Detection of cancer by liquid biopsy

Abstract

Described herein are methods and systems for non-invasive DNA capture assay to identify synovium-specific gene expression signatures in blood plasma from subjects having or suspected of having a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma).

Description

DETECTION OF CANCER BY LIQUID BIOPSYCROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application Nos. 63 / 661,001, filed on June 17, 2024; 63 / 680,001, filed on August 6, 2024; and 63 / 814,671 filed on May 30, 2025, each of which are incorporated by reference herein in their entireties.BACKGROUND

[0002] Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related deaths worldwide. In the U.S. alone, 154,270 new cases and 52,900 deaths are projected in 2025, with incidence rising among younger adults.SUMMARY

[0003] In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm from cell-free nucleic acid (cfNA) fragments derived from active chromatin in a sample obtained from the subject to obtain presence or absence data for the plurality of genomic regions; and (b) applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer and advanced adenoma. In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm from cell-free nucleic acid (cfNA) fragments derived from active chromatin in a sample obtained from the subject to obtain presence or absence data for the plurality of genomic regions; and (b) applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer and lacking colorectal cancer. In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regionsassociated with the colon neoplasm from cell-free nucleic acid (cfNA) fragments derived from active chromatin in a sample obtained from the subject to obtain presence or absence data for the plurality of genomic regions; and (b) applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses including advanced adenoma. In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm from cell-free nucleic acid (cfNA) fragments derived from active chromatin in a sample obtained from the subject to obtain presence or absence data for the plurality of genomic regions; and (b) applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer, advanced adenoma, and lacking colorectal cancer or advanced adenoma. In some embodiments, the sample is a plasma, serum, peripheral blood, or whole blood sample. In some embodiments, the sample is not a stool sample or derived from a stool sample. In some embodiments, the sample is a blood sample, and the method further comprises obtaining the blood sample from the subject prior to (a) by venipuncture, central line collection, or capillary collection. In some embodiments, the method further comprises obtaining the cfNA fragments from the sample from the subject prior to (a). In some embodiments, (a) further comprises: (i) contacting cfNA fragments derived from the sample obtained from the subject to an anionic surface to enrich the active chromatin, or (ii) performing a size selection to enrich the active chromatin. In some embodiments, the method further comprises performing a sequencing reaction on the cfNA fragments that have been enriched to obtain the obtain sequences of a plurality cfNA fragments derived from active chromatin. In some embodiments, the cfNA derived from active chromatin is about 200, 210, 250, 300, 350, or more base pairs (bp) or greater in length. In some embodiments, the cfNA fragments derived from active chromatin comprise cfDNA fragments. In some embodiments, the colon neoplasm is a colorectal cancer (CRC). In some embodiments, the colon neoplasm is an advanced adenoma. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise transcription factor binding sites, RNAP II pausing sites, DNAse I sensitive regions, exons, promoters, or enhancers. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise transcription factor binding sites, exons, promoters, or enhancers. In some embodiments, the plurality of genomic regionsassociated with the colon neoplasm comprise exons or promoters. In some embodiments, the method further comprises performing a size selection to enrich the cfNA fragments derived from the active chromatin from cfNA fragments derived from the sample obtained from the subject, wherein the size selection selects for cfNA fragments about 200 bp or greater in length. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer with at least 93% diagnostic sensitivity. In some embodiments, the computer- implemented algorithm is capable of performing a classification between the subject having stage I, II, or III of the colorectal cancer and the subject not having a colorectal cancer with at least 94% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having a stage IV of the colorectal cancer and the subject not having a colorectal cancer with at least 91% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma with at least 64% diagnostic sensitivity. In some embodiments, the method further comprises detecting the colon neoplasm in the subject via the computer-implemented algorithm and administering a chemotherapeutic agent to the subject, performing a surgical resection on the subject, or performing radiotherapy on the subject. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises an adjuvant chemotherapeutic agent. In some embodiments, the method further comprises reporting an identification of the subject as having the colon neoplasm to a physician, a caregiver, or the subject, wherein the identification is performed at least in part on the computer implemented algorithm. In some embodiments, the method further comprises recommending administration of a chemotherapeutic agent to a physician of the subject, recommending surgical resection of a colon of the subject to a physician of the subject, or recommending radiotherapy on the subject to a physician of the subject. In some embodiments, the detecting the presence or absence of the plurality of genomic regions comprises performing a next-generation sequencing procedure. In some embodiments, the detecting the presence of absence of the plurality of genomic regions comprises performing aquantitative reverse polymerase chain reaction (qPCR), a reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof. In some embodiments, the method further comprises detecting an abundance of the plurality of genomic regions associated with the colon neoplasm and applying the computer-implemented algorithm to the abundance of the plurality of genomic regions, wherein the computer-implemented algorithm has been trained on abundance data for the plurality of individuals having predetermined colon neoplasm statuses including the colorectal cancer and the advanced adenoma. In some embodiments, the computer-implemented algorithm comprises a logistic regression algorithm, a random forest algorithm, a lasso regression algorithm, a ridge regression algorithm, an elastic-net regression algorithm, a neural network algorithm, Naive Bayes algorithm, or any combination thereof. In some embodiments, the plurality of genomic regions comprises at least 10% of the genes listed in Table 1A, at least 10% of the genes listed in Table IB; or at least 10% of the genes listed in Table 1C. In some embodiments, the plurality of genomic regions are at least 5 in number In some embodiments, the method further comprises detecting a presence or absence of at least 5% of the loci listed in Table 2A, at least 5% of the loci listed in Table 2B, or at least 5% of the loci listed in Table 2C from the cfNA fragments and generating corresponding presence or absence data, wherein the computer-implemented algorithm is trained on presence or absence data for the loci. In some embodiments, the method does not comprise obtaining presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters from the cfNA fragments, or the method does not comprise obtaining presence or absence data for any of the transcription factor binding sites (TFBSs), exons, enhancers, or promoters of the genes in Table 2D.

