METHODS FOR AMPLIFYING NUCLEIC ACIDS CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of and priority to U.S. Provisional Patent Application No.63/409,528, filed on September 23, 2022, the entire contents of which are incorporated herein by reference. FIELD OF THE INVENTION [0002] The invention relates generally to methods of amplifying nucleic acids, and, more particularly, the invention relates to methods of distinguishing methylated and non-methylated nucleic acid residues in an amplification reaction. BACKGROUND [0003] DNA methylation is an epigenetic process by which a methyl group is added to DNA. In mammals, this typically occurs at the C5 position of a cytosine to form 5-methylcytosine. DNA methylation can change the activity of DNA, e.g., by repressing gene transcription, and functions in many biological processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging, and carcinogenesis. In mammals, methylation is frequently observed at CG (CpG) dinucleotides. CpG islands are generally defined as regions having a length greater than 200 bp, a GC content greater than 50% and a ratio of observed to expected CpG greater than 0.6. CpG islands are often found in promoter regions, where methylation is associated with transcriptional repression. [0004] Abnormal DNA methylation is associated with the development of health conditions, such as cancer. CpG islands can become abnormally methylated, with hypomethylation linked to chromosomal instability and hypermethylation associated with promoters and oncogene suppressor silencing. [0005] Accordingly, there is a need in the art for improved methods for detecting DNA methylation. Assessment of DNA methylation states can be used to predict risk for developing certain health conditions, such as cancer. SUMMARY OF THE INVENTION [0006] Disclosed herein are methods for the detection of methylated nucleotides (e.g., cytosines) in a nucleic acid using differential amplification, in which a nucleic acid having a methylated nucleotide (e.g., cytosine) is amplified at a different (e.g., faster) rate than an equivalent nucleic acid having an unmethylated nucleotide (e.g., cytosine) that has been converted to and replaced by another nucleotide. In certain embodiments, an unmethylated nucleotide is converted to another nucleotide (e.g., an unmethylated cytosine to a uracil according to FIG.1) and then amplified. The unmethylated nucleotide may be replaced by a replacement nucleotide (e.g., a thymine may replace a uracil) during the amplification reaction. Subsequently, amplification of the nucleic acid having the unmethylated nucleotide may be delayed as compared to amplification of an otherwise equivalent nucleic acid having a methylated nucleotide (e.g., cytosine) at that position by the use of a primer that binds more tightly to the nucleic acid that had the methylated nucleotide (see, e.g., the methylated cytosines in FIG.2, scheme 3). In certain embodiments, a probe that preferentially binds to a converted unmethylated cytosine in a region to be amplified is used to block extension of a primer in the region, and therefore delay, amplification of a nucleic acid having a converted unmethylated cytosine as compared to a nucleic acid having a methylated cytosine (see, e.g., FIG.2, scheme 2). Such primers and probes can be used as alternative methods or together in a single method (see, e.g., FIG.2, scheme 4). [0007] Prior to amplification of the nucleic acid, the nucleic acid may be treated to convert one or more unmethylated nucleotides to converted nucleotides (e.g., cytosines to uracils). The nucleic acid may then be amplified to produce copies of the nucleic acid in which the one or more converted nucleotides (e.g., uracils) are replaced with replacement nucleotides, (e.g., thymines). After such treatment and amplification, a nucleic acid having a methylated nucleotide (e.g., cytosine) at a position of interest will retain the cytosine at that position, whereas a nucleic acid having an unmethylated nucleotide (e.g., cytosine) will have a replacement nucleotide (e.g., thymine) at that position. Having different nucleotides at the position of interest allows for the use of a primer and/or probe to differentially bind to a nucleic acid having an unmethylated nucleotide (e.g., cytosine) at the position, thereby preferentially amplifying a methylated nucleic acid over an unmethylated nucleic acid. In certain embodiments, the primer and/or probe may preferentially amplify an unmethylated nucleic acid over a methylated nucleic acid. [0008] In one aspect, the disclosure relates to a method for differentially amplifying a nucleic acid having a methylated nucleotide at one or more positions as compared to a nucleic acid having an unmethylated nucleotide at the one or more positions. The method further includes providing a nucleic acid, wherein the nucleic acid is derived from a nucleic acid comprising a methylated nucleotide, wherein the nucleic acid has been (i) treated to convert one or more unmethylated nucleotides to a converted nucleotide and (ii) amplified to replace the converted nucleotide with a replacement nucleotide. The method further includes providing primers capable of amplifying a region comprising the previously methylated nucleotide or the replacement nucleotide. The method further includes providing a probe that either (i) preferentially binds to the region if the replacement nucleotide is present as compared to if the previously methylated nucleotide is present or (ii) preferentially binds to the region if the previously methylated nucleotide is present as compared to if the replacement nucleotide is present. The method further includes amplifying the region using the primers such that (i) if the replacement nucleotide is present, the probe binds to the replacement nucleotide and amplification is delayed, or (ii) if the previously methylated nucleotide is present, the probe binds to the previously methylated nucleotide and amplification is delayed. As used herein the term “previously methylated” refers to a non-methylated copy of a nucleotide that was methylated, e.g., from a sample. [0009] In certain embodiments, the probe comprises between about 5 and about 75 nucleotides. In certain embodiments, the probe comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 complementary nucleotides that bind to the at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 replacement nucleotides. In certain embodiments, the probe comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 adenosines that bind to the at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 thymines. In certain embodiments, the probe comprises exactly one complementary nucleotides that binds to the replacement nucleotides. In certain embodiments, the probe comprises exactly one adenosine that binds to the thymine. [0010] In another aspect, the disclosure relates to a method for differentially amplifying a nucleic acid having a methylated nucleotide at one or more positions as compared to a nucleic acid having an unmethylated nucleotide at one or more positions. The method includes providing a nucleic acid, wherein the nucleic acid is derived from a methylated nucleotide, wherein the nucleic acid has been (i) treated to convert one or more unmethylated nucleotides to a converted nucleotide and (ii) amplified to replace the converted nucleotide with a replacement nucleotide. The method further includes providing at least one primer that (i) preferentially binds to a region comprising the previously methylated nucleotide as compared to the replacement nucleotide or (ii) preferentially binds to a region comprising the replacement nucleotide as compared to the previously methylated nucleotide. The method further includes amplifying the region using the at least one primer, wherein amplification is delayed if (i) the primer preferentially binds to a region comprising the previously methylated nucleotide as compared to the replacement nucleotide and the replacement nucleotide is present or (ii) the primer preferentially binds to a region comprising the replacement nucleotide as compared to the previously methylated nucleotide and the previously methylated nucleotide is present. [0011] In another aspect, the disclosure relates to a method for differentially amplifying a nucleic acid having a methylated nucleotide at one or more positions as compared to a nucleic acid having an unmethylated nucleotide at the one or more positions. The method includes providing a first nucleic acid derived from a methylated nucleic acid in a sample, wherein the nucleic acid has been (A) treated to convert one or more unmethylated nucleotides to a converted nucleotide and (B) amplified to replace the converted nucleotide with a replacement nucleotide; (ii) providing primers capable of amplifying a region comprising the previously methylated nucleotide or the replacement nucleotide; providing a probe that either (A) preferentially binds to the region if the replacement nucleotide is present as compared to if the previously methylated nucleotide is present or (B) preferentially binds to the region if the previously methylated nucleotide is present as compared to if the replacement nucleotide is present; amplifying the region using the primers such that (A) if the replacement nucleotide is present, the probe binds to the replacement nucleotide and amplification is delayed, or (B) if the previously methylated nucleotide is present, the probe binds to the previously methylated nucleotide and amplification is delayed. The method further includes providing a second nucleic acid derived from the methylated nucleic acid in the sample, wherein the nucleic acid has not been treated to convert one or more unmethylated nucleotides to a converted nucleotide; providing primers capable of amplifying a region comprising the previously methylated nucleotide; providing the probe; and amplifying the region using the primers. The method further includes comparing the amplification levels of the first and second nucleic acids, wherein a difference in amplification levels is indicative of the presence and/or amount of the previously methylated nucleic acid in the sample. [0012] In yet another aspect, the disclosure relates to a method for differentially amplifying a nucleic acid having a methylated nucleotide at one or more positions as compared to a nucleic acid having an unmethylated nucleotide at the one or more positions. The method includes providing a first nucleic acid derived from a methylated nucleic acid in a sample, wherein the nucleic acid has been (A) treated to convert one or more unmethylated nucleotides to a converted nucleotide and (B) amplified to replace the converted nucleotide with a replacement nucleotide; ) providing at least one