namely, cleaved) using enzymes. Furthermore, action sites of enzymes on the cell-free DNA may not be experimentally controlled. Subsequently, the ends of the fragmented fetal cell-free DNA (cfDNA) are prepared such that adaptors can be ligated thereto. Optionally, the ends of the fragmented fetal cell-free DNA (cfDNA) may be polished using a polymerase, such as a Taq polymerase, and a single nucleotide is added to the ends of the fragmented fetal cell-free DNA (cfDNA) to facilitate ligation of the adaptors thereto. Adaptors are ligated to the fetal cell-free DNA (cfDNA) such that the fetal cell-free DNA (cfDNA) is individually and uniquely labelled. Optionally, labeling is achieved by utilizing a molecular barcode. Optionally, ligation of the adaptors to the fragments of the fetal cell- free DNA (cfDNA) occurs through single complementary nucleotides on the 3' end of a given strand of the adaptor to the corresponding end of the fetal cell- free DNA (cfDNA) fragment. In an example, the single complementary nucleotides include adenine and/or thymine (A/T). Referring to FIG. 2, there is shown an illustration of a Kalman filter equivalent representation 200 of the prenatal screening and diagnostic system (such as the prenatal screening and diagnostic system 100 of FIG. 1), in accordance with an embodiment of the present disclosure. The Kalman filter equivalent representation 200 includes the cell-free DNA readout data 202 and the information representative of combined test of the fetus 204 to a data processing arrangement 206 (such as data processing arrangement 104 of FIG. 1) . The data processing arrangement 206 may implement, when in operation, a Kalman filter on the cell-free DNA readout data 202 information representative of combined test of the fetus 204. The data processing arrangement 206 further includes a fuzzy logic module 208, a processing module 210, a genetic algorithm 212 for processing the cell-free DNA readout data with reference to the information stored in a database arrangement 214 (such as the database arrangement 106 of FIG. 1), a secondary database 216 (such as secondary database for storing the risk score 218 received from the processing module 210. In this embodiment, the data processing system 206 may be operable to implement the Kalman filter on the genetic information received after prenatal screening tests performed by the wet-laboratory arrangement 102. Furthermore, the genetic algorithm 212 may be operable to generate risk score by processing the cell-free DNA readout data with reference to the information stored in a database arrangement 214.

In an exemplary embodiment, a given plasma sample derived from the aforementioned blood sample includes DNA sequences that are enriched using hybridization. Specifically, the hybridization enrichment is performed using baits or primers targeted at genes that are susceptible to causing fetal illnesses. In this embodiment, the processing module 210 is operable to validate target positions of genes that are susceptible to causing genetic diseases. In an embodiment, the prenatal screening and diagnostic system 100 may differentiate, when in operation, maternal and fetal components of cell-free DNA. In this embodiment, such differentiation may be achieved by employing an assay design which enriches the fetal component and which aids in mapping of maternal and fetal reads.

In another exemplary embodiment, the prenatal screening and diagnostic system 100 may design baits, alternatively select baits from a library of such baits, and to employ the baits at targeted positions on the genes that are susceptible to causing fetal illnesses for enrichment by hybridization. Furthermore, the prenatal screening and diagnostic system 100 may avoid, when in operation, the maternal-specific regions in the blood sample.

Referring to FIG. 3, there is shown an illustration of molecular barcode-ligated DNA fragments 300, in accordance with an embodiment of the present disclosure. The prenatal screening and diagnostic system 100 ligates, when in operation, (namely, is operable to ligate) nucleic acid base molecular barcodes 302 to fragments of the cell-free DNA 304 present in the blood sample. Optionally, the nucleic acid base molecular barcodes 302 may be ligated to fragments of cell-free DNA 304 and may be followed by subsequent enrichment by hybridisation using baits targeted at genes that are susceptible to causing fetal illnesses.

In an embodiment, the prenatal screening and diagnostic system 100 implements, when in operation, the molecular barcode 302 as an n-mer. Optionally, n is in a range of 3 to 100. More optionally, A? is in a range of 4 to 20. Yet more optionally, n is substantially 10. Specifically, the molecular barcode 302 may be implemented in a range of 3-mer to 100-mer. Furthermore, the molecular barcode 302 may be synthesized during the ligation process. In an embodiment, the molecular barcode 302 includes a random sequence of nucleic acid bases. Specifically, the nucleic acid bases include adenine (A), cytosine (C), guanine (G), thymine (T). Furthermore, the molecular barcode 302 includes the random sequence of nucleic acid bases for identification of targeted genes that are susceptible to causing fetal illnesses.