[0004] In some aspects, the present disclosure provides for a method, the method comprising: detecting a presence or absence of at least 10% of the unique genes listed in Table 1A; at least 10% of the unique genes listed in Table IB; or at least 10% of the unique genes in Table 1C from cfNA fragments obtained from a blood sample or a fraction thereof from a subject suspected of having a colon neoplasm to generate presence or absence data, wherein the method involves detecting fewer than about 10,000 genes but greater than 4 genes. In some embodiments, the colon neoplasm comprises colorectal cancer. In some embodiments, the colon neoplasm comprises advanced adenoma. In some embodiments, the blood sample is a plasma, serum, peripheral blood, or whole blood sample. In some embodiments, the blood sample is not derived from a fecal sample. In some embodiments, the cfNA fragments are non-canonical or active chromatin fragments about 200 bp or greater in length. In some embodiments, the cfNA fragments are obtained by contacting the cfNA fragments obtained from the blood sample or thefraction thereof to an anionic surface or performing a size selection to enrich cfNA fragments derived from active chromatin. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, 2B, or 2C from the cfNA. In some embodiments, the method does not comprise generating presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters; or the method does not comprise generating presence or absence data for any of the genes in Table 2D. In some embodiments, wherein the cfNA fragments comprise cfDNA fragments. In some embodiments, the detecting comprises performing a next generation sequencing procedure. In some embodiments, the detecting comprises performing a quantitative reverse polymerase chain reaction (qPCR), reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof. In some embodiments, the plurality of genomic regions comprises transcription factor binding sites (TFBSs), exons, enhancers, promoters, RNAP II pausing sites, DNAse I sensitive regions, or any combination thereof. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise transcription factor binding sites, exons, promoters, or enhancers. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise exons or promoters. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, Table 2B, or Table 2C from the cfNA and generating corresponding presence or absence data. In some embodiments, the method further comprises applying a computer- implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma and absence colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having thecolorectal cancer. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer with at least 93% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having stage I, II, or III of the colorectal cancer and the subject not having a colorectal cancer with at least 94% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having a stage IV of the colorectal cancer and the subject not having a colorectal cancer with at least 91% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma with at least 64% diagnostic sensitivity. In some embodiments, the method further comprises detecting the colorectal cancer in the subject via the computer-implemented algorithm and administering a chemotherapeutic agent to the subject, performing a surgical resection on the subject, or performing radiotherapy on the subject. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises an adjuvant chemotherapeutic agent. In some embodiments, the method further comprises reporting an identification of the subject as having the colon neoplasm to a physician, a caregiver, or the subject, wherein the identification is performed at least in part on the computer implemented algorithm. In some embodiments, the method further comprises recommending administration of a chemotherapeutic agent to a physician of the subject, recommending surgical resection of a colon of the subject to a physician of the subject, or recommending radiotherapy on the subject to a physician of the subject.In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm in cell -free nucleic acid (cfNA) fragments derived from a sample of the subject; and (b) determining the subject has the colon neoplasm with a diagnostic sensitivity of at least 93% based on the presence or the absence of the plurality of genomic regions. In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having an advanced adenoma, the method comprising: (a)detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm in cell-free nucleic acid (cfNA) fragments derived from a sample of the subject; and (b) determining the subject has the advanced adenoma with a diagnostic sensitivity of at least 64% based on the presence or the absence of the plurality of genomic regions. In some aspects, the present disclosure provides for a method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising: (a) detecting a presence or an absence of a plurality of genomic regions associated with the colon neoplasm in cell-free nucleic acid (cfNA) fragments derived from a sample of the subject; and (b) determining the subject has the colon neoplasm with a diagnostic sensitivity of at least 60% based on the presence or the absence of the plurality of genomic regions, wherein the subject has an autoimmune disease. In some embodiments, the determining further comprises applying a computer-implemented algorithm to the presence or the absence of the plurality of genomic regions, wherein the computer implemented algorithm has been trained on presence or absence data for the plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses. In some embodiments, the sample is a plasma, serum, peripheral blood, or whole blood sample. In some embodiments, the method involves detecting fewer than about 10,000 genes but greater than 4 genes. In some embodiments, the colon neoplasm comprises colorectal cancer. In some embodiments, the colon neoplasm comprises advanced adenoma. In some embodiments, the blood sample is a plasma, serum, peripheral blood, or whole blood sample. In some embodiments, the blood sample is not derived from a fecal sample. In some embodiments, the cfNA fragments are non-canonical or active chromatin fragments about 200 bp or greater in length. In some embodiments, the cfNA fragments are obtained by contacting the cfNA fragments obtained from the blood sample or the fraction thereof to an anionic surface or performing a size selection to enrich cfNA fragments derived from active chromatin. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, 2B, or 2C from the cfNA. In some embodiments, the method does not comprise generating presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters; or the method does not comprise generating presence or absence data for any of the genes in Table 2D. In some embodiments, wherein the cfNA fragments comprise cfDNA fragments. In some embodiments, the detecting comprises performing a next generation sequencing procedure. In some embodiments, the detecting comprises performing a quantitative reverse polymerase chain reaction (qPCR), reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof. In some embodiments, the plurality of genomic regions comprises transcription factor binding sites(TFBSs), exons, enhancers, promoters, RNAP II pausing sites, DNAse I sensitive regions, or any combination thereof. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise transcription factor binding sites, exons, promoters, or enhancers. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise exons or promoters. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, Table 2B, or Table 2C from the cfNA and generating corresponding presence or absence data. In some embodiments, the method further comprises applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer- implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma and absence colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer- implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the computer- implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer with at least 93% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having stage I, II, or III of the colorectal cancer and the subject not having a colorectal cancer with at least 94% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having a stage IV of the colorectal cancer and the subject not having a colorectal cancer with at least 91% diagnostic sensitivity. In some embodiments, the computer- implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma with at least64% diagnostic sensitivity. In some embodiments, the method further comprises detecting the colorectal cancer in the subject via the computer-implemented algorithm and administering a chemotherapeutic agent to the subject, performing a surgical resection on the subject, or performing radiotherapy on the subject. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises an adjuvant chemotherapeutic agent. In some embodiments, the method further comprises reporting an identification of the subject as having the colon neoplasm to a physician, a caregiver, or the subject, wherein the identification is performed at least in part on the computer implemented algorithm. In some embodiments, the method further comprises recommending administration of a chemotherapeutic agent to a physician of the subject, recommending surgical resection of a colon of the subject to a physician of the subject, or recommending radiotherapy on the subject to a physician of the subject.In some aspects, the present disclosure provides for a method of treating a subject identified as having a colon neoplasm, the method comprising: administering to the subject a chemotherapeutic agent, performing a surgical resection on the subject, or performing radiotherapy on the subject, wherein the subject has been identified as having the colon neoplasm based at least in part on a computer-implemented algorithm capable of distinguishing between: (i) colorectal cancer; and (ii) advanced adenoma, based at least in part on detecting a presence or absence of a plurality of genomic regions associated with a colon neoplasm from active chromatin in cell -free nucleic acid (cfNA) fragments derived from a of the subject. In some embodiments, the sample is a plasma, serum, or peripheral blood, or whole blood sample. In some aspects, the present disclosure provides for a method of treating a subject identified as having a colon neoplasm, the method comprising: administering to the subject a chemotherapeutic agent, performing a surgical resection on the subject, or performing radiotherapy on the subject, wherein the subject has been identified as having the colon neoplasm based at least in part on a computer-implemented algorithm capable of distinguishing between: (i) colorectal cancer; and (ii) absence of colorectal cancer, based at least in part on detecting a presence or absence of a plurality of genomic regions associated with a colon neoplasm from active chromatin in cell-free nucleic acid (cfNA) fragments derived from a of the subject. In some aspects, the present disclosure provides for a method of treating a subject identified as having a colon neoplasm, the method comprising: administering to the subject a chemotherapeutic agent, performing a surgical resection on the subject, or performing radiotherapy on the subject, wherein the subject has been identified as having the colonneoplasm based at least in part on a computer-implemented algorithm capable of distinguishing between: (i) advanced adenoma; and (ii) absence of advanced adenoma, based at least in part on detecting a presence or absence of a plurality of genomic regions associated with a colon neoplasm from active chromatin in cell-free nucleic acid (cfNA) fragments derived from a sample of the subject. In some embodiments, the sample is a plasma, serum, or peripheral blood, or whole blood sample. In some embodiments, the sample is a plasma, serum, or peripheral blood, or whole blood sample. In some embodiments, the chemotherapeutic agent comprises neoadjuvant chemotherapy agent. In some embodiments, the chemotherapeutic agent comprises an adjuvant chemotherapy agent. In some embodiments, the detecting involves detecting fewer than about 10,000 genes but greater than 4 genes. In some embodiments, the colon neoplasm comprises colorectal cancer. In some embodiments, the colon neoplasm comprises advanced adenoma. In some embodiments, the blood sample is a plasma, serum, peripheral blood, or whole blood sample. In some embodiments, the blood sample is not derived from a fecal sample. In some embodiments, the cfNA fragments are non-canonical or active chromatin fragments about 200 bp or greater in length. In some embodiments, the cfNA fragments are obtained by contacting the cfNA fragments obtained from the blood sample or the fraction thereof to an anionic surface or performing a size selection to enrich cfNA fragments derived from active chromatin. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, 2B, or 2C from the cfNA. In some embodiments, the method does not comprise generating presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters; or the method does not comprise generating presence or absence data for any of the genes in Table 2D. In some embodiments, wherein the cfNA fragments comprise cfDNA fragments. In some embodiments, the detecting comprises performing a next generation sequencing procedure. In some embodiments, the detecting comprises performing a quantitative reverse polymerase chain reaction (qPCR), reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof. In some embodiments, the plurality of genomic regions comprises transcription factor binding sites (TFBSs), exons, enhancers, promoters, RNAP II pausing sites, DNAse I sensitive regions, or any combination thereof. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise transcription factor binding sites, exons, promoters, or enhancers. In some embodiments, the plurality of genomic regions associated with the colon neoplasm comprise exons or promoters. In some embodiments, the method further comprises detecting a presence of at least 10% of the loci listed in Table 2A, Table 2B, or Table 2C from the cfNA and generating corresponding presenceor absence data. In some embodiments, the method further comprises applying a computer- implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma and absence colorectal cancer or advanced adenoma. In some embodiments, the method further comprises applying a computer-implemented algorithm to the presence or the absence data, wherein the computer implemented algorithm has been trained on the presence or absence data for the plurality of genomic regions or the loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer or advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the colorectal cancer and the subject not having the colorectal cancer with at least 93% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having stage I, II, or III of the colorectal cancer and the subject not having a colorectal cancer with at least 94% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having a stage IV of the colorectal cancer and the subject not having a colorectal cancer with at least 91% diagnostic sensitivity. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma. In some embodiments, the computer-implemented algorithm is capable of performing a classification between the subject having the advanced adenoma and the subject not having the advanced adenoma with at least 64% diagnostic sensitivity. In some embodiments, the method further comprises detecting the colorectal cancer in the subject via the computer-implemented algorithm and administering a chemotherapeutic agent to the subject, performing a surgical resection on the subject, or performing radiotherapy on the subject. In some embodiments, the method further comprises administering a chemotherapeutic agent to the subject, wherein the chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent. In some embodiments, the method further comprises administering a chemotherapeutic agent tothe subject, wherein the chemotherapeutic agent comprises an adjuvant chemotherapeutic agent. In some embodiments, the method further comprises reporting an identification of the subject as having the colon neoplasm to a physician, a caregiver, or the subject, wherein the identification is performed at least in part on the computer implemented algorithm. In some embodiments, the method further comprises recommending administration of a chemotherapeutic agent to a physician of the subject, recommending surgical resection of a colon of the subject to a physician of the subject, or recommending radiotherapy on the subject to a physician of the subject.

[0005] Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.INCORPORATION BY REFERENCE

[0006] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS

[0007] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

[0008] FIG. 1 depicts circulating chromatin capture from plasma. The method is outlined in (A). Chromatin fragments from different cells are released to the bloodstream and non-canonical fragments that carry transcriptional footprint are enriched and sequenced as shown in (B).

[0009] FIG. 2 depicts active chromatin enrichment according to the methods described herein. Panel A shows a representative size distribution comparison of cfDNA sizes extracted by a solid-phase enrichment protocol and the active chromatin enrichment workflow described herein. Panel B shows a plot of normalized tissue RNA expression versus normalized cfDNA active chromatin blood signal for an experiment where matched RNA-seq and cfDNA activechromatin samples were collected from n=5 stage IV CRC subjects; in this analysis RNA levels were normalized to healthy whole blood expression profdes from the Gtex project (www. gtexportal.org) and cfDNA active chromatin blood signals were normalized to healthy donor cfDNA active chromatin blood signals.

[0010] FIG. 3 depicts KS feature selection for the classifier of Example 1. A distribution of the number iteration that passed the p-value cutoff is depicted in panel A and the top 20 features of the 876-feature set are shown in panel B.

[0011] FIG. 4 shows the average AUC from 10 repeated 5*5 CV RCE analysis in Example 1, demonstrating that less than all the classifier features can accurately classify CRC; the top identified features from the RCE analysis.

[0012] FIG. 5A shows a graph of the number of features relative to the area under the curve (AUC).

[0013] FIG. 5B shows results of a functional annotation of genes corresponding to the top 141 discriminating features from Example 1 performed using TCGA / GTEx / Protein Atlas. In an annotation of cancer specificity, 29.8% (n=42) of the genes were found to be cancer-specific, 64.5% (n=91) were found to have low cancer specificity, and 5.7% (n=8) were found to be not detected (panel A). In an analysis of immune specificity, 21.3% (n=30) were found to be immune -specific, 38.3% were found to have low immune specificity (n=54) and 40.4% (n=57) were found to be not detected (panel B). The enrichment for cancer specific genes and immune specific genes in the feature set suggested biological relevance to cancer.

[0014] FIG. 6 shows a receiver operating (ROC) curve for the 1997-feature classification model developed in Example 2.

[0015] FIG. 7 shows an over-representation analysis (ORA) of promoter and exon features selected in the majority of training models for the classifier development of Example 2. Shown are MSigDB Hallmark pathway annotations (panel A) and Reactome pathway annotations (panel B) versus -loglO(Adjusted P-value).

[0016] FIG. 8 depicts an example computer system for executing methods according to the disclosure.DETAILED DESCRIPTION

[0017] CRC can progress from normal epithelial tissue to adenocarcinoma through a well- defined sequence of molecular events. While current screening methods have reduced mortality, low compliance remains a critical barrier to early detection. Accordingly, there is a need for improved methods, compositions, and systems for non-invasive DNA capture assays toidentify expression signatures in blood plasma of patients suspected of having a colon neoplasm (e.g. colorectal cancer or advanced adenoma) which correlate to colon cancer or advanced adenoma or both. There is also a need for improved methods, compositions, and systems for non-invasive DNA capture assays to identify expression signatures in blood plasma of metabolically complex patients (e.g. patients with autoimmune diseases) suspected of having a colon neoplasm (e.g. colorectal cancer or advanced adenoma) which correlate to colon cancer or advanced adenoma or both.Definitions

[0018] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary proficiency in the fields of this application.

[0019] The practice of some methods disclosed herein employ, unless otherwise indicated, techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA. See for example Sambrook and Green, Molecular Cloning: A Laboratory Manual, 4thEdition (2012); the series Current Protocols in Molecular Biology (F. M. Ausubel, et al. eds.); the series Methods In Enzymology (Academic Press, Inc.), PCR 2: A Practical Approach (M.J. MacPherson, B.D. Hames and G.R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) Antibodies, A Laboratory Manual, and Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications, 6thEdition (R.I. Freshney, ed. (2010)) (which is entirely incorporated by reference herein).

[0020] As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including”, “includes”, “having”, “has”, “with”, or variants thereof are used in either the detailed description or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising”.

[0021] The term "or” as used herein and throughout the disclosure is intended as an inclusive “or”, meaning “and / or”.

[0022] The term “about” or “approximately” signifies within an acceptable error range for the particular value as determined by the application, which will 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 one or more than one standard deviation, per the practice in the art.Alternatively, “about” can mean a range of up to 20%, up to 15%, up to 10%, up to 5%, or up to 1% of a given value.

[0023] An average value can refer to any of a mean, median or mode.

[0024] Statistical significance generally refers to p < 0.05 or < 0.01 or even < 0.001 level.

[0025] The term “autoimmune disease” generally refers to a condition that results from an anomalous response of the immune system, wherein it mistakenly targets and attacks healthy, functioning parts of the body as if they were foreign organisms and causes inflammation and damage.

[0026] The term “sequencing,” generally refers to methods and technologies for determining the sequence of nucleotide bases in one or more polynucleotides. The polynucleotides can be, for example, deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), including variants or derivatives thereof (e.g., single stranded DNA). Sequencing can be performed by various systems currently available, such as, without limitation, a sequencing system by Illumina, Pacific Biosciences, Oxford Nanopore, or Life Technologies (Ion Torrent). As an alternative, sequencing may be performed using nucleic acid amplification, polymerase chain reaction (PCR) (e.g., digital PCR, quantitative PCR, or real time PCR) or isothermal amplification. Such devices may provide a plurality of raw genetic data corresponding to the genetic information or data of a subject (e.g., human), as generated by the device from a sample provided by the subject. In some situations, systems and methods provided herein may be used with proteomic information or data.