primer that (A) preferentially binds to a region comprising the previously methylated nucleotide as compared to the replacement nucleotide or (B) preferentially binds to a region comprising the replacement nucleotide as compared to the previously methylated nucleotide; amplifying the region using the at least one primer, wherein amplification is delayed if (A) the primer preferentially binds to a region comprising the previously methylated nucleotide as compared to the replacement nucleotide and the replacement nucleotide is present or (B) the primer preferentially binds to a region comprising the replacement nucleotide as compared to the previously methylated nucleotide and the previously methylated nucleotide is present. The method further comprises providing a second nucleic acid derived from the methylated nucleic acid in the sample, wherein the nucleic acid has not been treated to convert one or more unmethylated nucleotides to a converted nucleotide; providing the at least one primer; and amplifying the region using the primer. The method further includes comparing the amplification levels of the first and second nucleic acids, wherein a difference in amplification levels is indicative of the presence and/or amount of the previously methylated nucleic acid in the sample. [0013] In certain embodiments, the at least one primer is exactly one primer. In certain embodiments, the at least one primer is two primers. In certain embodiments, the at least one primer comprises at least one guanine at the 3’ end of the primer. In certain embodiments, the at least one primer comprises exactly one guanine at the 3’ end of the primer. [0014] In certain embodiments, the method further includes providing a probe that binds to the region if the replacement nucleotide is present, thereby delaying amplification. In certain embodiments, the method further includes providing a probe that binds to the region if the thymine is present, thereby delaying amplification. [0015] In certain embodiments of any of the differential amplification methods disclosed herein, the nucleic acid is DNA. In certain embodiments, the DNA is cell-free DNA. In certain embodiments, the nucleic acid is RNA. In certain embodiments, the nucleotide is selected from adenine, cytosine, thymine, uracil, and guanine. In certain embodiments, the methylated nucleotide is selected from N ⁶ -methyladenine (6mA), N ⁴ -methylcytosine (4mC), and 5- methylcytosine (5mC). [0016] In certain embodiments, the nucleic acid was treated with nitrite to convert one or more unmethylated nucleotides to a converted nucleotide. In certain embodiments, the unmethylated nucleotide is an unmethylated cytosine, the methylated nucleotide is 4mC, the converted nucleotide is a uracil, and the replacement nucleotide is a thymine. In certain embodiments, the unmethylated nucleotide is an adenine, the methylated nucleotide is a 6mA, the converted nucleotide is a inosine, and the replacement nucleotide is a guanine. [0017] In certain embodiments, the unmethylated nucleotide is a cytosine, the methylated nucleotide is a methylated cytosine, the converted nucleotide is a uracil, and the replacement nucleotide is a thymine. In certain embodiments, the probe preferentially binds to the region if the thymine is present as compared to if the methylated cytosine is present, and if the thymine is present, the probe binds to the thymine and amplification is delayed. [0018] In certain embodiments, the nucleic acid has been treated using bisulfite conversion to convert the unmethylated cytosine to uracil, and amplified to replace the uracil with thymine. [0019] In certain embodiments, the nucleic acid has been treated using enzymatic conversion to convert the unmethylated cytosine to uracil, and amplified to replace the uracil with thymine. In certain embodiments, the enzymatic conversion is selected from TET2 oxidation of cytosines and APOBEC conversion of cytosines. [0020] In certain embodiments, the nucleic acid was obtained from a sample. In certain embodiments, the sample comprises a blood sample, a stool sample, a urine sample, a mucous sample, or a saliva sample. [0021] In certain embodiments, the nucleic acid comprises at least 2, at least 3, at least 4, at least 5, at least 6 previously methylated nucleotides or replacement nucleotides, wherein the nucleic acid has been treated and amplified to convert unmethylated nucleotides to replacement nucleotides. In certain embodiments, the nucleic acid comprises at least 2, at least 3, at least 4, at least 5, at least 6 previously methylated cytosines or thymines, wherein the nucleic acid has been treated to convert unmethylated cytosines to thymines. [0022] In certain embodiments, the nucleic acid comprises at least a portion of a CpG island. In certain embodiments, the nucleic acid is informative of a health condition. In certain embodiments, the health condition is cancer or a risk of developing cancer. In certain embodiments, the cancer is preclinical or early stage cancer. In certain embodiments, the cancer is selected from acute lymphoblastic leukemia, acute myeloid leukemia, adrenocortical carcinoma, soft tissue sarcoma, lymphoma, anal cancer, gastrointestinal cancer, brain cancer, skin cancer, bile duct cancer, bladder cancer, bone cancer, breast cancer, lung cancer, cardiac cancer, central nervous system cancer, cervical cancer, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative neoplasms, colorectal cancer, uterine cancer, esophageal cancer, head and neck cancer, eye cancer, fallopian tube cancer, gallbladder cancer, gastric cancer, germ cell tumor, gestational trophoblastic cancer, hairy cell leukemia, liver cancer, Hodgkin lymphoma, intraocular melanoma, pancreatic cancer, kidney cancer, leukemia, mesothelioma, metastatic cancer, mouth cancer, multiple endocrine neoplasia syndromes, multiple myeloma neoplasms, myelodysplastic neoplasms, ovarian cancer, parathyroid cancer, penile cancer, pheochromocytoma, pituitary cancer, plasma cell neoplasm, primary peritoneal cancer, prostate cancer, rectal cancer, retinoblastoma, sarcoma, small intestine cancer, testicular cancer, throat cancer, thymoma and thymic carcinoma, thyroid cancer, urethral cancer, uterine cancer, vaginal cancer, and vulvar cancer. [0023] In certain embodiments, the health condition is selected from inflammatory disease, neurodegenerative disease, autoimmune disorder, neuromuscular disease, metabolic disorder, cardiac disease, or fibrotic disease, or a risk of developing any one of the foregoing. In certain embodiments, the neurodegenerative disease is one of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD). In certain embodiments, the health condition has an incidence of 1 in 100, 1 in 1,000, 1 in 10,000 individuals, 1 in 100,000 individuals, 1 in 1,000,000 individuals, 1 in 10,000,000 individuals, or 1 in 100,000,000 individuals. In certain embodiments, the health condition is a rare disease or disorder. [0024] In certain embodiments, if the replacement nucleotide is present, the amplifying step results in at least 2x, at least 5x, at least 10x, at least 20x, at least 50x, at least 100x, or at least 1000x as many amplicons containing previously methylated nucleotides as replacement nucleotides. In certain embodiments, if the thymine is present, the amplifying step results in at least 2x, at least 5x, at least 10x, at least 20x, at least 50x, at least 100x, or at least 1000x as many amplicons containing cytosines as thymines. [0025] In certain embodiments, the amplification comprises PCR, RT-PCR, digital PCR, nicking endonuclease amplification (NEAR), transcription-mediated amplification (TMA), loop- mediated isothermal amplification (LAMP), helicase-dependent amplification (HAD), or strand displacement amplification (SDA). [0026] These and other aspects and features of the invention are described in the following detailed description and claims. BRIEF DESCRIPTION OF THE DRAWINGS [0027] The foregoing and other objects, features and advantages of the invention will become apparent from the following description of preferred embodiments, as illustrated in the accompanying drawings. The drawings are not necessarily to scale, with emphasis instead being placed on illustrating the principles of the present invention, in which: [0028] FIGURE 1 provides a overview of bisulfite conversion. [0029] FIGURE 2 is a schematic showing methods for enriching amplification for nucleic acid sequences having methylated residues, e.g., hypermethylation sites. [0030] FIGURE 3 shows the results of nitrite conversion on select nucleotides. Figure adapted from Li et al. (2022) Genome Biology 23:122. DETAILED DESCRIPTION [0031] Disclosed herein are methods for the detection of methylated nucleotides (e.g., cytosines) in a nucleic acid using differential amplification, in which a nucleic acid having a methylated nucleotide (e.g., a methylated cytosine) is amplified at a faster rate than an equivalent nucleic acid having an unmethylated nucleotide. The invention is based, in part, upon the discovery that nucleic acids comprising methylated nucleotides can be amplified at a different rate (e.g., a faster rate) than nucleic acids comprising unmethylated nucleotides using amplification methods that, for example, use amplification primers that preferentially bind methylated nucleotides and/or blocking probes that preferentially bind unmethylated nucleotides (or vice versa), resulting in a faster rate of amplification of methylated nucleic acids. [0032] In certain embodiments, amplification of a nucleic acid having an unmethylated cytosine (e.g., that has been converted to a uracil according to FIG.1) at a given position may be delayed as compared to amplification of an otherwise equivalent nucleic acid having a methylated cytosine at that position by the use of a primer that binds more tightly to the nucleic acid having the methylated cytosine (see, e.g., FIG.2, scheme 3). In certain embodiments, a probe that preferentially binds to an unmethylated cytosine in a region to be amplified is used to block extension of a primer in the region, and therefore delay, amplification of a nucleic acid having an unmethylated cytosine as compared to a nucleic acid having a methylated cytosine (see, e.g., FIG.2, scheme 2). Such primers and probes can be used as alternative methods or together in a single method (see, e.g., FIG.2, scheme 4). In certain embodiments where the primers and probes are used together in a single method, the probe may also block binding of a primer, e.g., in instances where the binding sequence of the probe overlaps at least partially with the binding sequence of the primer. [0033] Prior to amplification of the nucleic acid, the nucleic acid may be treated to convert one or more unmethylated