In an embodiment, the molecular barcode 302 includes adapters (namely, linkers). Specifically, adapters are short, chemically synthesized, single- stranded or double-stranded oligonucleotide. More specifically, such adapters may be comprised in the molecular barcode 302 and may facilitate ligation thereof.

According to an embodiment, start sites for ligating the molecular barcode 302 are determined by endogenous enzymatic digestion. As aforementioned, fragments of cell-free DNA are generated in the prenatal screening and diagnostic system 100 by employing enzymic digestion. Furthermore, start sites may be generated on the fragments of cell-free DNA during enzymatic shearing of the cell-free DNA.

Referring to FIG. 4, there is shown an illustration of amplified molecular barcode-ligated fragment 400, in accordance with an embodiment of the present disclosure. The prenatal screening and diagnostic system 100 amplifies, when in operation, (namely, is operable to amplify) the molecular barcode-ligated DNA fragments 300 for sequencing the amplified molecular barcode-ligated fragments 400. Specifically, the molecular barcode-ligated DNA fragments 300 are amplified by the prenatal screening arrangement 100. The adaptor-ligated fetal cell-free DNA (cfDNA) are subsequently amplified to produce a suitable amount of material for subsequent use. In an embodiment, primers that target the adaptor-ligated fetal cell-free DNA (cfDNA) are utilized for amplification. Specifically, the primers target a universal sequence that is common to at least some of the adaptor-ligated fetal cell-free DNA (cfDNA). More specifically, the primers target the universal sequence at the 5' end of the molecular barcode labelled adaptor-ligated fetal cell-free DNA (cfDNA). Optionally, the amplification may include using a Polymerase Chain Reaction (PCR) technique. Specifically, such amplification techniques may amplify a single copy or a few copies of molecular barcode- ligated DNA fragments 300 by several orders of magnitude, thereby generating potentially thousands of millions of copies of the particular given DNA sequence. Furthermore, such amplification techniques may provide an error, such as duplication of a nucleic acid base, in such an amplification process, which may be incorrectly represented as indicative of a genetic abnormality. Furthermore, such error may be corrected during analysis of sequencing data from the amplified molecular barcode-ligated fragments 400. Consequently, the cell-free DNA readout data generated from sequencing process of the amplified molecular barcode-ligated fragments 400 may take into account the amplification error when generating, namely computing, the risk score.

In an embodiment, the amplified molecular barcode-ligated fragments 400 comprise the molecular barcodes 402 (such as the molecular barcodes 302), fragments of the cell-free DNA 404 (such as the fragments of the cell-free DNA 304). Furthermore, the amplified molecular barcode-ligated fragments 400 may comprise a sample-specific index 408. Specifically, the sample- specific index 408 comprises a pre-defined sequence and a random 8-mer molecular barcode. Furthermore, if an error, such as the duplication of a nucleic acid base, is generated during the amplification process, the sample- specific index may be used during sequencing to identify the amplification error. Additionally, sites 410 may represent sites for amplification, wherein amplified DNA may be attached to the sites 410. Alternatively or additionally, optionally, the sites 410 may comprise baits or primers used to perform enrichment of targeted genes that are susceptible to causing genetic disease. The amplified molecular barcode-ligated fragments 400 are sequenced to generate cell-free DNA readout data. Optionally, a sequencing process employed may account for errors generated during an amplification process or processes. More optionally, the cell-free DNA readout data is indicative of whether or not there are genetic abnormalities in the blood sample. Optionally, the skeletal abnormality and/or the cardiac abnormality is caused by a de novo mutation. Furthermore, the molecular barcode-ligated fragments are useful to employ for reducing stochastic noise (namely, stochastic error) generated during aforementioned sequencing process and/or during processing in the data processing arrangement 104.

Additionally, the cell-free DNA readout data, generated subsequent to ligation, amplification and sequencing processes is used to generate, namely to compute, a risk score which provides an accurate indication of whether or not there are genetic abnormalities in the blood sample.

In an embodiment, the wet-laboratory arrangement 102 incorporates, when in operation, the molecular barcode to a cell-free DNA library containing a fetal component, and uses the cell-free DNA library thereby obtained in hybridisation-based enrichment for identifying de novo variants when computing the risk score. Specifically, the wet-laboratory arrangement prepares, when in operation, a cell-free DNA library comprising information about cell-free DNA readout data and the molecular barcodes. Furthermore, the cell-free DNA library may be used in achieving a higher accuracy of identification of de novo variants in a given fetal DNA.