[0027] The term “colon neoplasm” generally refers to a new or abnormal growth of tissue in the colon (e.g. the intestinal tract below the small intestine including the cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum) of a subject. The term generally encompasses both colorectal cancer and advanced adenoma.

[0028] The term “colorectal cancer” generally refers to a malignant neoplasm of the colon within a subject. Colorectal cancer can be defined according to its type, stage, or grade.

[0029] The term “advanced adenoma” generally refers to a colon growth that exhibits the first indications of relatively abnormal, uncontrolled, and / or autonomous growth but is not yet classified as cancerous. The growth can show signs of high-grade dysplasia, a size that is >=10mm, a villous histological type, or a serrated histological type with any type of dysplasia. The term can encompass a tubovillous adenoma, a tubular adenoma, a serrated adenoma, or an adenoma with high grade dysplasia.

[0030] As used herein “obtaining a sample” includes obtaining a sample directly or indirectly. In some embodiments, the sample is taken from the subject by the same party (e.g. a testing laboratory) that subsequently acquires biomarker data from the sample. In some embodiments, the sample is received (e.g. by a testing laboratory) from another entity that collected it from the subject (e.g. a physician, nurse, phlebotomist, or medical caregiver). In some embodiments, the sample is taken from the subject by a medical professional under direction of a separate entity(e.g. a testing laboratory) and subsequently provided to the entity (e.g. the testing laboratory). In some embodiments, the sample is taken by the subject or the subject’s caregiver at home and subsequently provided to the party that acquires biomarker data from the sample (e.g. a testing laboratory). A variety of kits suitable for self or home collection of biological samples have been described commercially and in the literature such as e.g., US20170023446A1 and US4777964A.

[0031] The term “nucleic acid” or “NA” generally refers 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 (e.g., blood or interstitial fluid) or a solid sample (e.g., a cell or tissue sample). In some examples, the sample is obtained from a cell- free bodily fluid, such as plasma. In such instance, the sample may include cell-free DNA or cell-free RNA. In some examples, the majority of DNA in a biological sample that may be enriched for cfDNA (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). In some examples, nucleic acid is derived from circulating tumor cells or circulating fetal cells. Throughout the disclosure the use of cell-free nucleic acid or cfNA may be used interchangeably with nucleic acid or NA.

[0032] The term “whole blood sample", as used herein, generally refers to a whole blood sample that has not been fractionated or separated into its component parts. Whole blood may be combined with an anticoagulant such as ethylenediaminetetraacetic acid (EDTA) or acid citrate dextrose (ACD) during the collection process but is generally otherwise unprocessed. "Whole Blood" may refer to a specific standardized product for transfusion or further processing, or to any unmodified collected blood.

[0033] The terms "blood plasma" or "plasma", as used herein, generally refer to a straw- colored / pale-yellow liquid component of blood that holds the blood cells in whole blood in suspension. Blood plasma can make up about 55% of total blood by volume. It can comprise up to about 93% by volume water, and can contain dissolved proteins including albumins, immunoglobulins, and fibrinogen, glucose, clotting factors, electrolytes (Na+, Ca2+, Mg2+, HCO3 Cl etc.), hormones and carbon dioxide. Blood serum generally refers to blood plasma without fibrinogen or the other clotting factors (e.g., whole blood minus both the cells and the clotting factors).

[0034] The term “chaotropic agent” generally refers to a compound that disrupts hydrogen bonds between water molecules and disrupts the tertiary structure of biopolymers. In some embodiments, the chaotropic agent comprises a guanidinium ion (e.g. guanidinium chloride orguanidine thiocyanate), thiourea, or urea. In some embodiments, the chaotropic agent is a sulfur atom-free agent.

[0035] As used herein, a “cell” generally refers to a biological cell. A cell may be the basic structural, functional or biological unit of a living organism. A cell may originate from any organism having one or more cells. Some non-limiting examples include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant, an algal cell, an animal cell, a cell from an invertebrate animal, a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), or a cell from a mammal (e.g., a pig, a cow, a goat, a sheep, a rodent, a rat, a mouse, a non-human primate, a human, etc.).

[0036] The term “binding agent” generally refers to a molecule that has selective affinity for a biomolecule. Binding agents may comprise aptamers, antibodies, lectins and enzymes.

[0037] The term "antibody" generally includes polyclonal antiserum, monoclonal antibodies, fragments of antibodies (e.g. single chain or Fab fragments), and engineered derivatives carrying binding components of antibodies (e.g. single chain variable fragments or ScFvs)

[0038] The term "aptamer" generally includes affinity agents with selectivity for a specific target and which are polymers of nucleic acids.

[0039] The term “alcohol” generally refers to an organic compound that carries at least one hydroxyl functional group ( — OH) bound to a saturated carbon atom. Examples include mono, di, tri, tetra or penta alcohols. Examples further include ethanol or isopropanol. Examples still further include methanol, ethanol, isopropanol, propanol, butanol, ethylene glycol, propylene glycol, butylene glycol, pentylene glycol, glycerol, tetritol, pentitol, 1,3 propane diol, and the like, or mixtures thereof.

[0040] The term “chromatin" generally refers to nucleoprotein complexes with nucleic acid which can compact and organize great lengths of cellular genetic material to contain it within cells. The nucleosome, in which double-stranded DNA (dsDNA) is wound approximately twice around a core of conserved histone or histone-like proteins, can comprise a primary level of chromatin organization in the nucleus of eukaryotic cells. Higher-order chromatin organization can involve further compaction of nucleosomes around additional chromatin-associated proteins and can employ a variety of chromatin assembly factors.

[0041] The term “heterochromatin” or “inactive chromatin” generally refers to a subset of chromatin that is most densely compacted and is generally transcriptionally silent.

[0042] As used herein, “euchromatin” or “active chromatin” generally refers to more extended chromatin domains that are often transcriptionally active, accessible portions of the genome.

[0043] As used herein, the term “receiver operating characteristic” or “ROC” generally refers to a graph showing the performance of a classification model at all classification thresholds. This curve generally plots two parameters: True Positive Rate (Y -axis) and False Positive Rate (X- axis). Generally, a steeper curve can indicate a more accurate test.

[0044] As used herein, the term “area under the curve” or “AUC” generally refers to the entire two-dimensional area underneath the entire ROC curve from (0,0) to (1,1). Accordingly, the AUC ranges from zero to one.

[0045] As used herein, the term “sensitivity” or “diagnostic sensitivity” generally refers to the degree to which a test accurately identifies the presence of a condition (e.g., a colon neoplasm). It is generally expressed as a percentage of true positive predictions over the sum of true positive and false negative predictions. In general, higher sensitivity indicates better ability to accurately assign the presence of the condition (e.g. a colon neoplasm).

[0046] As used herein, the term “specificity” or “diagnostic specificity” generally refers to the degree to which a test accurately identifies the absence of a condition (e.g., a colon neoplasm). It is generally expressed as a percentage of true negative predictions over the sum of true negative and false positive predictions. In general, higher specificity indicates better ability to accurately assign the absence of the condition (e.g. a colon neoplasm).

[0047] The term “neoadjuvant chemotherapeutic agents” generally relates to a variety of hormonal, chemotherapeutic and / or antibody agents, which is aimed to shrink the primary tumor, thereby rendering local therapy (surgery or radiotherapy) less destructive or more effective, enabling colon conserving surgery and evaluation of responsiveness of tumor sensitivity towards specific agents in vivo.

[0048] The term “adjuvant chemotherapeutic agent” generally relates to chemotherapeutic agents used after surgery where all detectable disease has been removed, but where there still remains a risk of small amounts of remaining cancer. Adjuvant chemotherapeutic agents can include cisplatin, carboplatin, vinorelbine, gemcitabine, docetaxel, paclitaxel, and navelbine, or any of the agents describe in Table 2E.

[0049] In some aspects, the present disclosure provides for a method of enriching cell-free nucleic acids (cfNA) comprising active chromatin comprising a sequence of a genomic region. In some embodiments, the cfNA comprises cfDNA, cf-mtDNA (mitochondrial DNA), cfRNA, or any combination thereof. Non-limiting examples of cfRNA include miRNA, IncRNA, circRNA, piRNA, YRNA, and vtRNA. In some embodiments, the cfNAs are produced by cell death. In some embodiments, the cfNAs are produced by cleavage of nuclear DNA. In some embodiments, the cfNA produced from cleavage of nuclear DNA is canonical. In some embodiments, the canonical nuclear DNA is about 170 base pairs (bp). In some embodiments,the cfNA produced from cleavage of nuclear DNA is non-canonical. In some embodiments, the non-canonical nuclear DNA greater than 300 bp in length. In some embodiments, the cfNA originates from tumor cells. In some embodiments, the cfNA originates from lymphoid cells. In some embodiments, the cfNA originates from myeloid cells. In some embodiments, the cfNA originates from fetal cells. In some embodiments, the cfNA originates from microbial cells.

[0050] In some embodiments, the cfNA comprises DNA. In some embodiments, the cfNA comprises RNA. In some embodiments, the cfNA is between 10 and 21,000 base pairs in length. In some embodiments, the cfNA is between 15 and 10,000 base pairs in length. In some embodiments, the cfNA is canonical. A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 base pairs in length. A canonical fragment may comprise about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20. 25. 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 230, or more than 230 base pairs in length. A canonical fragment may comprise about less than 230, 200, 150, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 base pair. A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 base pairs in length. In some embodiments, the cfNA is non-canonical. A non-canonical cfNA fragment may comprise at least 185, 255, 270, or 310 base pairs in length. A non-canonical cfNA fragment may comprise about 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more than 1000 base pairs in length. A non-canonical cfNA fragment may comprise about 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, or less than 200 base pairs in length. In some embodiments the cfNA is between 300 and 1,500 base pairs in length. In some embodiments, the cfNA may comprise about 170, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, or more than 1500 base pairs in length. In some embodiments, the cfNA may comprise about 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, 170, or less than 170 base pairs in length.

[0051] In some embodiments, the cfNA is between 10 and 21,000 nucleotides. In some embodiments, the cfNA is between 15 and 10,000 nucleotides. In some embodiments, the cfNA is canonical. A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 nucleotides. A canonical fragment may comprise about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20. 25. 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 230, or more than 230 nucleotides. A canonical fragment may comprise about less than 230, 200, 150, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide(s). A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 nucleotides. In some embodiments, the cfNA is non-canonical. A non-canonical cfNA fragment may comprise at least 185, 255, 270, or 310 nucleotides. A non-canonical cfNA fragment may comprise about 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more than 1000 nucleotides. A non-canonical cfNA fragmentmay comprise about 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, or less than 200 nucleotides. In some embodiments the cfNA is between 300 and 1,500 nucleotides. In some embodiments, the cfNA may comprise about 170, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, or more than 1500 nucleotides. In some embodiments, the cfNA may comprise about 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, 170, or less than 170 nucleotides.

[0052] In some embodiments, the cfNA is extracted from blood, urine, stool, any subfraction of the aforementioned, or any combination thereof. In some embodiments, the cfNA is extracted from blood. In some embodiments, the cfNA is extracted from blood plasma. In some embodiments, the blood is collected by venipuncture, a finger stick, arterial draw, or any combination thereof. In some embodiments, the blood is collected in a clinical setting. Nonlimiting examples of clinical settings includes hospital, urgent care, doctor’s office, and laboratories. In some embodiments, the blood is collected in a blood collection tube. In some embodiments, the blood collection tube is a STRECK tube. In some cases, the cfNA is extracted from serum or plasma.