cytosines to uracils, while preserving methylated cytosines as methylated cytosines. The nucleic acid may then be amplified to produce copies of the nucleic acid in which the one or more uracils are replaced with thymines and the methylated cytosines are replaced with cytosines. After such treatment and amplification, a nucleic acid having a methylated cytosine at a position of interest will have a cytosine at that position, whereas a nucleic acid having an unmethylated cytosine will have a thymine at that position. Having different nucleotides at the position of interest allows for the use of a primer and/or probe to differentially bind to a nucleic acid having a cytosine at the position in contrast to having a thymine at the position, thereby preferentially amplifying a methylated original template nucleic acid over an unmethylated original template nucleic acid. I. Definitions [0034] As used herein, the term “about” or “approximately” can mean within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which can depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the art. “About” can mean a range of ±20%, ±10%, ±5%, or ±1% of a given value. The term “about” or “approximately” can mean within an order of magnitude, within 5-fold, or within 2-fold, of a value. Where a particular value is described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value can be assumed. The term “about” can have the meaning as commonly understood by one of ordinary skill in the art. The term “about” can refer to ±10%. The term “about” can refer to ±5%. [0035] As used herein, the term “biological sample,” or “sample” refers to any sample taken from a subject, which can reflect a biological state associated with the subject, and that includes cell free DNA. A biological sample can take any of a variety of forms, such as a liquid biopsy (e.g., blood, urine, stool, saliva, or mucous), or a tissue biopsy, or other solid biopsy. Examples of biological samples include, but are not limited to, blood, whole blood, plasma, serum, urine, cerebrospinal fluid, fecal, saliva, sweat, tears, pleural fluid, pericardial fluid, or peritoneal fluid of the subject. A biological sample can include any tissue or material derived from a living or dead subject. A biological sample can be a cell-free sample. A biological sample can comprise a nucleic acid (e.g., DNA or RNA) or a fragment thereof. The term “nucleic acid” can refer to deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or any hybrid or fragment thereof. The nucleic acid in the sample can be a cell-free nucleic acid. A sample can be a liquid sample or a solid sample (e.g., a cell or tissue sample). A biological sample can be a bodily fluid, such as blood, plasma, serum, urine, vaginal fluid, fluid from a hydrocele (e.g., of the testis), vaginal flushing fluids, pleural fluid, ascitic fluid, cerebrospinal fluid, saliva, sweat, tears, sputum, bronchoalveolar lavage fluid, discharge fluid from the nipple, aspiration fluid from different parts of the body (e.g., thyroid, breast), etc. A biological sample can be a stool sample. In various embodiments, the majority of DNA in a biological sample that has been enriched for cell-free DNA (e.g., a plasma sample obtained via a centrifugation protocol) can be cell-free (e.g., greater than 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the DNA can be cell-free). A biological sample can be treated to physically disrupt tissue or cell structure (e.g., centrifugation and/or cell lysis), thus releasing intracellular components into a solution which can further contain enzymes, buffers, salts, detergents, and the like which can be used to prepare the sample for analysis. [0036] As used herein, the terms “nucleic acid” and “nucleic acid molecule” are used interchangeably. The terms refer to nucleic acids of any composition form, such as deoxyribonucleic acid (DNA, e.g., complementary DNA (cDNA), genomic DNA (gDNA) and the like), and/or DNA analogs (e.g., containing base analogs, sugar analogs and/or a non-native backbone and the like), and/or ribonucleic acid (RNA) and or RNA analogs, all of which can be in single- or double-stranded form. Unless otherwise limited, a nucleic acid can comprise known analogs of natural nucleotides, some of which can function in a similar manner as naturally occurring nucleotides. A nucleic acid can be in any form useful for conducting processes herein (e.g., linear, circular, supercoiled, single-stranded, double-stranded and the like). A nucleic acid in some embodiments can be from a single chromosome or fragment thereof (e.g., a nucleic acid sample may be from one chromosome of a sample obtained from a diploid organism). In certain embodiments nucleic acids comprise nucleosomes, fragments or parts of nucleosomes or nucleosome-like structures. Nucleic acids can comprise protein (e.g., histones, DNA binding proteins, and the like). Nucleic acids analyzed by processes described herein can be substantially isolated and are not substantially associated with protein or other molecules. Nucleic acids can also include derivatives, variants and analogs of DNA synthesized, replicated or amplified from single-stranded (“sense” or “antisense,” “plus” strand or “minus” strand, “forward” reading frame or “reverse” reading frame) and double-stranded polynucleotides. Deoxyribonucleotides can include deoxyadenosine, deoxycytidine, deoxyguanosine and deoxythymidine. A nucleic acid may be prepared using a nucleic acid obtained from a subject as a template. [0037] As used herein, the term “cell-free nucleic acids” refers to nucleic acid molecules that can be found outside cells, in bodily fluids such as blood, whole blood, plasma, serum, urine, cerebrospinal fluid, fecal, saliva, sweat, sweat, tears, pleural fluid, pericardial fluid, or peritoneal fluid of a subject. Cell-free nucleic acids originate from one or more healthy cells and/or from one or more cancer cells, or from non-human sources such bacteria, fungi, viruses. Examples of the cell-free nucleic acids include but are not limited to cell-free DNA (“cfDNA”), including mitochondrial DNA or genomic DNA, and cell-free RNA. In certain embodiments herein, instruments for assessing the quality of the cell-free nucleic acids, such as the TapeStation System from Agilent Technologies (Santa Clara, CA) can be used. Concentrating low- abundance cfDNA can be accomplished, for example using a Qubit Fluorometer from Thermofisher Scientific (Waltham, MA). [0038] As used herein, the term “methylation” refers to a modification of a nucleic acid where a hydrogen atom on the pyrimidine ring of a cytosine base is converted to a methyl group, forming 5-methylcytosine. Methylation can occur at dinucleotides of cytosine and guanine referred to herein as “CpG sites”. Methylation of cytosine can occur in cytosines in other sequence contexts, for example, 5ƍ-CHG-3ƍ and 5ƍ-CHH-3ƍ, where H is adenine, cytosine or thymine. Cytosine methylation can also be in the form of 5-hydroxymethylcytosine. Methylation of DNA can include methylation of non-cytosine nucleotides, such as N ⁶ -methyladenine (6mA). Anomalous cfDNA methylation can be identified as hypermethylation or hypomethylation, both of which may be indicative of cancer status. As is well known in the art, DNA methylation anomalies (compared to healthy controls) can cause different effects, which may contribute to cancer. [0039] In certain embodiments, the term “methylated”, e.g., “methylated nucleotide” refers to a nucleic acid or a nucleotide that has undergone methylation. In certain embodiments, as will be clear from the context, the term “methylated”, e.g., “methylated nucleotide” refers to a non- methylated copy of a nucleotide that was methylated, e.g., that was methylated in its native state in a sample. [0040] Certain portions of a genome comprise regions with a high frequency of CpG sites. A CpG site is portion of a genome that has cytosine and guanine separated by only one phosphate group and is often denoted as “5'-C-phosphate-G-3'”, or “CpG” for short. Regions with a high frequency of CpG sites are commonly referred to as “CpG islands”, “CG islands” or “CGIs”. It has been found that certain CGIs and certain features of certain CGIs in tumor cells tend to be different from the same CGIs or features of the CGIs in healthy cells. Herein, such CGIs and features of the genome are referred to herein as “cancer informative CGIs”, which is defined and described in more detail below. An “informative CpG” can be specified by reference to a specific CpG site, or to a collection of one or more CpG sites by reference to a CG island that contains the collection. These cancer informative CGIs tend to have methylation patterns in tumor cells that are different from the methylation patterns in healthy cells. DNA fragments from other CGIs may not express such differences. Exemplary cancer informative CGIs are identified in, e.g., Table 1 of U.S. Patent Publication 2020/0109456A1 and Tables 2 and 3 of WO2022/133315, which are hereby incorporated by reference. Other exemplary cancer informative CGIs are identified at Tables 1-4 herein. [0041] As used herein, the term “methylation profile” (also called methylation status) can include information related to DNA methylation for a region. Information related to DNA methylation can include a methylation index of a CpG site, a methylation density of CpG sites in a region, a distribution of CpG sites over a contiguous region, a pattern or level of methylation for each individual CpG site within a region that contains more than one CpG site, and non-CpG methylation. A methylation profile of a substantial part of the genome can be considered equivalent to the methylome. “DNA methylation” in mammalian genomes can refer to the addition of a methyl group to position 5 of the heterocyclic ring of cytosine (e.g., to produce 5- methylcytosine) among CpG dinucleotides. Methylation of cytosine can occur in cytosines in other sequence contexts, for example, 5ƍ-CHG-3ƍ and 5ƍ-CHH-3ƍ, where H is adenine, cytosine or thymine. Cytosine methylation can also be in the form of 5-hydroxymethylcytosine. Methylation of DNA can include methylation of non-cytosine nucleotides, such as N ⁶ - methyladenine (6mA). [0042] As used herein, the term “amplifying” means performing an amplification reaction. In one aspect, an amplification reaction is “template-driven” in that base pairing of reactants, either nucleotides or oligonucleotides, have complements in a template polynucleotide that are required for the creation of reaction products. In one aspect, template-driven reactions are primer extensions with a nucleic acid polymerase, or oligonucleotide ligations with a nucleic acid ligase. Such reactions include, but are not limited to, polymerase chain