In an embodiment, the prenatal screening and diagnostic system 100 utilizes in operation the adaptor-ligated cell-free DNA fragments and the adaptor- ligated molecular barcodes to perform enrichment by hybridization using baits targeted at genes, or primers targeted at genes that are susceptible to causing one or more diseases. Specifically, the enrichment of the specific genes susceptible to causing one or more diseases comprises isolating the desired adaptor-ligated cell-free DNA fragments which include such genes. Optionally, the enrichment may include using a hybridization technique. More optionally, oligonucleotide probes of known sequence may be exposed to separate collections of fetal, maternal and/or paternal adaptor-ligated cell-free DNA fragments. The probes may be of any suitable length, such that they recognize a particular desired sequence. In an embodiment, the probes target particular regions of the genes, for example such as genes associated with monogenic Mendelian disorder, and the like. In another embodiment, the probes target exon coding sequences. In yet another embodiment, the probes may be labeled. In an example, a probe may be labeled with a first binding agent, such as biotin, that binds with a second binding agent, such as avidin. Upon the binding of the biotin-labeled probe with the avidin-labeled probe, the desired adaptor-ligated cell-free DNA fragments are isolated from adaptor- ligated cell-free DNA fragments that lack the targeted gene.

Referring to FIG. 5, there is shown an illustration of steps of a method 500 of (for) using a prenatal screening and diagnostic system (such as the prenatal screening and diagnostic system 100 of FIG. 1), in accordance with an embodiment of the present disclosure. At a step 502, a blood sample is processed to determine cell-free DNA readout data from the blood sample. At a step 504, the cell-free DNA readout data is processed with reference to information stored in a database arrangement to generate, namely to compute, a risk score indicative of whether or not there are genetic abnormalities in the blood sample that are indicative of fetal abnormalities. At a step 506, nucleic acid base molecular barcodes are ligated to fragments of the cell-free DNA present in the blood sample. At a step 508, the molecular barcode-ligated fragments are amplified. At a step 510, the amplified molecular barcode-ligated fragments are sequenced to generate the cell-free DNA readout data. The steps 502 to 510 are only illustrative and other alternatives can also be provided where one or more steps are added, one or more steps are removed, or one or more steps are provided in a different sequence without departing from the scope of the claims herein. Optionally, the method 500 includes operating the prenatal screening and diagnostic system to implement the molecular barcode as an n-mer, wherein n is in a range 3 to 100. Optionally, the method 500 includes arranging for the molecular barcode to include a random sequence of nucleic acid bases. More optionally, the method 500 includes using fragments of cell-free DNA in the prenatal screening and diagnostic system generated by enzymatic digestion. Yet more optionally, the method 500 includes determining start sites for ligating the molecular barcode by the enzymatic digestion.

Optionally, the method 500 includes operating the wet-laboratory arrangement to incorporate the molecular barcode to a cell-free DNA library containing a fetal component, and to use the cell-free DNA library thereby obtained in hybridisation-based enrichment for identifying de novo variants when computing the risk score. Optionally, the method 500 includes operating the prenatal screening and diagnostic system to generate the cell- free DNA fragments by employing enzymic digestion, to ligate nucleic acid base molecular barcodes to the fragments to generate corresponding barcoded fragments, and to perform enrichment by hybridization using baits targeted at genes which for one or more diseases that are susceptible to causing fetal illnesses. More optionally, the method 500 includes operating the prenatal screening and diagnostic system to perform non-invasive molecular diagnosis of a fetus which on ultrasound investigation (for example, non-invasive ultrasound imaging) presents with, for example, a skeletal abnormality and/or a cardiac abnormality. Yet more optionally, the skeletal abnormality and/or the cardiac abnormality is caused by a de novo mutation. Optionally, the aforementioned method 500 of (for) using the prenatal screening and diagnostic system is implemented by using a computer program product comprising a non-transitory computer-readable storage medium having computer-readable instructions stored thereon, the computer-readable instructions being executable by a computerized device comprising processing hardware.

Although use of the prenatal screening and diagnostic system 100 is described in the foregoing for executing prenatal screening tasks, it will be appreciated that the prenatal screening and diagnostic system may be used for investigating other types of biological problems, and not merely restricted to prenatal screening tasks, for example: cancer risk determination; autistic risk determination; verification of organism performance after performing gene therapy; ionizing radiation damage identification to cell DNA; and/or diabetes risk determination.

Modifications to embodiments described in the foregoing are possible without departing from the scope of the invention as defined by the accompanying claims. Expressions such as "including", "comprising", "incorporating", "consisting of", "have", "is" used to describe and claim the present invention are intended to be construed in a non-exclusive manner, namely allowing for items, components or elements not explicitly described also to be present. Reference to the singular is also to be construed to relate to the plural. Numerals included within parentheses in the accompanying claims are intended to assist understanding of the claims and should not be construed in any way to limit subject matter claimed by these claims. REFERENCES

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