[0053] In some embodiments, the cfNA is collected from urine. In some embodiments, the urine is collected by a subject urinating in a container or through use of a foley catheter. In some embodiments, the container is sterile. In some embodiments, the container is non-sterile. In some embodiments, the container has a lid or seal. The lid may be a cover, a screw top, or pop top. In some embodiments, the seal may be a plug. In some embodiments, the seal may be a zip top. In some embodiments, urine is collected directly from the foley catheter. In some embodiments, the urine is collected from a urinary drainage bag. Urine may be collected in a clinical setting or a personal setting of the subject. Non-limiting examples of clinical settings includes hospital, urgent care, doctor’s office, and laboratories. Non-limiting examples of personal settings of the subject may include a house, an office, or a business. In some embodiments, the subject brings the collected urine sample to the clinical setting. In some embodiments, the subject collects the urine by themselves. In some embodiments, the urine is collected by the subject with the help of another person. In some embodiments, the urine is collected by another person. Non-limiting examples of another person includes medical staff such as a nurse, doctor, orderly or a personal contact of the subject such as a family member or friend. In some embodiments, the cfNA is extracted from stool. In some embodiments, the stool is collected by a subject excreting in a container or on to a holder. In some embodiments, the container is sterile. In some embodiments, the container is non-sterile. In some embodiments, the container has a lid or seal. The lid may be a cover, a screw top, or pop top. In some embodiments, the seal may be a plug. In some embodiments, the seal may be a zip top. In someembodiments, the holder is a stick. Stool may be collected in a clinical setting or a personal setting of the subject. Non-limiting examples of clinical settings includes hospital, urgent care, doctor’s office, and laboratories. Non-limiting examples of personal settings of the subject may include a house, an office, or a business. In some embodiments, the subject brings the collected stool sample to the clinical setting. In some embodiments, the subject collects the stool by themselves. In some embodiments, the stool is collected by the subject with the help of another person. In some embodiments, the stool is collected by another person. Non-limiting examples of another person includes medical staff such as a nurse, doctor, orderly or a personal contact of the subject such as a family member or friend.

[0054] In some embodiments, the nucleic acid (NA) is extracted from blood, urine, stool, interstitial fluid, any subfraction of the aforementioned, or any combination thereof. In some embodiments, the NA is extracted from tissue. In some embodiments, the cfNA is extracted from blood, urine, stool, interstitial fluid, any subfraction of the aforementioned, or any combination thereof. In some embodiments, the NA is extracted from blood. In some embodiments, the NA is extracted from blood plasma. In some embodiments, the cfNA is extracted from blood. In some embodiments, the cfNA is extracted from blood plasma. In some embodiments, the blood is collected by venipuncture, a finger stick, arterial draw, or any combination thereof. In some embodiments, the blood is collected in a clinical setting. Nonlimiting examples of clinical settings includes hospital, urgent care, doctor’s office, and laboratories. In some embodiments, the blood is collected in a blood collection tube. In some embodiments, the blood collection tube is a STRECK tube. In some cases, the cfNA is extracted from serum or plasma. In some embodiments, the NA is collected from urine.

[0055] In some embodiments, the cfNA or NA is extracted from interstitial fluid. In some embodiments, the cfNA or NA is extracted from interstitial fluid. In some embodiments, the interstitial fluid is collected using a needle. In some embodiments, the interstitial fluid is collected in a clinical setting. Non-limiting examples of clinical settings includes hospital, urgent care, doctor’s office, and laboratories. In some embodiments, the interstitial fluid is collected in a collection tube. In some embodiments, the interstitial fluid is collected in a container. In some embodiments, the container is sterile. In some embodiments, the container is non-sterile. In some embodiments, the container has a lid or seal. The lid may be a cover, a screw top, or pop top. In some embodiments, the seal may be a plug. In some embodiments, the seal may be a zip top.

[0056] In some embodiments, a composition comprising cfNA or NA in solution is contacted with an anionic solid surface in the presence of a chaotropic agent. In some embodiments, a composition comprising cfNA or NA in solution is contacted with an anionic solid surface in thepresence of a chaotropic agent. The anionic solid surface can be any anionic surface. In some embodiments, the anionic solid surface is planar or spherical. In some embodiments, the anionic solid surface is a slide, a flow cell, a well, a bead, or any combination thereof.

[0057] An anionic solid surface may be a planar surface. A planar surface may be the interior of a well. A well may have a dimension of x by y by z, where x, y, and z are each independently at least about 0.1 pm, 1 pm, 5 pm, 10 pm, 15 pm, 20 pm, 25 pm, 30 pm, 35 pm, 40 pm, 45 pm, 50 pm, 55 pm, 60 pm, 65 pm, 70 pm, 75 pm, 80 pm, 85 pm, 90 pm, 95 pm, 100 pm, 110 pm, 120 pm, 130 pm, 140 pm, 150 pm, 160 pm, 170 pm, 180 pm, 190 pm, 200 pm, 250 pm, 300 pm, 400 pm, 500 pm, 600 pm, 700 pm, 800 pm, 900 pm, 1,000 pm, or more micrometers. A well may have a dimension of x by y by z, where x, y, and z are each independently at most about 1,000 pm, 900 pm, 800 pm, 700 pm, 600 pm, 500 pm, 400 pm, 300 pm, 250 pm, 200 pm, 190 pm, 180 pm, 170 pm, 160 pm, 150 pm, 140 pm, 130 pm, 120 pm, 110 pm, 100 pm, 95 pm, 90 pm, 85 pm, 80 pm, 75 pm, 70 pm, 65 pm, 60 pm, 55 pm, 50 pm, 45 pm, 40 pm, 35 pm, 30 pm, 25 pm, 20 pm, 15 pm, 10 pm, 5 pm, 1 pm, 0.1 pm, or less micrometers. For example, a well can have an x dimension of 434 pm, a y dimension of 30 pm, and a z dimension of 510 pm. In another example, a well can have an x and y dimension of 16 pm and a z dimension of 1 pm. The planar surface may be a well among a plurality of wells. The plurality of wells may comprise at least two wells. The plurality of wells may comprise at least 1,000 wells. There may be 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 1000, 1500, 2000, 3000, 4000, 5000, 10,000, 100,000, 1,000,000 or more than 1,000,000 wells in a plurality of wells. A well may comprise a bead or a planar surface may incorporate a bead.

[0058] An anionic solid surface may be a bead or nanoparticle. A bead may be a polymer such as a polystyrene bead or polystyrene cross-linked with divinylbenzene. In some embodiments, the bead comprises a single composition. A bead may be cellulose, cellulose derivatives, gelatin, acrylic resins, glass, silica gels, polyvinyl pyrrolidine (PVP), co-polymers of vinyl and acrylamide, polyacrylamides, latex gels, dextran, crosslinked dextran (e.g., Sephadex™), rubber, silicon, plastics, nitrocellulose, natural sponges, metal, and agarose gel (Sepharose™). Nonlimiting examples of single compositions include silicon dioxide (e.g., glass), metal, and plastic. In some embodiments, the bead comprises multiple components. In some embodiments, the bead comprises a bead core and an outer shell.

[0059] In some embodiments, the bead core comprises metal. In some embodiments, the metal bead core is magnetic. In some embodiments, the magnetic metal bead core comprises metal oxide. In some embodiments, the metal oxide is iron oxide. In some embodiments, the iron oxide is iron (II, III) oxide. In some embodiments, the iron oxide is black iron oxide. In some embodiments, the iron oxide molecule further comprises an additional metal element. In someembodiments, the metal element is an alkaline earth metal. Non limiting examples of alkaline earth metals includes magnesium, calcium, and barium. In some embodiments, the metal element is a transition metal. Non-limiting examples of transition metals includes manganese, cobalt, copper, zinc, nickel, and chromium. A bead may comprise a metal salt such as a copper salt, a magnesium salt, a calcium salt, or a manganese salt.

[0060] In some embodiments, an outer shell covers the bead core. In some embodiments, the outer shell of the bead is the anionic solid surface. In some embodiments, the outer shell comprises polymer, such as polyethylene glycol, polyacrylic acid, polyacrylamide, polyvinyl alcohol, poly-methyl methacrylate, polystyrene, poly-4-vinylphenol, polyester, polyimide, polyethylene, polypropylene, polyethylene vinyl acetate, polyacrylates, polysaccharide, etc. In some embodiments, the polymer has different molecular weight. In various embodiments, the polymer has an average molecular weight of 100 to 500000 Dalton, such as 200 to 100000 Dalton, 300 to 50000 Dalton, 400 to 20000 Dalton, 500 to 10000 Dalton, or 600 to 5000 Dalton. In some embodiments, the polymer comprises one monomer unit. In some of these embodiments, the monomer is ethylene glycol, acrylic acid, acrylamide, or styrene. In some embodiments, the polymer is a copolymer comprising two or more different monomer units. In some of these embodiments, the two or more different monomer units are selected from ethylene glycol, acrylic acid, acrylamide, and styrene. In some embodiments, the polymer has a linear structure. In some embodiments, the polymer has a branched structure. In some embodiments, the polymer is cross-linked.

[0061] In some embodiments, the outer shell has a thickness of less than 300 nm, such as less than 250 nm, less than 200 nm, less than 150 nm, less than 100 nm, less than 80 nm, less than 50 nm, less than 20 nm, less than 10 nm, less than 5 nm, less than 2 nm, or less than 1 nm. In various embodiments, the outer shell has a thickness of 1 nm to 300 nm, such as 1 nm to 250 nm, 1 nm to 200 nm, 1 nm to 150 nm, 1 nm to 100 nm, 1 nm to 50 nm, 1 nm to 10 nm, 10 nm to 300 nm, 10 nm to 250 nm, 10 nm to 200 nm, 10 nm to 150 nm, 10 nm to 100 nm, 10 nm to 50 nm, 50 nm to 300 nm, 50 nm to 250 nm, 50 nm to 200 nm, 50 nm to 150 nm, 50 nm to 100 nm, 100 nm to 300 nm, 100 nm to 250 nm, 100 nm to 200 nm, 100 nm to 150 nm, 150 nm to 300 nm, 150 nm to 250 nm, 150 nm to 200 nm, 200 nm to 300 nm, 200 nm to 250 nm, or 250 nm to 300 nm. In certain embodiments, the outer shell has a thickness of about 250 nm. In certain embodiments, the outer shell has a thickness of about 200 nm. In certain embodiments, the outer shell has a thickness of about 150 nm. In certain embodiments, the outer shell has a thickness of about 100 nm. In certain embodiments, the outer shell has a thickness of about 80 nm. In certain embodiments, the outer shell has a thickness of about 60 nm. In certain embodiments, the outer shell has a thickness of about 40 nm. In certain embodiments, the outer shell has a thickness ofabout 20 nm. In certain embodiments, the outer shell has a thickness of about 10 nm. In certain embodiments, the outer shell has a thickness of about 5 nm. In certain embodiments, the outer shell has a thickness of about 2 nm. In certain embodiments, the outer shell has a thickness of about 1 nm.

[0062] In some embodiments, the shell is a single layer. In other embodiments, the shell comprises a plurality of layers. In certain embodiments, the shell comprises a layer of silicon dioxide and a layer of titanium dioxide. In certain embodiments, the shell comprises a layer of silicon dioxide and a layer of polymer. In certain embodiments, the shell comprises a layer of titanium dioxide and a layer of polymer.

[0063] In some embodiments, the shell comprises at least one nonporous layer. In certain embodiments, the shell comprises a nonporous silicon dioxide layer. In certain embodiments, the shell comprises a nonporous titanium dioxide layer. In certain embodiments, the shell comprises a nonporous polymer layer. In certain embodiments, the shell comprises a layer of nonporous silicon dioxide and a layer of nonporous titanium dioxide. In certain embodiments, the shell comprises a layer of nonporous silicon dioxide and a layer of nonporous polymer. In certain embodiments, the shell comprises a layer of nonporous titanium dioxide and a layer of nonporous polymer.