reactions (PCRs), linear polymerase reactions, nucleic acid sequence-based amplification (NASBAs), rolling circle amplifications, nicking endonuclease amplification (NEAR), transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HAD), or strand displacement amplification (SDA) and the like, disclosed in the following references, each of which are incorporated herein by reference herein in their entirety: Mullis et al., U.S. Pat. Nos.4,683,195; 4,965,188; 4,683,202; 4,800,159 (PCR); Gelfand et al., U.S. Pat. No.5,210,015 (real-time PCR with “taqman” probes); Wittwer et al., U.S. Pat. No. 6,174,670; Kacian et al., U.S. Pat. No.5,399,491 (“NASBA”); Lizardi, U.S. Pat. No.5,854,033; Aono et al., Japanese patent publ. JP 4-262799 (rolling circle amplification); and the like. In one aspect, the amplification reaction is PCR. An amplification reaction may be a “real-time” amplification if a detection chemistry is available that permits a reaction product to be measured as the amplification reaction progresses, e.g., “real-time PCR”, or “real-time NASBA” as described in Leone et al., Nucleic Acids Research, 26: 2150-2155 (1998), and like references. [0043] The terms “polymerase chain reaction” or “PCR”, as used interchangeably herein, mean a reaction for the in vitro amplification of specific DNA sequences by the simultaneous primer extension of complementary strands of DNA. In other words, PCR is a reaction for making multiple copies or replicates of a target nucleic acid flanked by primer binding sites, such reaction comprising one or more repetitions of the following steps: (i) denaturing the target nucleic acid, (ii) annealing primers to the primer binding sites, and (iii) extending the primers by a nucleic acid polymerase in the presence of nucleoside triphosphates. Usually, the reaction is cycled through different temperatures optimized for each step in a thermal cycler instrument. Particular temperatures, durations at each step, and rates of change between steps depend on many factors that are well-known to those of ordinary skill in the art, e.g., exemplified by the following references: McPherson et al., editors, PCR: A Practical Approach and PCR2: A Practical Approach (IRL Press, Oxford, 1991 and 1995, respectively). For example, in a conventional PCR using Taq DNA polymerase, a double stranded target nucleic acid may be denatured at a temperature>90° C, primers annealed at a temperature in the range 50-75° C, and primers extended at a temperature in the range 72-78° C. The term “PCR” encompasses derivative forms of the reaction, including, but not limited to, RT-PCR, real-time PCR, nested PCR, quantitative PCR, multiplexed PCR, and the like. The particular format of PCR being employed is discernible by one skilled in the art from the context of an application. Reaction volumes can range from a few hundred nanoliters, e.g., 200 nL, to a few hundred ^L, e.g., 200 ^L. “Reverse transcription PCR,” or “RT-PCR,” means a PCR that is preceded by a reverse transcription reaction that converts a target RNA to a complementary single stranded DNA, which is then amplified, an example of which is described in Tecott et al., U.S. Pat. No. 5,168,038, the disclosure of which is incorporated herein by reference in its entirety. “Real-time PCR” means a PCR for which the amount of reaction product, i.e., amplicon, is monitored as the reaction proceeds. There are many forms of real-time PCR that differ mainly in the detection chemistries used for monitoring the reaction product, e.g., Gelfand et al., U.S. Pat. No. 5,210,015 (“taqman”); Wittwer et al., U.S. Pat. Nos.6,174,670 and 6,569,627 (intercalating dyes); Tyagi et al., U.S. Pat. No.5,925,517 (molecular beacons); the disclosures of which are hereby incorporated by reference herein in their entireties. Detection chemistries for real-time PCR are reviewed in Mackay et al., Nucleic Acids Research, 30: 1292-1305 (2002), which is also incorporated herein by reference. “Nested PCR” means a two-stage PCR wherein the amplicon of a first PCR becomes the sample for a second PCR using a new set of primers, at least one of which binds to an interior location of the first amplicon. As used herein, “initial primers” in reference to a nested amplification reaction mean the primers used to generate a first amplicon, and “secondary primers” mean the one or more primers used to generate a second, or nested, amplicon. “Asymmetric PCR” means a PCR wherein one of the two primers employed is in great excess concentration so that the reaction is primarily a linear amplification in which one of the two strands of a target nucleic acid is preferentially copied. The excess concentration of asymmetric PCR primers may be expressed as a concentration ratio. Typical ratios are in the range of from 10 to 100. “Multiplexed PCR” means a PCR wherein multiple target sequences (or a single target sequence and one or more reference sequences) are simultaneously carried out in the same reaction mixture, e.g., Bernard et al., Anal. Biochem., 273: 221-228 (1999) (two- color real-time PCR). Usually, distinct sets of primers are employed for each sequence being amplified. Typically, the number of target sequences in a multiplex PCR is in the range of from 2 to 50, or from 2 to 40, or from 2 to 30. “Quantitative PCR” means a PCR designed to measure the abundance of one or more specific target sequences in a sample or specimen. Quantitative PCR includes both absolute quantitation and relative quantitation of such target sequences. Quantitative measurements are made using one or more reference sequences or internal standards that may be assayed separately or together with a target sequence. The reference sequence may be endogenous or exogenous to a sample or specimen, and in the latter case, may comprise one or more competitor templates. Typical endogenous reference sequences include segments of transcripts of the following genes: ȕ-actin, GAPDH, ȕ2-microglobulin, ribosomal RNA, and the like. “Digital PCR” refers to a method in which a PCR reaction is partitioned into thousands (e.g., tens of thousands) of nanoliter sized droplets, where a separate PCR reaction takes place in each one. Using Poisson’s law of small numbers, the distribution of target molecule within the sample can be accurately approximated allowing for a quantification of the target strand in the PCR product. Techniques for quantitative PCR are well-known to those of ordinary skill in the art, as exemplified in the following references, which are incorporated by reference herein in their entireties: Freeman et al., Biotechniques, 26: 112-126 (1999); Becker- Andre et al., Nucleic Acids Research, 17: 9437-9447 (1989); Zimmerman et al., Biotechniques, 21: 268-279 (1996); Diviacco et al., Gene, 122: 3013-3020 (1992); Becker-Andre et al., Nucleic Acids Research, 17: 9437-9446 (1989); and Baker et al., Nature Methods, 9(6): 541-544 (2012). [0044] “Cycle threshold” or “Ct” refers to the number of amplification (e.g., PCR) cycles needed for a sample to amplify and cross a threshold, e.g., to be considered detected. [0045] A “reaction mixture” means a solution containing all the necessary reactants for performing a reaction, which may include, but is not be limited to, buffering agents to maintain pH at a selected level during a reaction, salts, co-factors, scavengers, and the like. [0046] The terms “fragment” or “segment”, as used interchangeably herein, refer to a portion of a larger polynucleotide molecule. A polynucleotide, for example, can be broken up, or fragmented into, a plurality of segments. Various methods of fragmenting nucleic acid are well known in the art. These methods may be, for example, either chemical or physical or enzymatic in nature. Enzymatic fragmentation may include partial degradation with a DNase; partial depurination with acid; the use of restriction enzymes; intron-encoded endonucleases; DNA- based cleavage methods, such as triplex and hybrid formation methods, that rely on the specific hybridization of a nucleic acid segment to localize a cleavage agent to a specific location in the nucleic acid molecule; or other enzymes or compounds which cleave a polynucleotide at known or unknown locations. Physical fragmentation methods may involve subjecting a polynucleotide to a high shear rate. High shear rates may be produced, for example, by moving DNA through a chamber or channel with pits or spikes, or forcing a DNA sample through a restricted size flow passage, e.g., an aperture having a cross sectional dimension in the micron or submicron range. Other physical methods include sonication and nebulization. Combinations of physical and chemical fragmentation methods may likewise be employed, such as fragmentation by heat and ion-mediated hydrolysis. See, e.g., Sambrook et al., “Molecular Cloning: A Laboratory Manual,” 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001) (“Sambrook et al.) which is incorporated herein by reference for all purposes. These methods can be optimized to digest a nucleic acid into fragments of a selected size range. [0047] The term “primer” as used herein means an oligonucleotide, either natural or synthetic, that is capable, upon forming a duplex with a polynucleotide template, of acting as a point of initiation of nucleic acid synthesis and being extended from its 3ƍ end along the template so that an extended duplex is formed. Extension of a primer is usually carried out with a nucleic acid polymerase, such as a DNA or RNA polymerase. The sequence of nucleotides added in the extension process is determined by the sequence of the template polynucleotide. Usually, primers are extended by a DNA polymerase. Primers usually have a length in the range of from about 5 to about 75 nucleotides, for example, from about 14 to about 40 nucleotides, or in the range of from about 18 to about 36 nucleotides. Primers are employed in a variety of nucleic amplification reactions, for example, linear amplification reactions using a single primer, or polymerase chain reactions, employing two or more primers. Guidance for selecting the lengths and sequences of primers for particular applications is well known to those of ordinary skill in the art, as evidenced by the following reference that is incorporated by reference herein in its entirety: Dieffenbach, editor, PCR Primer: A Laboratory Manual, 2nd Edition (Cold Spring Harbor Press, New York, 2003). [0048] As used herein, the term “subject” refers to any living or non-living organism, including but not limited to a human (e.g., a male human, female human, fetus, pregnant female, child, or the like), a non-human animal, a plant, a bacterium, a fungus or a protist. Any human or non- human animal can serve as a subject, including but not limited to mammal, reptile, avian, amphibian, fish, ungulate, ruminant, bovine (e.g., cattle), equine (e.g., horse), caprine and ovine (e.g., sheep, goat), swine (e.g., pig), camelid (e.g., camel, llama, alpaca), monkey, ape (e.g., gorilla, chimpanzee), ursid (e.g., bear), poultry, dog, cat, mouse, rat, fish, dolphin, whale and shark. In some embodiments, a subject is a male or female of any age (e.g., a man, a women or a child). II. Nucleic Acids A. Source of Nucleic Acids [0049] Nucleic acids used in the methods described herein can be derived from any source, such as a sample taken from the environment or from a subject (e.g., a human subject). A biological sample can be treated to physically disrupt tissue or cell structure (e.g., centrifugation and/or cell lysis), thus releasing intracellular components into a solution which can further contain enzymes, buffers, salts, detergents, and the like which can be used to prepare the sample for analysis. A biological sample can take any of a variety of forms, such as a liquid biopsy (e.g., blood, urine, stool, saliva, or mucous), or a tissue biopsy, or other solid biopsy. Examples of biological samples include, but are not limited to, blood, whole blood, plasma, serum, urine, cerebrospinal fluid, fecal, saliva, sweat, tears, pleural fluid, pericardial fluid, or peritoneal fluid of the subject. A biological sample can include any tissue or material derived from a living or dead subject. A biological sample can be a cell-free sample. A sample can be a liquid sample or a solid sample (e.g., a cell or tissue sample). A biological sample can be a bodily fluid, such as blood, plasma, serum, urine, vaginal fluid, fluid from a hydrocele (e.g., of the testis), vaginal flushing fluids, pleural fluid, ascitic fluid, cerebrospinal fluid, saliva, sweat, tears, sputum, bronchoalveolar lavage fluid, discharge fluid from the nipple, aspiration fluid from different parts of the body (e.g., thyroid, breast), etc. [0050] The nucleic acid can be of any composition form, such as deoxyribonucleic acid (DNA, e.g., complementary DNA (cDNA), genomic DNA (gDNA) and the like), and/or DNA analogs (e.g., containing base analogs, sugar analogs and/or a non-native backbone and the like), and/or ribonucleic acid (RNA) and or RNA analogs, all of which can be in single- or double-stranded form. Unless otherwise limited, a nucleic acid can comprise known analogs of natural nucleotides, some of which can function in a similar manner as naturally occurring nucleotides. A nucleic acid can be in any form useful for conducting processes herein (e.g., linear, circular, supercoiled, single-stranded, double-stranded and the like). A nucleic acid in some embodiments can be from a single chromosome or fragment thereof (e.g., a nucleic acid sample may be from one chromosome of a sample obtained from a diploid organism). In certain embodiments nucleic acids comprise nucleosomes, fragments or parts of nucleosomes or nucleosome-like structures. Nucleic acids can comprise protein (e.g., histones, DNA binding proteins, and the like). Nucleic acids analyzed by processes described herein can be substantially isolated and are not substantially associated with protein or other molecules. Nucleic acids can also include derivatives, variants and analogs of DNA synthesized, replicated or amplified from single-stranded (“sense” or “antisense,” “plus” strand or “minus” strand, “forward” reading frame or “reverse” reading frame) and double-stranded polynucleotides. Deoxyribonucleotides can include deoxyadenosine, deoxycytidine, deoxyguanosine and deoxythymidine. A nucleic acid may be prepared using a nucleic acid obtained from a subject as a template. [0051] In certain embodiments, the nucleic acid is a cell-free nucleic acid, which can be found in bodily fluids such as blood, whole blood, plasma, serum, urine, cerebrospinal fluid, fecal, saliva, sweat, sweat, tears, pleural fluid, pericardial fluid, or peritoneal fluid of a subject. Cell-free nucleic acids originate from one or more healthy cells and/or from one or more cancer cells, or from non-human sources such bacteria, fungi, viruses. Examples of the cell-free nucleic acids include but are not limited to cell-free DNA (“cfDNA”), including mitochondrial DNA or genomic DNA, and cell-free RNA. In certain embodiments herein, instruments for assessing the quality of the cell-free nucleic acids, such as the TapeStation System from Agilent Technologies (Santa Clara, CA) can be used. Concentrating low-abundance cfDNA can be accomplished, for example using a Qubit Fluorometer from Thermofisher Scientific (Waltham, MA). [0052] In various embodiments, the majority of DNA in a biological sample that has been enriched for cell-free DNA (e.g., a plasma sample obtained via a centrifugation protocol) can be cell-free (e.g., greater than 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the DNA can be cell- free). B. Methylation of Nucleic Acids [0053] A methylated nucleic acid is a nucleic acid having a modification in which a hydrogen atom on the pyrimidine ring of a cytosine base is converted to a methyl group, forming 5- methylcytosine. Methylation can occur at dinucleotides of cytosine and guanine referred to herein as “CpG sites”. Methylation of cytosine can occur in cytosines in other sequence contexts, for example, 5ƍ-CHG-3ƍ and 5ƍ-CHH-3ƍ, where H is adenine, cytosine or thymine. Cytosine methylation can also be in the form of 5-hydroxymethylcytosine. Methylation of DNA can include methylation of non-cytosine nucleotides, such as N ⁶ -methyladenine (6mA). Anomalous cfDNA methylation can be identified as hypermethylation or hypomethylation, both of which may be indicative of cancer status. As is well known in the art, DNA methylation anomalies (compared to healthy controls) can cause different effects, which may contribute to cancer. [0054] In certain embodiments, the nucleic acid comprises a CpG site (i.e., cytosine and guanine separated by only one phosphate group). In certain embodiments, the nucleic acid comprises a CpG island (also referred to as a “CG islands” or “CGI”) or a portion thereof. Because certain CGIs and certain features of certain CGIs in tumor cells tend to be different from the same CGIs or features of the CGIs in healthy cells, detection of such CGIs can be informative of a health condition. In certain embodiments, the CGI is a “cancer informative CGIs”, which is defined and described in more detail below. In certain embodiments, the CpG is an “informative CpG”, e.g., a “cancer informative CGI”. Such CGIs may have methylation patterns in tumor cells that are different from the methylation patterns in healthy cells. Accordingly, detection of a cancer informative CGI can be informative regarding a subject’s risk of developing cancer or can be indicative that the subject has cancer. Exemplary cancer informative CGIs are identified in, e.g., Table 1 of U.S. Patent Publication 2020/0109456A1 and Tables 2 and 3 of WO2022/133315. Other exemplary cancer informative CGIs are identified at Tables 1-4 herein. C. Converting Unmethylated Nucleic Acids [0055] In certain aspects, the nucleic acids of the invention have been treated to convert one or more unmethylated nucleotides (e.g., cytosines) to another nucleotide (a “converted nucleotide”, as used herein), for example, prior to amplification. In certain embodiments, one or more unmethylated cytosines are converted to a nucleotide that pairs with adenine (e.g., the unmethylated cytosine may be converted to uracil). In certain embodiments, one or more unmethylated adenines are converted to a base that pairs with cytosine (e.g., the unmethylated adenine may be converted to inosine (I)). In certain embodiments, one or more methylated cytosines (e.g., a 5-methylcytosine (5mC)) is converted to a thymine, which pairs with adenine. In certain embodiments, methylated cytosines are protected from conversion (e.g., deamination) during the conversion step. [0056] After a nucleic acid has been treated to convert unmethylated, or, in some cases, methylated nucleotides, into another nucleotide, the nucleic acid may be amplified. During amplification, the converted nucleotide pairs with its complementary nucleotide, and in the next round of amplification, the complementary nucleotide pairs with a replacement nucleotide. For example, following the conversion of an unmethylated cytosine to a uracil, the nucleic acid may be amplified such that an adenine pairs with the uracil in the first round of replication, and in the second round of replication, the adenine pairs with a thymine. Accordingly, the thymine replaces the uracil in the original nucleic acid sequence, and is referred to herein as a “replacement nucleotide”. [0057] In certain aspects, the nucleic acids of the invention have been selectively deaminated. Selective deamination refers to a process in which unmethylated cytosine residues are selectively deaminated over methylated cytosine (5-methylcytosine) residues. In certain embodiments, deamination of cytosine forms uracil, effectively inducing a C to T point mutation to allow for detection of methylated cytosines or unmethylated cytosines. Methods of deaminating cytosine are known in the art, and include bisulfite conversion and enzymatic conversion. In certain embodiments, the enzymatic conversion comprises subjecting the nucleic acid to TET2, which oxidizes methylated cytosines, thereby protecting them, and subsequent exposure to APOBEC, which converts unprotected (i.e., unmethylated) cytosines to uracils. [0058] In some embodiments, the conversion, for example, bisulfite conversion or enzymatic conversion, uses commercially available kits. Bisulfite conversion can be performed using commercially available technologies, such as EZ DNA Methylation-Gold, EZ DNAMethylation- Direct or an EZ DNAMethylation-Lighting kit (Zymo Research Corp (Irvine, California)) or EpiTect Fast available from Qiagen (Germantown, MD). In another example a kit such as APOBECSeq (NEBiolabs) or OneStep qMethyl-PCR Kit (Zymo Research Corp (Irvine, California)) is used. i. Bisulfite conversion [0059] Bisulfite conversion is performed on DNA by denaturation using high heat, preferential deamination (at an acidic pH) of unmethylated cytosines, which are then converted to uracil by desulfonation (at an alkaline pH). Methylated cytosines remain unchanged on the single- stranded DNA (ssDNA) product. An overview of bisulfite conversion is provided in FIG.1. [0060] In some embodiments the methods include treatment of the sample with bisulfite (e.g., sodium bisulfite, potassium bisulfite, ammonium bisulfite, magnesium bisulfite, sodium metabisulfite, potassium metabisulfite, ammonium metabisulfite, magnesium metabisulfite and the like). Unmethylated cytosine is converted to uracil through a three-step process during sodium