[0064] In certain embodiments, the outer shell comprises at least one layer with mesoporous structure. In certain embodiments, the outer shell comprises a layer of mesoporous silicon dioxide. In certain embodiments, the outer shell comprises a layer of mesoporous titanium dioxide. In certain embodiments, the outer shell comprises a layer of mesoporous polymer. In some embodiments, the outer shell comprises a layer of nonporous material and a layer of mesoporous material. In some of these embodiments, the layer of mesoporous material covers the layer of nonporous material. In some embodiments, the outer shell comprises a layer of nonporous silicon dioxide and a layer of mesoporous silicon dioxide. In some of these embodiments, the layer of mesoporous silicon dioxide covers the layer of nonporous silicon dioxide. In some embodiments, the outer shell comprises a layer of nonporous titanium dioxide and a layer of mesoporous titanium dioxide. In some of these embodiments, the layer of mesoporous titanium dioxide covers the layer of nonporous titanium dioxide. In some embodiments, the outer shell comprises a layer of nonporous polymer and a layer of mesoporous polymer. In some of these embodiments, the layer of mesoporous polymer covers the layer of nonporous polymer. In some embodiments, the outer shell comprises a layer of nonporous silicon dioxide and a layer of mesoporous titanium dioxide. In some of these embodiments, the layer of mesoporous titanium dioxide covers the layer of nonporous silicon dioxide. In some embodiments, the outer shell comprises a layer of nonporous titanium dioxide and a layer ofmesoporous silicon dioxide. In some of these embodiments, the layer of mesoporous silicon dioxide covers the layer of nonporous titanium dioxide. In some embodiments, the outer shell comprises a layer of nonporous polymer and a layer of mesoporous silicon dioxide. In some of these embodiments, the layer of mesoporous silicon dioxide covers the layer of nonporous polymer. In some embodiments, the outer shell comprises a layer of nonporous silicon dioxide and a layer of mesoporous polymer. In some of these embodiments, the layer of mesoporous polymer covers the layer of nonporous silicon dioxide. In some embodiments, the outer shell comprises a layer of nonporous polymer and a layer of mesoporous titanium dioxide. In some of these embodiments, the layer of mesoporous titanium dioxide covers the layer of nonporous polymer. In some embodiments, the outer shell comprises a layer of nonporous titanium dioxide and a layer of mesoporous polymer. In some of these embodiments, the layer of mesoporous polymer covers the layer of nonporous titanium dioxide.

[0065] In some embodiments, the outer shell contains a coating. In some embodiments, the outer shell contains functional groups. In some embodiments, the functional group is attached to the outer shell. In some embodiments, the functional group is covalently attached to the outer shell. In some embodiments, the functional group is attached to the outer shell non-covalently. In some embodiments, the functional group is capable of binding directly to a target molecule, such as a nucleic acid, a protein, a peptide, a carbohydrate, a lipid, or an organic molecule. In certain embodiments, the functional group is capable of binding to a molecular probe, such as a nucleic acid probe or a protein probe. In some of these latter embodiments, the molecular probe is capable, in turn, of binding to a target molecule, such as a nucleic acid, a protein, a peptide, a carbohydrate, or a lipid. In various embodiments, the functional group is carboxyl, hydroxyl, epoxy, carbonyl, aldehyde, amine, maleimide, N-hydroxysuccinimide, carbodiimide, anhydride, hydrazide, polyethylene glycol, azide, nitrile, sulfhydryl, thiocyanate, phosphate, borono, thioester, cysteine, disulfide, alkyl and acyl halide, glutathione, maltose, isocyanate, sulfonyl chloride, tosylate ester, carbonate, arylating agent, imidoester, fluorophenyl ester, or Schiff base. In some embodiments, the functional group can be carboxyl, hydroxyl, epoxy, carbonyl, aldehyde, amine, maleimide, N-hydroxysuccinimide, carbodiimide, anhydride, hydrazide, or biotin. In some embodiments, the magnetic particle comprises a plurality of functional group species. In some embodiments, each of the plurality of functional groups is attached to the outer shell. In various embodiments, the functional group lead to the creation of surface charge of the magnetic nanoparticle. In some embodiments, the surface charge of the magnetic nanoparticle is positive. In some embodiments, the surface charge of the magnetic nanoparticle is negative. In some embodiments, the surface charge of the magnetic nanoparticle can be tuned by changing the pH of the solution.

[0066] In some embodiments, the bead has a maximum diameter of less than 1 pm, such as less than 900 nm, less than 800 nm, less than 700 nm, less than 600 nm, less than 500 nm, less than 400 nm, less than 300 nm, or less than 200 nm. In various embodiments, the magnetic nanoparticle has a maximum diameter of 100 nm to 1000 nm, such as 100 nm to 900 nm, 100 nm to 800 nm, 100 nm to 700 nm, 100 nm to 600 nm, 100 nm to 500 nm, 100 nm to 400 nm, 100 nm to 300 nm, 100 nm to 200 nm, 200 nm to 1000 nm, 200 nm to 900 nm, 200 nm to 800 nm, 200 nm to 700 nm, 200 nm to 600 nm, 200 nm to 500 nm, 200 nm to 400 nm, 200 nm to 300 nm, 300 nm to 1000 nm, 300 nm to 900 nm, 300 nm to 800 nm, 300 nm to 700 nm, 300 nm to 600 nm, 300 nm to 500 nm, 300 nm to 400 nm, 400 nm to 1000 nm, 400 nm to 900 nm, 400 nm to 800 nm, 400 nm to 700 nm, 400 nm to 600 nm, 400 nm to 500 nm, 500 nm to 1000 nm, 500 nm to 900 nm, 500 nm to 800 nm, 500 nm to 700 nm, 500 nm to 600 nm, 600 nm to 1000 nm, 600 nm to 900 nm, 600 nm to 800 nm, 600 nm to 700 nm, 700 nm to 1000 nm, 700 nm to 900 nm, 700 nm to 800 nm, 800 nm to 1000 nm, 800 nm to 900 nm, or 900 nm to 1000 nm. In certain embodiments, the magnetic core has a maximum diameter of about 900 nm. In certain embodiments, the magnetic core has a maximum diameter of about 800 nm. In certain embodiments, the magnetic core has a maximum diameter of about 700 nm. In certain embodiments, the magnetic core has a maximum diameter of about 600 nm. In certain embodiments, the magnetic core has a maximum diameter of about 500 nm. In certain embodiments, the magnetic core has a maximum diameter of about 400 nm. In certain embodiments, the magnetic core has a maximum diameter of about 300 nm. In certain embodiments, the magnetic core has a maximum diameter of about 200 nm. The bead diameter may depend on the sample assayed requiring smaller or larger beads. The solid support may be of a specific size diameter to allow for the selective binding of non-canonical fragments. The solid support may be modified with various functional groups such as carboxyl, hydroxyl, amino, etc. to promote nucleic acid isolation.

[0067] In some embodiments, the magnetic core has a maximum diameter of less than 1 pm, such as less than 800 nm, less than 700 nm, less than 600 nm, less than 500 nm, less than 400 nm, less than 300 nm, or less than 200 nm. In various embodiments, the magnetic core has a maximum diameter of 100 nm to 800 nm, such as 100 nm to 700 nm, 100 nm to 600 nm, 100 nm to 500 nm, 100 nm to 400 nm, 100 nm to 300 nm, 100 nm to 200 nm, 200 nm to 800 nm, 200 nm to 700 nm, 200 nm to 600 nm, 200 nm to 500 nm, 200 nm to 400 nm, 200 nm to 300 nm, 300 nm to 800 nm, 300 nm to 700 nm, 300 nm to 600 nm, 300 nm to 500 nm, 300 nm to 400 nm, 400 nm to 800 nm, 400 nm to 700 nm, 400 nm to 600 nm, 400 nm to 500 nm, 500 nm to 800 nm, 500 nm to 700 nm, 500 nm to 600 nm, 600 nm to 800 nm, 600 nm to 700 nm, or 700 nm to 800 nm. In certain embodiments, the magnetic core has a maximum diameter of about 700nm. In certain embodiments, the magnetic core has a maximum diameter of about 600 nm. In certain embodiments, the magnetic core has a maximum diameter of about 500 nm. In certain embodiments, the magnetic core has a maximum diameter of about 450 nm. In certain embodiments, the magnetic core has a maximum diameter of about 400 nm. In certain embodiments, the magnetic core has a maximum diameter of about 350 nm. In certain embodiments, the magnetic core has a maximum diameter of about 300 nm. In certain embodiments, the magnetic core has a maximum diameter of about 250 nm. In certain embodiments, the magnetic core has a maximum diameter of about 200 nm.

[0068] A bead may be a single bead or may be among a plurality of beads. The plurality of beads may comprise at least 1,000 wells. There may be 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 1000, 1500, 2000, 3000, 4000, 5000, 10,000, 100,000, 1,000,000 or more than 1,000,000 wells in a plurality of beads.

[0069] In some embodiments, the extraction of NAs utilizes a lysis buffer. In some embodiments, the extraction of cfNAs utilizes a lysis buffer. In some embodiments, the lysis buffer comprises a chaotropic agent. The chaotropic agent can be any chaotropic agent. Nonlimiting examples of chaotropic agents include guanidinium -based solutions (e.g., guanidinium hydrochloride, guanidinium chloride, guanidinium thiocyanate, guanidinium isothiocyanate), urea-based solutions (e.g., urea, thiourea), lithium-based solutions (e.g., lithium perchlorate, lithium acetate), propylene glycol, phenol, and DMSO. In some embodiments, the chaotropic agent is a salt. In some embodiments, the chaotropic agent is a guanidinium salt. In some embodiments, the guanidinium salt is guanidinium isothiocyanate. In some embodiments, the concentration of the chaotropic agent is about 0.40 M to about 0.20 M. In some embodiments, the concentration of the chaotropic agent is about 0.35 M to about 0.25 M. In some embodiments, the concentration of the chaotropic agent is about 0.30 M to about 0.25 M. In some embodiments, the concentration of the chaotropic agent is about 0.25 M. In some embodiments, the concentration of the chaotropic agent is about 0.26 M. In some embodiments, the lysis buffer contains an enzyme. In some embodiments the enzyme is a protease (e.g., proteolytic enzyme). In some embodiments, the protease is proteinase K. In some embodiments, the amount of proteinase K used in a reaction is no more than about 3 %. In some embodiments, the amount of proteinase K used in a reaction is no less than about 1 %. In some embodiments, the amount of proteinase K used in a reaction is about 3 % to about 1 %. In some embodiments, the amount of proteinase K used in a reaction is about 2 % to about 1 %. In some embodiments, the amount of proteinase K used in a reaction is about 1.75 % to about 1.25 %. In some embodiments, the amount of proteinase K used in a reaction is about 1.75 % to about 1.50 %. In some embodiments, the amount of proteinase K used in a reaction is about 1.7 % to about 1.6 %.In some embodiments, the lysis buffer has a pH from about 6 to about 9. In some embodiments, the lysis buffer has a pH no more than 9. In some embodiments, the lysis buffer has a pH no less than 6. In some embodiments, lysis buffer has a pH of about 8. In some embodiments, the lysis buffer has a pH of 6.5 or less or 6.0 or less. In some embodiments, lysis buffer has a pH of 8. In some embodiments, the lysis buffer has a pH of between 6.0 and 8.5, between 6.0 and 8.0, between 6.0 and 7.5, between 6.0 and 7.0, or between 6.0 and 6.5. In some embodiments, the lysis buffer incubates with the sample at a temperature higher than room temperature. In some embodiments, the lysis buffer incubates with the sample at a temperature no higher than 70°C. In some embodiments, the lysis buffer incubates with the sample at a temperature no lower than 50°C. In some embodiments, the lysis buffer incubates with the sample at a temperature from about 70°C to about 50°C. In some embodiments, the lysis buffer incubates with the sample at a temperature from about 65 °C to about 55 °C. In some embodiments, the lysis buffer incubates with the sample at a temperature from about 60°C to about 55°C. In some embodiments, the lysis buffer incubates with the sample at a temperature of about 58°C. In some embodiments, the lysis buffer incubates with the sample for no more than 60 minutes. In some embodiments, the lysis buffer incubates with the sample for no less than 15 minutes. In some embodiments, the lysis buffer incubates with the sample for about 60 minutes to about 15 minutes. In some embodiments, the lysis buffer incubates with the sample for about 40 minutes to about 20 minutes. In some embodiments, the lysis buffer incubates with the sample for about 35 minutes to about 25 minutes. In some embodiments, the lysis buffer incubates with the sample for about 30 minutes.

[0070] In some embodiments, the extraction of NAs utilizes a binding buffer. In some embodiments, the extraction of cfNAs utilizes a binding buffer. In some embodiments, the binding buffer comprises a chaotropic agent. The chaotropic agent can be any chaotropic agent. Non-limiting examples of chaotropic agents include guanidinium-based solutions (e.g., guanidinium hydrochloride, guanidinium chloride, guanidinium thiocyanate, guanidinium isothiocyanate), urea-based solutions (e.g., urea, thiourea), lithium-based solutions (e.g., lithium perchlorate, lithium acetate), propylene glycol, phenol, and DMSO. In some embodiments, the chaotropic agent is a salt. In some embodiments, the chaotropic agent is a guanidinium salt. In some embodiments, the guanidinium salt is guanidinium isothiocyanate. In some embodiments, the concentration of the chaotropic agent is about 2.5 M to about 1.5 M. In some embodiments, the concentration of the chaotropic agent is about 2 M to about 1.5 M. In some embodiments, the concentration of the chaotropic agent is about 1.8 M. In some embodiments, the binding buffer has a pH of 6.5 or less or 6.0 or less. In some embodiments, lysis buffer has a pH of 8. In some embodiments, the lysis buffer has a pH of between 6.0 and 8.5, between 6.0 and 8.0,between 6.0 and 7.5, between 6.0 and 7.0, or between 6.0 and 6.5. In some embodiments, the binding buffer comprises an alcohol. The alcohol can be any alcohol, such as ethyl alcohol or isopropyl alcohol. In some embodiments, the alcohol is isopropyl alcohol. In some embodiments, the concentration of alcohol mixed with the sample is no more than about 15 %, 14%, 13%, 12%, 11%, 10%, 9.5%, 9%, 8.5%, 8%, 7.5%, 7%, 6.5%, 6%, 5.5%, 5%, 4.5%, 4%, 3.5%, 3%, 2.5%, 2%, 1.5% or 1%, or any range between these values. In some embodiments, the concentration of alcohol mixed with the sample is no less than about 2 %, 2.5%, 3%, or 3.5%. In some embodiments, the concentration of alcohol mixed with the sample is about 15 % to about 2 %. In some embodiments, the concentration of alcohol mixed with the sample is about 11 % to about 3.5 %. In some embodiments, the concentration of alcohol mixed with the sample is about 9 % to about 6 %. In some embodiments, the concentration of alcohol mixed with the sample is about 8 % to about 7 %. In some embodiments, the concentration of alcohol mixed with the sample is about 7.5 % to about 7 %. In some embodiments, the concentration of alcohol mixed with the sample is about 7.25 %. In some embodiments, the concentration of alcohol mixed with the sample is about 7.3 %. In some embodiments, the binding buffer comprises a detergent. The detergent can be any suitable detergent used to solubilize biological samples. In some embodiments, the detergent is an ionic detergent (e.g. an anionic or cationic detergent). Non-limiting examples of ionic detergents include dodecylsulfide salts (e.g. sodium dodecylsulfide or SDS), bile acid salts (e.g. Sodium cholate and sodium deoxy cholate), and quaternary ammonium detergents (e.g. cetyltrimethylammonium bromide or CTAB). In some embodiments, the detergent is a nonionic detergent. Non-limiting examples of classes of nonionic detergents include hydrophilic polyethylene oxide derivatives (e.g. Triton™ X-100, Triton™ X-I02, Triton™ X-l 14, Triton™ CG-110, Triton™ X-405, Triton™ X-165, Triton™ X-45, Triton™ N-57, Triton™ N-60), lipid-like nonionic detergents (e.g. n-Dodecyl-beta- Maltoside or DDM), steroidal nonionic detergents (e.g. digitonin), nonionic polyoxyethylene detergents (e.g. Tween®-20, Tween®40, Tween®- 60, Tween®-80, Tween®65, Tween®-85, Tagat TO, Cremophore RH 40, Cremophore EL, Alpha-tocopherol TGPS, Brij®-96, Brij®-S20, Brij®-S100, Brij®-35, Brij®-58, Brij®-020, Brij®-L23, Brij®-S10, Brij®-010, Brij®-C10, Brij®-93, Brij®-L4, SP Brij® C2 MBAL-SO-(SG), and SP Brij® S2 MBAL), and nonionic ethoxylated nonylphenol detergents (e.g. NP-40). In some embodiments the nonionic detergent is a hydrophilic polyethylene oxide derivative. In some embodiments, the nonionic detergent is a lipid-like nonionic detergent. In some embodiments, the nonionic detergent is a steroidal nonionic detergent. In some embodiments, the nonionic detergent is a polysorbate-type nonionic detergent. In some embodiments, the nonionic detergent is a nonionic polyoxyethylene detergent. In some embodiments, the nonionic detergent is an ethoxylated nonylphenoldetergent (e.g. NP-40). In some embodiments, the concentration of detergent mixed with the sample is no more than about 6 %. In some embodiments, the concentration of detergent mixed with the sample is no less than about 2 %. In some embodiments, the concentration of detergent mixed with the sample is about 6 % to about 2 %. In some embodiments, the concentration of detergent mixed with the sample is about 5 % to about 3 %. In some embodiments, the concentration of detergent mixed with the sample is about 4 % to about 3 %. In some embodiments, the concentration of detergent mixed with the sample is about 3.5 % to about 3 %. In some embodiments, the concentration of detergent mixed with the sample is about 3.25 %. In some embodiments, the concentration of detergent mixed with the sample is about 3.3 %. In some embodiments, the binding buffer has a pH from about 6 to about 9. In some embodiments, the binding buffer has a pH from about 6 to about 8.5. In some embodiments, the binding buffer has a pH of about 8. In some embodiments, the binding buffer has a pH of 7.8. In some embodiments, the binding buffer incubates with the sample at a temperature no higher than about 25°C. In some embodiments, the binding buffer incubates with the sample at a temperature no lower than 15°C. In some embodiments, the binding buffer incubates with the sample at a temperature from about 25°C to about 15°C. In some embodiments, the binding buffer incubates with the sample at a temperature from about 22°C to about 18°C. In some embodiments, the binding buffer incubates with the sample at a temperature of about 20°C. In some embodiments, the binding buffer incubates with the sample at room temperature. In some embodiments, the binding buffer incubates with the sample for no more than 60 minutes. In some embodiments, the binding buffer incubates with the sample for no less than 15 minutes. In some embodiments, the binding buffer incubates with the sample for about 60 minutes to about 15 minutes. In some embodiments, the binding buffer incubates with the sample for about 40 minutes to about 20 minutes. In some embodiments, the binding buffer incubates with the sample for about 35 minutes to about 25 minutes. In some embodiments, the binding buffer incubates with the sample for about 30 minutes. In some embodiments, the binding buffer incubates with the sample undisturbed. In some embodiments, the binding buffer incubates with the sample with disruption. In some embodiments, the disruption is shaking. In some embodiments, the disruption is on a tube rotator.

[0071] In some embodiments, cfNA or NA not bound to the anionic solid surface is removed. In some embodiments, cfNA not bound to the anionic solid surface is removed. In some embodiments, the unbound cfNA or NA is removed with a wash buffer comprising a wash operation. In some embodiments, the unbound cfNA or NA is removed with a wash buffer comprising a wash operation. In some embodiments, more than one wash operation is performed. In some embodiments, more than one wash buffer is used. In some embodiments, theextraction of cfNAs or Nas utilizes a wash buffer. In some embodiments, the extraction of cfNAs utilizes a wash buffer. In some embodiments, the extraction of cfNAs or NAs utilizes more than 1 wash buffer. In some embodiments, the extraction of cfNAs or Nas utilizes two different wash buffers. In some embodiments, the first wash buffer comprises a chaotropic agent. The chaotropic agent can be any chaotropic agent. Non-limiting examples of chaotropic agents include guanidinium-based solutions (e.g., guanidinium hydrochloride, guanidinium chloride, guanidinium thiocyanate, guanidinium isothiocyanate), urea-based solutions (e.g., urea, thiourea), lithium-based solutions (e.g., lithium perchlorate, lithium acetate), propylene glycol, phenol, and DMSO. In some embodiments, the chaotropic agent is a salt. In some embodiments, the chaotropic agent is a guanidinium salt. In some embodiments, the guanidinium salt is guanidinium isothiocyanate. In some embodiments, the concentration of the chaotropic agent is about 4M (molar), about 3.75M, about 3.5M, about 3.25M, about 3.0 M, about 2.75M, about 2.5M, about 2.0M, about 1.75M, about 1.5M, about 1.25M, about 1 M, about 0.75M, about 0.5 M, or about 0.25M, or any range between these values. In some embodiments, the concentration of the chaotropic agent is about 3.5 M to about 1.5 M. In some embodiments, the concentration of the chaotropic agent is about 3 M to about 2 M. In some embodiments, the concentration of the chaotropic agent is about 2.5 M. In some embodiments, the first wash buffer comprises an alcohol. The alcohol can be any alcohol, such as ethyl alcohol or isopropyl alcohol. In some embodiments, the alcohol is ethyl alcohol. In some embodiments, the concentration of alcohol mixed with the sample is no more than about 30 %, 25%, 20%, 15%, 10%, 5%, or 1%, or any range between these values. In some embodiments, the concentration of alcohol mixed with the sample is no less than about 5 %. In some embodiments, the concentration of alcohol mixed with the sample is about 30 % to about 5 %. In some embodiments, the concentration of alcohol mixed with the sample is about 25 % to about 5 %. In some embodiments, the concentration of alcohol mixed with the sample is about 20 % to about 10 %. In some embodiments, the concentration of alcohol mixed with the sample is about 16 % to about 14 %. In some embodiments, the concentration of alcohol mixed with the sample is about 15 %. In some embodiments, the first wash buffer comprises a detergent. The detergent can be any suitable detergent used to solubilize biological samples. In some embodiments, the detergent is an ionic detergent (e.g. an anionic or cationic detergent). Non-limiting examples of ionic detergents include dodecylsulfide salts (e.g. sodium dodecylsulfide or SDS), bile acid salts (e.g. Sodium cholate and sodium deoxy cholate), and quaternary ammonium detergents (e.g. cetyltrimethylammonium bromide or CTAB). In some embodiments, the detergent is a nonionic detergent. Non-limiting examples of classes of nonionic detergents include hydrophilic polyethylene oxide derivatives (e.g. Triton™ X-100, Triton™ X-102, Triton™ X-l 14, Triton™CG-110, Triton™ X-405, Triton™ X-165, Triton™ X-45, Triton™ N-57, Triton™ N-60), lipid-like nonionic detergents (e.g. n-Dodecyl-beta-Maltoside or DDM), steroidal nonionic detergents (e.g. digitonin), nonionic polyoxyethylene detergents (e.g. Tween®-20, Tween®40, Tween®- 60, Tween®-80, Tween®65, Tween®-85, Tagat TO, Cremophore RH 40, Cremophore EL, Alpha-tocopherol TGPS, Brij®-96, Brij®-S20, Brij®-S100, Brij®-35, Brij®- 58, Brij®-020, Brij®-L23, Brij®-S10, Brij®-010, Brij®-C10, Brij®-93, Brij®-L4, SP Brij® C2 MBAL-SO-(SG), and SP Brij® S2 MB AL), and nonionic ethoxylated nonylphenol detergents (e.g. NP-40). In some embodiments the nonionic detergent is a hydrophilic polyethylene oxide derivative. In some embodiments, the nonionic detergent is a lipid-like nonionic detergent. In some embodiments, the nonionic detergent is a steroidal nonionic detergent. In some embodiments, the nonionic detergent is a polysorbate -type nonionic detergent. In some embodiments, the nonionic detergent is a nonionic polyoxyethylene detergent. In some embodiments, the nonionic detergent is an ethoxylated nonylphenol detergent (e.g. NP-40). In some embodiments, the concentration of detergent mixed with the sample is no more than about 5 %, 4.5%, 4%, 3.5%, 3%, 2.5%, 2%, 1.5%, 1%, or 0.5%, or any range between these values. In some embodiments, the concentration of detergent mixed with the sample is no less than about 1 %. In some embodiments, the concentration of detergent mixed with the sample is about 5 % to about 1 %. In some embodiments, the concentration of detergent mixed with the sample is about 4 % to about 2 %. In some embodiments, the concentration of detergent mixed with the sample is about 3.5 % to about 2.5 %. In some embodiments, the concentration of detergent mixed with the sample is about 3 %. In some embodiments, the first wash buffer has a pH from about 6 to about 9. In some embodiments, the first wash buffer has a pH from about 6 to about 8.5. In some embodiments, the first wash buffer has a pH of about 8, 7.75, 7.5. 7.25, 7.0, 6.75, 6.5, or 6, or any range between these values. In some embodiments, the first wash buffer has a pH of 8.1. In some embodiments, the first wash buffer has a pH of greater than or equal to about 6.5 or 6.0. In some embodiments, the first wash buffer is used to wash the sample once. In some embodiments, the second wash buffer comprises an alcohol. The alcohol can be any alcohol, such as ethyl alcohol or isopropyl alcohol. In some embodiments, the alcohol is ethyl alcohol. In some embodiments, the concentration of alcohol mixed with the sample is no more than about 90 %, 88%, 86%, 84%, 82%, 80%, 78%, 76%, 74%, 72%, or 70%, or any range between these values. In some embodiments, the concentration of alcohol mixed with the sample is no less than about 70 %. In some embodiments, the concentration of alcohol mixed with the sample is about 90 % to about 70 %. In some embodiments, the concentration of alcohol mixed with the sample is about 85 % to about 75 %. In some embodiments, the concentration of alcohol mixed with the sample isabout 80 %. In some embodiments, the second wash buffer is used to wash the sample at least once. In some embodiments, the second wash buffer is used to wash the sample twice. In some embodiments, the second wash buffer has a pH from about 6 to about 9. In some embodiments, the second wash buffer has a pH of 6.0, 6.25, 6.5, 6.75, 7.0, 7.25, 7.5, 8.0, 8.25, 8.5, 8.75, or 9.0, or any range between these values. In some embodiments, the second wash buffer has a pH from about 6 to about 8.5. In some embodiments, the second wash buffer has a pH of about 8.