bisulfite modification. As shown in FIG.1, the steps are sulfonation to convert cytosine to cytosine sulphonate, deamination to convert cytosine sulphonate to uracil sulphonate and alkali desulfonation to convert uracil sulphonate to uracil. Conversion on methylated cytosine is much slower and is not observed at significant levels in a 4-16 hour reaction. (See Clark et al., Nucleic Acids Res., 22(15):2990-7 (1994).) If the cytosine is methylated it will remain a methylated cytosine. If the cytosine is unmethylated it will be converted to uracil. When the modified strand is copied, for example, through extension of a locus specific primer, a random or degenerate primer or a primer to an adaptor, a G will be incorporated in the interrogation position (opposite the C being interrogated) if the C was methylated and an A will be incorporated in the interrogation position if the C was unmethylated and converted to U. When the double stranded extension product is amplified those Cs that were converted to Us and resulted in incorporation of A in the extended primer will be replaced by Ts during amplification. Those Cs that were not converted (i.e., the methylated Cs) and resulted in the incorporation of G will be replaced by unmethylated Cs during amplification. ii. Enzymatic conversion [0061] In certain embodiments, the enzymatic treatment with a cytidine deaminase enzyme is used to convert cytosine to uracil. Enzymatic conversion can include an oxidation step, in which Tet methylcytosine dioxygenase 2 (TET2) catalyzes the oxidation of 5mC to 5hmC to protect methylated cytosines from conversion by subsequent exposure to a cytidine deaminase. Other protection steps known in the art can be used in addition to or in place of oxidation by TET2. After the oxidation step, the nucleic acid is treated with the cytidine deaminase to convert one or more unmethylated cytosines to uracils. As with bisulfite conversion, when the modified strand is copied, a G will be incorporated in the interrogation position (opposite the C being interrogated) if the C was methylated and an A will be incorporated in the interrogation position if the C was unmethylated. When the double stranded extension product is amplified those Cs that were converted to Us and resulted in incorporation of A in the extended primer will be replaced by Ts during amplification. Those Cs that were not modified and resulted in the incorporation of G will remain as C. [0062] In certain embodiments the cytidine deaminase may be APOBEC. In certain embodiments the cytidine deaminase includes activation induced cytidine deaminase (AID) and apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBEC). In certain embodiments, the APOBEC enzyme is selected from the human APOBEC family consisting of: APOBEC-1 (Apo1), APOBEC-2 (Apo2), AID, APOBEC-3A, -3B, -3C, -3DE, -3F, -3G, -3H and APOBEC-4 (Apo4). In certain embodiments, the APOBEC enzyme is APOBEC-seq. iii. Nitrite Conversion [0063] In certain embodiments, nitrite treatment is used to deaminate adenine and cytosine. As shown in FIG.3, deamination of an A results in conversion to an inosine (I), which is read by a polymerase as a G, whereas deamination of a methylated A (N ⁶ -methyladenine (6mA)) results in a nitrosylated 6mA (6mA-NO), which causes the base to be read by a polymerase as an A. Deamination of a C results in conversion to a uracil, which is read by a polymerase as a T, whereas deamination of a N ⁴ -methylcytosine (4mC) to 4mC-NO or a 5-methylcytosine (5mC) to a T causes the base to be read by a polymerase as a C or a T, respectively. For 5mC bases, the C to T ratio at the 5mC position is about 40% higher than other cytosine positions, allowing 5mC to be differentiated from C. (See, Li et al. (2022) Genome Biology 23:122.) III. Methods of Differentially Amplifying Methylated Nucleic Acids A. Amplification Reactions [0064] Amplification reactions suitable for use with the methods disclosed herein include “template-driven” reactions in which reactants (i.e., nucleotides or oligonucleotides) have complements in a template polynucleotide that are required for the creation of reaction products. Template-driven reactions can be, e.g., primer extensions with a nucleic acid polymerase or oligonucleotide ligations with a nucleic acid ligase. Such reactions include, but are not limited to, polymerase chain reactions (PCRs), linear polymerase reactions, nucleic acid sequence-based amplification (NASBAs), rolling circle amplifications, nicking endonuclease amplification (NEAR), transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HAD), or strand displacement amplification (SDA) and the like. In one aspect, the amplification reaction is PCR, such as quantitative PCR or digital PCR. An amplification reaction may be a “real-time” amplification if a detection chemistry is available that permits a reaction product to be measured as the amplification reaction progresses, e.g., “real-time PCR”, or “real-time NASBA”. [0065] In certain embodiments, the amplification reaction comprises one or more repetitions of the following steps: (i) denaturing a target nucleic acid, (ii) annealing primers to primer binding sites, and (iii) extending the primers by a nucleic acid polymerase in the presence of nucleoside triphosphates. The reaction is performed in a solution containing all the necessary reactants, which may include, but is not limited to, buffering agents to maintain pH at a selected level during a reaction, salts, co-factors, scavengers, and the like. [0066] In certain embodiments, the reaction is cycled through different temperatures optimized for each step in a thermal cycler instrument. In other embodiments, the reaction is isothermal, e.g., in a LAMP reaction. Particular temperatures, durations at each step, and rates of change between steps depend on many factors that are well-known to those of ordinary skill in the art, e.g., exemplified by the following references: McPherson et al., editors, PCR: A Practical Approach and PCR2: A Practical Approach (IRL Press, Oxford, 1991 and 1995, respectively). For example, in a conventional PCR using Taq DNA polymerase, a double stranded target nucleic acid may be denatured at a temperature >90° C, primers annealed at a temperature in the range 50-75° C, and primers extended at a temperature in the range 72-78° C. The particular format of PCR being employed is discernible by one skilled in the art from the context of an application. Reaction volumes can range from a few hundred nanoliters, e.g., 200 nL, to a few hundred ^L, e.g., 200 ^L. [0067] In certain embodiments, the amplification reaction is preceded by a reverse transcription reaction that converts a target RNA to a complementary single stranded DNA, which is then amplified. In certain embodiments, the amount of reaction product, i.e., amplicon, is monitored as the reaction proceeds (e.g., in a real-time-PCR (RT-PCR) reaction). In certain embodiments, the amplification reaction is designed to measure the abundance of one or more specific target sequences in a sample or specimen (e.g., an absolute quantitation and/or relative quantitation of such target sequences). In certain embodiments, such quantitative measurements are made using one or more reference sequences or internal standards that may be assayed separately or together with a target sequence. The reference sequence may be endogenous or exogenous to a sample or specimen, and in the latter case, may comprise one or more competitor templates. Typical endogenous reference sequences include segments of transcripts of the following genes: ȕ-actin, GAPDH, ȕ2-microglobulin, ribosomal RNA, and the like. [0068] “Cycle threshold” or “Ct” refers to the number of amplification (e.g., PCR) cycles needed for a sample to amplify and cross a threshold, e.g., to be considered detected. i. Methods of Preferentially Amplifying a Methylated Nucleic Acid using a Probe [0069] The methods disclosed herein can be used to determine whether one or more cytosines in a region of interest is methylated or unmethylated using a probe designed to delay amplification of the region if one or more cytosines in the region are unmethylated. The region of interest may comprise a specific cytosine that may be methylated or unmethylated, multiple cytosines that may be methylated or unmethylated, a CpG island, etc. Following conversion of unmethylated cytosines to thymines, the nucleic acid can include 1 methylated cytosine or thymine, or at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 50, at least 100, or at least 200 methylated cytosines or thymines. [0070] As shown in FIG.2 (scheme 2), a nucleic acid is subjected to an amplification reaction using a probe, wherein the probe preferentially binds to a thymine (which was derived from an unmethylated cytosine), thereby blocking amplification of the region comprising the thymine and reducing the rate of its amplification. The rate of amplification can be compared to a positive and/or negative control to determine whether the nucleic acid is methylated or unmethylated in the region of interest. In certain embodiments, the delta-Ct between a negative control, a positive control, and a sample are calculated to determine presence or absence of a methylated cytosine or an unmethylated cytosine (a thymine) in the sample. [0071] In certain embodiments, the method includes providing a sample comprising a nucleic acid having a methylated cytosine or a thymine, wherein the nucleic acid has been (i) treated to convert one or more unmethylated cytosines to uracils and (ii) amplified to convert the uracils to thymines. The method further includes providing primers capable of amplifying a region comprising the methylated cytosine or the thymine, providing a probe that preferentially binds to the region if the thymine is present as compared to if the methylated cytosine is present, and amplifying the region using the primers, wherein, if the thymine is present, the probe binds to the thymine and amplification is delayed (i.e., the rate of amplification is reduced). [0072] As will be understood by one of skill in the art, the reverse method can also be performed, in which a probe preferentially binds to the region if a methylated cytosine is present, such that amplification is delayed if the region comprises the methylated cytosine. [0073] In certain embodiments, the rate of amplification is determined as the “Cycle threshold” or “Ct”, which refers to the number of amplification (e.g., PCR) cycles needed for a sample to amplify and cross a threshold, e.g., to be considered detected. The Ct of the reaction may be compared to that of a control reaction. An amplification may be considered delayed if it has a higher Ct than a control reaction. [0074] In certain embodiments, the probe