[0072] In some embodiments, the cfNA or NA bound the anionic solid surface are eluted. In some embodiments, the cfNA or NA bound to the anionic solid surface are eluted. In some embodiments, the cfNA or NA bound is eluted with an elution operation. In some embodiments, the cfNA or NA bound is eluted with an elution operation. In some embodiments, the elution operation utilizes an elution buffer. In some embodiments, the elution solution is basic. In some embodiments, the extraction of cfNAs or NAs utilizes an elution buffer. In some embodiments, the elution buffer comprises tris-base buffer. In some embodiments, the elution buffer has a pH from about 6 to about 9. In some embodiments, the elution buffer has a pH of 6.0, 6.25, 6.5, 6.75, 7.0, 7.25, 7.5, 8.0, 8.25, 8.5, 8.75, or 9.0, or any range between these values. In some embodiments, the elution buffer has a pH from about 6.5 to about 9. In some embodiments, the elution buffer has a pH of about 9. In some embodiments, the elution buffer has a pH of 9.

[0073] In some embodiments, the buffers used for NA extraction have a pH that is basic. In some embodiments, the buffers used for NA extraction have a pH that is slightly acidic. In some embodiments, the buffers used for NA extraction have a pH that is neutral. In some embodiments, the pH range of the buffers used for NA extraction have a pH from about 6 to about 9. In some embodiments, the pH of the buffers used for NA extraction is 6.0, 6.25, 6.5, 6.75, 7.0, 7.25, 7.5, 8.0, 8.25, 8.5, 8.75, or 9.0, or any range between these values. In some embodiments, all the buffers used for NA extraction have the same pH. In some embodiments, none of the buffers used for NA extraction have the same pH. In some embodiments, 1 or more buffers used for NA extraction have the same pH. Non-limiting examples of buffers that may be used in cfNA extraction include lysis buffer, binding buffer, wash buffer, and elution buffer.

[0074] In some embodiments, the eluted cfNA or NA fragments are analyzed. In some embodiments, the NA fragments are analyzed using a nucleic acid-based detection assay. In some embodiments, the eluted cfNA or NA fragments are analyzed. In some embodiments, the cfNA or NA fragments are analyzed using a nucleic acid-based detection assay. In some embodiments, the nucleic acid-based detection assay comprises qPCR, gel electrophoresis (including for e.g., Northern or Southern blot), immunochemistry, in situ hybridization such as fluorescent in situ hybridization (FISH), cytochemistry, or sequencing. In some embodiments, the sequencing technique comprises next generation sequencing. In some embodiments, themethods involve a hybridization assay such as Anorogenic qPCR (e.g., TaqMan™ or SYBR green), which involves a nucleic acid amplification reaction with a specific primer pair, and hybridization of the amplified nucleic acid probes comprising a detectable moiety or molecule that is specific to a predetermined nucleic acid sequence. In some embodiments, the electrophoresis is automated. In some embodiments, the electrophoresis utilizes a TapeStation system.

[0075] In some embodiments, the eluted cfNA fragments contain no less than 50 % non- canonical fragments. In some embodiments, the eluted cfNA fragments contain no less than 55 % non-canonical fragments. In some embodiments, the eluted cfNA fragments contain no less than 60 % non-canonical fragments. In some embodiments, the eluted cfNA fragments contain no less than 65 % non-canonical fragments. In some embodiments, the eluted cfNA fragments contain no less than 70 % non-canonical fragments. In some embodiments, the eluted cfNA fragments contain at least 70 % non-canonical fragments.

[0076] In some embodiments, the eluted NA fragments contain no less than 50 % non-canonical fragments. In some embodiments, the eluted NA fragments contain no less than 55 % non- canonical fragments. In some embodiments, the eluted NA fragments contain no less than 60 % non-canonical fragments. In some embodiments, the eluted NA fragments contain no less than 65 % non-canonical fragments. In some embodiments, the eluted NA fragments contain no less than 70 % non-canonical fragments. In some embodiments, the eluted NA fragments contain at least 70 % non-canonical fragments.

[0077] In some embodiments, the eluted cfNA fragments are analyzed. In some embodiments, the cfNA fragments are analyzed using a nucleic acid-based detection assay. In some embodiments, the eluted cfNA fragments are analyzed. In some embodiments, the cfNA fragments are analyzed using a nucleic acid-based detection assay. In some embodiments, the nucleic acid-based detection assay comprises qPCR, gel electrophoresis (including for e.g., Northern or Southern blot), immunochemistry, in situ hybridization such as Auorescent in situ hybridization (FISH), cytochemistry, or sequencing. In some embodiments, the sequencing technique comprises next generation sequencing. In some embodiments, the methods involve a hybridization assay such as Auorogenic qPCR (e.g., TaqManTM or SYBR green), which involves a nucleic acid amplification reaction with a specific primer pair, and hybridization of the amplified nucleic acid probes comprising a detectable moiety or molecule that is specific to a predetermined nucleic acid sequence. In some embodiments, the electrophoresis is automated. In some embodiments, the electrophoresis utilizes a TapeStation system.

[0078] In some embodiments, the cfNA fragments are analyzed to identify a disorder, a disease, a condition, or any combination thereof. In some embodiments, the cfNA fragments areanalyzed to identify more than one disorder, disease, condition, or any combination thereof. Non-limiting examples of conditions indicated by cfNA include cancer or absence thereof, colorectal cancer (e.g. Stage I, II, III, or IV colorectal cancer) or absence thereof, or advanced adenoma or absence thereof.

[0079] In some embodiments, the cfNA fragments are analyzed to identify a disorder, a disease, a condition, or any combination thereof. In some embodiments, the cfNA fragments are analyzed to identify more than one disorder, disease, condition, or any combination thereof. Non-limiting examples of conditions indicated by cfNA include cancer or absence thereof, colorectal cancer (e.g. Stage I, II, III, or IV colorectal cancer) or absence thereof, or advanced adenoma or absence thereof. In some embodiments, the cfNA fragments are analyzed to identify overabundance of a cell type (e.g. via identification of a sequence present in an overexpressed gene characteristic of the cell type). The overabundance can comprise pathological cells (e.g. cells attributed to colorectal cancer or advanced adenoma).