comprises between about 5 and about 75 nucleotides. For example, the probe can comprise between about 5 and about 15 nucleotides, about 5 and 30 nucleotides, about 5 and about 45 nucleotides, about 5 and about 60 nucleotides, about 5 and about 75 nucleotides, about 15 and 30 nucleotides, about 15 and about 45 nucleotides, about 15 and about 60 nucleotides, about 15 and about 75 nucleotides, about 30 and about 45 nucleotides, about 30 and about 60 nucleotides, about 30 and about 75 nucleotides, about 45 and about 60 nucleotides, about 45 and about 75 nucleotides, and about 60 and about 75 nucleotides. [0075] In certain embodiments, the probe comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 adenosines that bind to the at least at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 thymines. In certain embodiments, the probe comprises exactly one adenosine that binds to the thymine. If the reverse method is used, the probe can comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 guanosines that bind to the at least at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 methylated cytosines. In certain embodiments, the probe comprises exactly one guanosine that binds to the methylated cytosine. ii. Methods of Preferentially Amplifying a Methylated Nucleic Acid using Primers [0076] The methods disclosed herein can be used to determine whether a cytosine in a region of interest is methylated or unmethylated using one or more (e.g., 2) primers designed to preferentially bind a cytosine (e.g., a methylated cytosine) as compared to a thymine (e.g., that was converted from an unmethylated cytosine), thereby preferentially amplifying the region if one or more cytosines in the region are methylated. The region of interest may comprise a specific cytosine that may be methylated or unmethylated, multiple cytosines that may be methylated or unmethylated, a CpG island, etc. Following conversion of unmethylated cytosines to thymines, the nucleic acid can include 1 methylated cytosine or thymine, or at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 50, at least 100, or at least 200 methylated cytosines or thymines. [0077] As shown in FIG.2 (scheme 3), a nucleic acid is subjected to an amplification reaction using one or more primers that preferentially bind to a cytosine (a methylated cytosine), thereby preferentially amplifying the region if one or more cytosines in the region are methylated. If the region comprises a thymine (which was derived from an unmethylated cytosine), the rate of amplification is reduced (or in some cases, no amplification product is produced). The rate of amplification can be compared to a positive and/or negative control to determine whether the nucleic acid is methylated or unmethylated in the region of interest. In certain embodiments, the delta-Ct between a negative control, a positive control, and a sample are calculated to determine presence or absence of a methylated cytosine or an unmethylated cytosine (a thymine) in the sample. [0078] In certain embodiments, the method further comprises providing a probe that binds to the region if the thymine is present, thereby delaying amplification. For example, as shown in FIG. 2 (scheme 4), both the probes of section (i) and the primers of section (ii) can be combined in the same amplification reaction to increase preferential amplification of a region comprising one or more methylated cytosines. As will be understood by the skilled artisan, an alternative method can be practiced in which the probes and primers are designed to preferentially bind to cytosines and increase the rate of amplification of the region if the region comprises one or more methylated cytosines relative to one or more unmethylated cytosines. [0079] In certain embodiments, the method includes providing a sample comprising a nucleic acid, wherein the nucleic acid has been (i) treated to convert one or more unmethylated cytosines to uracils and (ii) amplified to convert the uracils to thymines. The method further includes providing at least one primer that preferentially binds to a region comprising the methylated cytosine as compared to the thymine; and amplifying the region using the at least one primer, wherein amplification is delayed if the thymine is present. In certain embodiments, the at least one primer is exactly one primer. In certain embodiments, the at least one primer is two primers. [0080] In certain embodiments, the at least one primer comprises at least one guanosine, for example, one guanosine, two guanosines, three guanosines, four guanosines, five guanosines, six guanosines, seven guanosines, eight guanosines, nine guanosines, or ten guanosines, or any range therein. In certain embodiments, the at least one primer comprises at least one guanosine at the 3’ end of the primer, for example, one guanosine, two guanosines, three guanosines, four guanosines, five guanosines, six guanosines, seven guanosines, eight guanosines, nine guanosines, or ten guanosines, or any range therein. In certain embodiments, the at least one primer comprises exactly one guanine at the 3’ end of the primer. IV. Health Conditions [0081] In certain embodiments, the methods disclosed herein can be used to determine whether a cytosine in a specific position of a nucleic acid, e.g., a position known to be associated with a health condition, is methylated or unmethylated, thereby providing information regarding the health status of the subject from which the nucleic acid was obtained. For example, in certain embodiments, determining that a cytosine is methylated or unmethylated is indicative that a subject has, or is at risk of developing, a health condition. [0082] In certain embodiments, the nucleic acid is informative of a health condition. In certain embodiments, the methylation status of a nucleic acid (e.g., whether a cytosine in the nucleic acid is methylated or unmethylated) is informative of a health condition. For example, certain regions of interest (e.g., CGIs) can have methylation patterns in tumor cells that are different from the methylation patterns in healthy cells (e.g., cancer informative CGIs). Specific cancer informative CGIs are identified in, e.g., Table 1 of U.S. Patent Publication 2020/0109456A1, Tables 2 and 3 of WO2022/133315, and Tables 1-4 herein, and such CGIs can be evaluated using the methods described herein. [0083] In addition to cancer, other health conditions are known to be associated with methylation status of certain regions of interest, as are known in the art. Accordingly, in certain embodiments, the health condition is selected from inflammatory disease, neurodegenerative disease, autoimmune disorder, neuromuscular disease, metabolic disorder, cardiac disease, or fibrotic disease, or a risk of developing any one of the foregoing. In certain embodiments neurodegenerative disease is one of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD). [0084] In certain embodiments, the health condition is cancer or a risk of developing cancer. In certain embodiments, the cancer is preclinical or early stage cancer. In certain embodiments, the cancer is selected from acute lymphoblastic leukemia, acute myeloid leukemia, adrenocortical carcinoma, soft tissue sarcoma, lymphoma, anal cancer, gastrointestinal cancer, brain cancer, skin cancer, bile duct cancer, bladder cancer, bone cancer, breast cancer, lung cancer, cardiac cancer, central nervous system cancer, cervical cancer, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative neoplasms, colorectal cancer, uterine cancer, esophageal cancer, head and neck cancer, eye cancer, fallopian tube cancer, gallbladder cancer, gastric cancer, germ cell tumor, gestational trophoblastic cancer, hairy cell leukemia, liver cancer, Hodgkin lymphoma, intraocular melanoma, pancreatic cancer, kidney cancer, leukemia, mesothelioma, metastatic cancer, mouth cancer, multiple endocrine neoplasia syndromes, multiple myeloma neoplasms, myelodysplastic neoplasms, ovarian cancer, parathyroid cancer, penile cancer, pheochromocytoma, pituitary cancer, plasma cell neoplasm, primary peritoneal cancer, prostate cancer, rectal cancer, retinoblastoma, sarcoma, small intestine cancer, testicular cancer, throat cancer, thymoma and thymic carcinoma, thyroid cancer, urethral cancer, uterine cancer, vaginal cancer, and vulvar cancer. V. Kits [0085] Also disclosed herein are kits for differentially amplifying methylated nucleic acids. Such kits can include equipment to draw a sample from a subject. For example, kits can include syringes and/or needles for obtaining a sample from a subject. Kits can include detection reagents for detecting amplified nucleic acids from the sample obtained from the subject. [0086] For example, detection reagents can include a set of primers, or a set of primers and at least one probe, that, when combined with the sample, allows for preferential amplification of a methylated (or an unmethylated cytosine (thymine)) from the sample. In certain embodiments, the detection reagents may be primers that target specific known sequences of target sites, thereby enabling nucleic acid amplification of the target sites. Thus, the use of the detection reagents results in generation of methylation information of the subject corresponding to the target sites. In certain embodiments, the detection reagents enable detection of methylated or unmethylated informative CpGs including one or more CGI’s described in Table 1 of U.S. Patent Publication 2020/0109456A1, Tables 2 and 3 of WO2022/133315, and Tables 1-4 herein. [0087] In certain embodiments, the detection reagents include one or more enzymes for processing the nucleic acid and/or performing the amplification reaction, such as a polymerase, reverse transcriptase, nicking enzyme, etc. In certain embodiments, the detection reagents include a detection moiety, e.g., a fluorescent or a chemiluminescent moiety, allowing for the detection of amplified product. In certain embodiments, the detection reagents include dNTPs, salts, inhibitors, or other regents for performing the amplification reaction. [0088] A kit can include instructions for use of one or more sets of detection reagents. For example, a kit can include instructions for performing at least one nucleic acid amplification assay (e.g., polymerase chain reaction assay including any of real-time PCR assays, quantitative real-time PCR (qPCR) assays, allele-specific PCR assays, and reverse-transcription PCR assays). [0089] Kits can further include instructions for accessing computer program instructions stored on a computer storage medium. In various embodiments, the computer program instructions, when executed by a processor of a computer system, cause the processor to perform a screen and/or perform a diagnostic analysis to detect presence of a health condition in a subject. For example, kits can include instructions that, when executed by a processor of a computer system, cause the processor to perform an analysis of methylation information comprising data of the plurality of methylation sites to identify whether the subject is not at risk of having a health condition. [0090] Instructions can be present as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc. Yet another means would be a computer readable medium, e.g., diskette, CD, hard-drive, network data storage, etc., on which the information has been recorded. Yet another means that can be present is a website address which can be used via the internet to access the information at a removed site. Any convenient means can be present in the kits. [0091] Throughout the description, where apparatus, devices, and systems are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are apparatus, devices, and systems of the present invention that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present invention that consist essentially of, or consist of, the recited processing steps. [0092] Practice of the invention will be more fully understood from the foregoing examples, which are presented herein for illustrative purposes only, and should not be construed as limiting the invention in any way. EXAMPLES Example 1 – Hypermethylation-Specific PCR [0093] This example describes a process overview for hypermethylation-specific PCR. [0094] Using the chemistry of PCR, hypermethylation-specific PCR enriches amplification products for hypermethylation sites by biologically or intentionally delaying PCR rates by inhibiting PCR steps at non-methylated sites. Specific embodiments of the method are shown in FIG.2. Prepare target specimen [0095] The target specimen type (e.g., DNA or RNA) is isolated from a biological source (e.g., tissue, blood, plasma, serum, saliva, feces, etc.). Target specimens are assayed for quality and quantity measurements. Convert Unmethylated Cytosines to Uracils [0096] Bisulfite conversion is performed on DNA by denaturation using high heat, preferential deamination (at an acidic pH) of unmethylated cytosines, which are then converted to uracil by desulfonation (at an alkaline pH). Methylated cytosines remain unchanged on the single-stranded DNA (ssDNA) product. An overview of bisulfite conversion is provided in FIG.1. Differential PCR Control [0097] As a negative control, differential PCR is performed by combining library DNA with PCR reagents and primers specific for target sequences. (Lang et al., “Optimized Allele-Specific Real-Time PCR Assays for the Detection of Common Mutations in KRAS and BRAF” J. Mol. Diag: 13(1):23-28 (2011).) A schematic is shown in Part 1 of FIG.2. [0098] Real-time PCR (or digital PCR) is performed for 30-50 cycles and the output for signal via fluorescence from amplified target DNA is monitored. Cycle threshold values (Ct) are recorded and exported for analysis. The delta-Ct between negative control, positive control, and sample are calculated to determine presence or absence of hypermethylated DNA. (Mitchell et al., “Circulating microRNAs as stable blood-based markers for cancer detection” PNAS 105(30):10513-10518 (2008); Chubarov et al., “Allele-Specific PCR for KRAS Mutation Detection Using Phosphoryl Guanidine Modified Primers” Diagnostics: 10:872-886 (2020); Fox et al., “The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system” British J. Cancer: 77(8):1267-1274 (1998).) As shown in Part 1 of FIG.2, enrichment of methyl-C sequences is not observed. Probe-mediated delay PCR [0099] Probe-mediated delay PCR is performed by combining library DNA with PCR reagents, targeted probes for non-methylated sites (bisulfite converted sites) and primers specific for target sequences. A schematic is shown in Part 2 of FIG.2. [00100] Real-time PCR (or digital PCR) is performed for 30-50 cycles and the output for signal via fluorescence from amplified target DNA is monitored. Cycle threshold values (Ct) are recorded and exported for analysis. The delta-Ct between negative control, positive control, and sample are calculated to determine presence or absence of hypermethylated DNA. Slight modifications of this protocol will allow for end-point PCR detection of RNA or DNA of hypermethylated sequences. Methyl-C Chimeric enriched PCR [00101] Methyl-C Chimeric PCR is performed by combining library DNA with PCR reagents, and methyl-C chimeric primers specific for target sequences. A schematic is shown in Part 3 of FIG.2. [00102] Real-time PCR (or digital PCR) is performed for 30-50 cycles and the output for signal via fluorescence from amplified target DNA is monitored. Cycle threshold values (Ct) are recorded and exported for analysis. The delta-Ct between negative control, positive control, and sample are calculated to determine presence or absence of hypermethylated DNA. Slight modifications of this protocol will allow for end-point PCR detection of RNA or DNA of hypermethylated sequences. Probe-mediated delay and Methyl-C Chimeric enriched PCR [00103] Combined Probe-mediated delay PCR and Methyl-C Chimeric PCR is performed by combining library DNA with PCR reagents, targeted probes for non-methylated sites (bisulfite converted sites) and methyl-C chimeric primers specific for target sequences. A schematic is shown in Part 4 of FIG.2. [00104] Real-time PCR (or digital PCR) is performed for 30-50 cycles and the output is monitored for signal via fluorescence from amplified target DNA. Cycle threshold values (Ct) are recorded and exported for analysis. The delta-Ct between negative control, positive control, and sample are calculated to determine presence or absence of hypermethylated DNA. Slight modifications of this protocol will allow for end-point PCR detection of RNA or DNA of hypermethylated sequences. [00105] Interpretation of results 1. Positive results for hypermethylation target sites will produce a result of the delta-Ct between sample and negative control is greater than or equal to 3. 2. Negative results for hypermethylation target sites will produce a result of delta-Ct between sample and negative control is less than 2. 3. Inconclusive results for hypermethylation target sites will produce a result of delta-Ct between the sample and negative control is greater than or equal to 2 but less than 3. INCORPORATION BY REFERENCE [00106] The entire disclosure of each of the patent and scientific documents referred to herein is incorporated by reference for all purposes. EQUIVALENTS [00107] The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.

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chr16:51183699^51188763 37 chr5:140346105^140346931 38 chr9:23820691^23822135 39 chr20:690575^691099 40 chr1:177133392^177133846 41 chr5:45695394^45696510 42 chr2:45395869^45398186 43 chr20:48184193^48184833 44 chr6:6002471^6005125 45 chr14:101192851^101193499 46 chr8:4848968^4852635 47 chr8:53851701^53854426 48 chr12:186863^187610 49 chr5:54519054^54519628 50 chr6:108485671^108490539 51 chr3:157815581^157816095 52 chr11:626728^628037 53 chr2:177012371^177012675 54 chr17:59531723^59535254 55 chr16:55364823^55365483 56 chr8:99960497^99961438 57 chr7:42267546^42267823 58 chr17:14202632^14203258 59 chr10:102891010^102891794 60 chr5:174158680^174159729 61 chr14:33402094^33404079 62 chr2:177036254^177037213 63 chr10:106399567^106402812 64 chr6:166579973^166583423 65 chr11:123066517^123066986 66 chr11:44327240^44327932 67 chr14:95237622^95238211 68 chr9:102590742^102591303 69 chr15:76630029^76630970 70 chr4:24801109^24801902 71 chr8:97169731^97170432 72 chr3:6902823^6903516 73 chr22:48884884^48887043 74 chr15:45408573^45409528 75 chr9:100610696^100611517 76 chr4:174448333^174448845 77 chr16:20084707^20085305 78 chr4:174439812^174440249 79 chr6:10381558^10382354 80 chr15:35046443^35047480 81 chr10:119494493^119494991 82 chr5:72676120^72678421 83 chr11:44325657^44326517 84 chr17:46670522^46671458 85 chr14:92789494^92790712 86 chr4:174459200^174460054 87 chr2:80549578^80549798 88 chr7:153748407^153750444 89 chr6:1389139^1391393 90 chr16:49314037^49316543 91 chr2:105459127^105461770 92 chr21:38079941^38081833 93 chr4:174427891^174428192 94 chr14:60973772^60974123 95 chr8:99985733^99986983 96 chr2:63281034^63281347 97 chr12:101109863^101111622 98 chr1:119549144^119551320 99 chr5:38257825^3825913600 chr5:54522302^5452353301 chr1:165324191^16532632802 chr15:33602816^3360400303 chr10:118030732^11803423004 chr2:45240372^4524157905 chr4:174430386^17443086106 chr6:50810642^5081099407 chr5:122430676^12243144308 chr10:109674196^10967496409 chr8:97172634^9717388010 chr8:11536767^1153896111 chr5:180486154^18048689212 chr2:38301276^3830451813 chr10:1778784^178001814 chr12:54424610^5442517315 chr17:46669434^4666981116 chr11:8190226^819067117 chr8:25900562^2590584218 chr12:81102034^8110271619 chr7:27199661^2720096020 chr10:119311204^11931210421 chr12:130387609^13038913922 chr7:155258827^15526140323 chr6:117591533^11759227924 chr10:111216604^11121708325 chr1:29585897^2958659826 chr2:144694666^14469518027 chr12:48397889^4839873128 chr5:2748368^2757024 29 chr12:114845861^11484765030 chr2:80529677^8053084631 chr5:1874907^1879032 32 chr6:100905952^10090668633 chr15:96904722^9690505034 chr5:134374385^13437675135 chr2:66652691^6665421836 chr12:54440642^5444154337 chr6:108495654^10849598638 chr17:70112824^7011427139 chr3:87841796^87842563 40 chr7:96650221^9665155141 chr4:110222970^11022425742 chr6:78172231^7817408843 chr7:155164557^15516785444 chr12:113900750^11390644245 chr9:112081402^11208290546 chr12:114886354^11488657947 chr5:3590644^3592000 48 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chr2:176977284^17697754063 chr4:4868440^4869173 64 chr6:137809342^13781020465 chr12:54321301^5432172166 chr2:105468851^10547348867 chr8:55366180^5536762868 chr12:72665683^7266755169 chr4:54966163^5496806370 chr5:134366913^13436743871 chr1:226075150^22607568072 chr20:17206528^1720695273 chr4:172733734^17273511874 chr18:55019707^5502160575 chr2:162279835^16228070976 chr6:1381743^1385211 77 chr7:103968783^10396995978 chr6:150358872^15035939479 chr2:119914126^11991666380 chr7:27278945^27279469 81 chr12:114851957^11485236082 chr16:24267040^2426752783 chr6:7229877^7230865 84 chr2:45227644^4522878385 chr4:174450046^17445146986 chr4:154712073^15471270687 chr3:22413492^2241436588 chr20:21694472^2169534489 chr6:1378445^1379318 90 chr8:70981873^7098488891 chr12:53107912^5310847192 chr10:102996034^10299664693 chr3:157821232^15782160494 chr4:111554965^11155550495 chr13:58206526^5820893096 chr10:22634000^2263486297 chr9:22005887^2200622998 chr5:159399004^15939992899 chr2:31805293^3180640300 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able 3: Additional Example CGIs

able 4: Additional Example CGIs