[0080] In some aspects, the present disclosure provides for a method of enriching cell-free nucleic acid (cfNA) fragments comprising active chromatin, comprising: (a) contacting a composition comprising the cfNA fragments in solution with an anionic solid surface in the presence of a chaotropic agent, (b) removing unbound cfNA not enriched for active chromatin from the anionic solid surface; and (c) obtaining cfNA bound to the anionic solid surface, thereby enriching the cfNA fragments comprising active chromatin, wherein the method does not involve the use of an biomolecule binding agent directed against the active chromatin. In some embodiments, the active chromatin does not comprise heterochromatin. In some embodiments, the active chromatin comprises at least part of a promotor, an insulator, a transcriptional start site, a DNase hypersensitive site, a DNAse-I hypersensitive site, a Pol II pausing site, a first exon, or an intron to exon boundary, a transcription factor binding site, or any combination thereof. In some embodiments, the active chromatin comprises chromatin comprising an H3K4mel modification, a H3K27ac modification, an H4K4me2 modification, an H3K4me3 modification, or any combination thereof. In some embodiments, the cfNA fragments comprising active chromatin are at least 1000 nucleotides in length, at least 400 nucleotides in length, or at least 300 nucleotides in length. In some embodiments, the solution is configured to favor capture of cfNA fragments of at least 1000 nucleotides in length, at least 400 nucleotides in length, or at least 300 nucleotides in length on the anionic solid surface. In some embodiments, a pH of the composition is less than about 6.5 or 6.0. In some embodiments, the solution comprises at least about 3.5% to about 11% alcohol. In some embodiments, the chaotropic agent comprises a guanidinium salt or the composition comprises between 1.5 M and 2 M of the guanidinium salt. In some embodiments, the method enriches the cfNA fragmentscomprising active chromatin by at least 7-fold compared to cfNA fragments of less than 300 nucleotides in length. In some embodiments, (b) further comprises washing the anionic solid surface with a wash solution. In some embodiments, the wash solution comprises less than or equal to 30%, 25%, 20%, 15%, 10%, or 5% alcohol. In some embodiments, the wash solution displays a pH of greater than or equal to about 6.5 or 6.0. In some embodiments, the wash solution comprises a nonionic surfactant. In some embodiments, the method further comprises eluting the cfNA fragments comprising active chromatin bound to the anionic solid surface. In some embodiments, the anionic solid surface is a surface of a bead or nanoparticle. In some embodiments, a particle size of the bead or nanoparticle is 200 nm to 600 nm. In some embodiments, the anionic solid surface comprises silicon dioxide (SiCh). In some embodiments, the bead or nanoparticle comprises a hydroxyl -derivatized surface layer and a ferric core. In some embodiments, the composition comprising the cfNA fragments in solution is plasma or interstitial fluid. In some embodiments, the plasma is prepared by low-speed centrifugation of whole blood to separate red blood cells from a first supernatant; transferring the first supernatant to a new consumable vessel, and high-speed centrifugation of the first supernatant to separate the plasma from white blood cells and plasma. In some embodiments, the low speed centrifugation comprises a relative centrifugal force (RCF) of equal to or less than about 300 x g. In some embodiments, the high speed centrifugation comprises an RCF of equal to or greater than 5000 x g. In some embodiments, the method further comprises digesting the plasma with a proteolytic enzyme. In some embodiments, the proteolytic enzyme is Proteinase K. In some embodiments, the method results in an enrichment of the cfNA comprising active chromatin of at least about 7- to 10-fold relative to cfNA not comprising active chromatin. In some embodiments, the cfNA fragments comprising active chromatin comprise cfDNA. In some embodiments, the method further comprises dissociating the enriched cfNA fragments comprising active chromatin from the solid surface. In some embodiments, the enriched cfNA fragments comprise an individual genomic region, further comprising contacting the enriched cfNA fragments with a first oligonucleotide bait that hybridizes to a first portion of the individual genomic region. In some embodiments, the first oligonucleotide bait is configured to hybridize a cfNA of the enriched cfNA fragments comprising an individual genomic region of greater than 200 or 210 nucleotides in length preferentially over a cfNA of the enriched cfNA fragments comprising an individual genomic region of less than 200 or 210 nucleotides in length. In some embodiments, the method further comprises contacting the enriched cfNA fragments with a second oligonucleotide bait that hybridizes to a second portion of the individual genomic region. In some embodiments, the second nucleotide bait is configured to hybridize to a cfNA of the enriched cfNA fragments comprising an individual genomic region ofless than 200 or 210 nucleotides in length and a cfNA of the enriched cfNA fragments comprising an individual genomic region of greater than 200 or 210 nucleotides in length. In some embodiments, the first genomic region and the second genomic region are overlapping. In some embodiments, the first genomic region and the second genomic region are nonoverlapping. In some embodiments, the genomic region comprises at least part of a promotor, a transcriptional start site, a DNAse I-hypersensitive site, a Pol II pausing site, an exon, a transcription factor binding site, an insulator, or an intron to exon boundary. In some embodiments, the method further comprises amplifying the first portion of the genomic region or the second portion of the genomic region. In some embodiments, the amplifying comprises an isothermal amplification method. In some embodiments, the amplifying comprises loop mediated isothermal amplification, nucleic acid sequence -based amplification, strand displacement amplification, or multiple displacement amplification. In some embodiments, the amplifying comprises polymerase chain reaction (PCR). In some embodiments, the first oligonucleotide bait or the second oligonucleotide bait is conjugated to an affinity tag. In some embodiments, the affinity tag is biotin. In some embodiments, the first oligonucleotide bait and the second oligonucleotide bait are conjugated to a solid surface. In some embodiments, the solid surface is a bead. In some embodiments, the solid surface is a planar surface. In some embodiments, the method further comprises detecting an amount of the cfNA that hybridizes with the first oligonucleotide bait or an amount of the cfNA that hybridizes with the second oligonucleotide bait by sequencing or fluorimetry. In some embodiments, the method further comprises detecting an amount of the cfNA that hybridizes with the first oligonucleotide bait or an amount of the cfNA that hybridizes with the second oligonucleotide bait by quantitative polymerase chain reaction (qPCR) or reverse transcriptase polymerase chain reaction (rtPCR). In some embodiments, the method further comprises identifying individual cfNA molecules within the enriched cfNA. In some embodiments, the method further comprises evaluating the individual cfNA molecules, wherein the evaluating comprises comparing an amount of the individual cfNA derived from a first genomic region with an additional amount of individual cfNA derived from a second genomic region. In some embodiments, the first genomic region and the second genomic region are non-overlapping. In some embodiments, the first genomic region and the second genomic region are non-contiguous. In some embodiments, the first genomic region is present in cfNA fragments of 200 or 210 nucleotides in length or less and in cfNA fragments of 200 or 210 nucleotides in length or more. In some embodiments, the second genomic region is preferentially present in cfNA fragments of 200 or 210 nucleotides in length or more. In some embodiments, the evaluating comprises sequencing the individual cfNA molecules. In some embodiments, the sequencing comprises next-generation sequencing orDNA nanoball sequencing. In some embodiments, the evaluating is performed within a droplet reaction environment. In some embodiments, the evaluating comprises quantitative reverse polymerase chain reaction (qPCR) or reverse transcriptase PCR (rtPCR), or any combination thereof. In some embodiments, the individual cfNA molecules comprise at least part of a gene associated with a pathological condition. In some embodiments, the individual cfNA molecules comprise at least part of a gene with overexpression in a cell type associated with inflammation. In some embodiments, the cell type associated with inflammation is a neutrophil. In some embodiments, the gene with overexpression in a cell type associated with inflammation comprises CXCR4, CXCR2, SELL / CD62L, or any combination thereof. In some embodiments, the method further comprises identifying individual cfNA molecules from the enriched cfNA fragments, wherein the individual cfNA molecules have a length greater than about 200 nucleotides, about 210 nucleotides, about 250 nucleotides, or about 300 nucleotides. In some embodiments, the method further comprises identifying individual cfNA molecules from the enriched cfNA fragments that are less than about 1000 nucleotides in length. In some embodiments, the identifying comprises next-generation sequencing or DNA nanoball sequencing. In some embodiments, the identifying is performed within a droplet reaction environment. In some embodiments, the identifying comprises quantitative reverse polymerase chain reaction (qPCR) or reverse transcriptase PCR (rtPCR), or any combination thereof. In some embodiments, the method further comprises evaluating the individual cfNA molecules identified against a reference sequence associated with a pathological condition or a cell type associated with inflammation. In some embodiments, the method further comprises evaluating the individual cfNA molecules identified against a reference sequence associated with a pathological condition. In some embodiments, the method further comprises evaluating the individual cfNA molecules identified against a reference locus (or gene) or a plurality of reference loci (or genes) associated with a pathological condition. In some embodiments, the pathological condition is a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma).Sample and subject

[0081] Methods described herein comprise processing a sample of nucleic acids from a subject. The term subject or patient can include human or non-human animals. Thus, the methods and described herein are applicable to both human and veterinary disease and animal models.Preferred subjects are "patients," e.g., living humans that are receiving medical care for a disease or condition. This includes persons with no defined illness who are being investigated for signsof pathology. Preferably the subject is a human, but in some cases the subject is a non-human mammal, such as a non-human primate (e.g., ape, monkey, chimpanzee), cat, dog, rabbit, goat, horse, cow, pig, rodent, mouse, SCID mouse, rat, guinea pig, or sheep. The subject may be male or female. In some cases, the subject may be an infant, child, adolescent, teenager or adult.

[0082] Methods described herein comprising processing a sample of nucleic acids from a subject suspected of, or having (e.g. having at least one symptom of) a colon neoplasm. In some embodiments, the colon neoplasm comprises colorectal cancer (e.g. class I, II, III, or IV colorectal cancer) or advanced adenoma. Methods described herein comprising processing a sample of nucleic acids from a subject suspected of, or having at least one symptom of, a colon neoplasm.

[0083] Methods described herein comprising processing a sample of nucleic acids from a subject of suspected having at least one symptom of a colon neoplasm comprising detecting from a blood sample for a plurality of genomic regions associated with the colon neoplasm. In some embodiments, the colon neoplasm comprises colorectal cancer or advanced adenoma.

[0084] The methods described herein comprising detecting from samples for a plurality of genomic regions associated with a colon neoplasm a relative abundance of nucleic acid fragments indicative of a first fragmentation pattern compared to nucleic acid fragments indicative of a second fragmentation pattern. In some embodiments, the samples may comprise blood, urine, saliva, synovial fluid, skin biopsies, muscle biopsies, nerve biopsies, cerebrospinal fluid (CSF), stool, tissue biopsies, nasal swabs, respiratory secretions, or tears. In some embodiments, the sample is a blood sample, which refers to whole blood or fractions thereof. In some embodiments, blood sample fractions comprise plasma, serum, platelet-rich plasma or DNA blood sample. In some cases, a plurality of genomic regions is associated with a colon neoplasm (e.g. colorectal cancer generally, a specific stage of colorectal cancer, or advanced adenoma). In some cases, the plurality of genomic regions associated with a colon neoplasm (e.g. colorectal cancer generally, a specific stage of colorectal cancer, or advanced adenoma) comprise transcription factor binding sites, RNAP II pausing sites, and DNAse I sensitive regions.

[0085] The methods described herein comprising obtaining samples from a subject suspected of having (e.g. having at least one symptom of) a colon neoplasm. In some embodiments, the samples are obtained from blood draw (venipuncture), fingerstick, heel stick, urine collection, saliva collection, swabs, tissue biopsy, fine needle aspiration, nasal swab, stool collection, lumbar puncture, bronchoscopy, or endoscopy. In some embodiments, blood sample are obtained by venipuncture, central line collection, or capillary collection.cfNA fragments

[0086] The methods disclosed herein may comprise obtaining cfNA fragments from a sample from a subject. In some aspects, the present disclosure provides for a method of enriching cell- free nucleic acids (cfNA) comprising active chromatin comprising a sequence of a genomic region. In some embodiments, the cfNA comprises cfDNA, cf-mtDNA (mitochondrial DNA), cfRNA, or any combination thereof. Non-limiting examples of cfRNA include miRNA, IncRNA, circRNA, piRNA, YRNA, and vtRNA. In some embodiments, the cfNAs are produced by cell death. In some embodiments, the cfNAs are produced by cleavage of nuclear DNA. In some embodiments, the cfNA produced from cleavage of nuclear DNA is canonical. In some embodiments, the canonical nuclear DNA is about 170 base pairs (bp). In some embodiments, the cfNA produced from cleavage of nuclear DNA is non-canonical. In some embodiments, the non-canonical nuclear DNA greater than 300 bp in length. In some embodiments, the cfNA originates from tumor cells. In some embodiments, the cfNA originates from lymphoid cells. In some embodiments, the cfNA originates from myeloid cells. In some embodiments, the cfNA originates from fetal cells. In some embodiments, the cfNA originates from microbial cells.

[0087] The methods disclosed herein may further comprise size selecting the cfNA fragments to obtain fragments. In some embodiments, the cfNA is between 10 and 21,000 nucleotides. In some embodiments, the cfNA is between 15 and 10,000 nucleotides. In some embodiments, the cfNA is canonical. A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 nucleotides. A canonical fragment may comprise about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 230, or more than 230 nucleotides. A canonical fragment may comprise about less than 230, 200, 150, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide(s). A canonical cfNA fragment may comprise less than 220, 205, 190, or 175 nucleotides. In some embodiments, the cfNA is non-canonical. A non-canonical cfNA fragment may comprise at least 185, 255, 270, or 310 nucleotides. A non-canonical cfNA fragment may comprise about, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more than 1000 nucleotides. A non-canonical cfNA fragment may comprise about 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, or less than 200 nucleotides. In some embodiments the cfNA is between 300 and 1,500 nucleotides. In some embodiments, the cfNA may comprise about 170, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, or more than 1500 nucleotides. In some embodiments, the cfNA may comprise about 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 250, 200, 170, or less than 170 nucleotides.

[0088] In some embodiments, the selected cfNA fragments are analyzed. In some embodiments, the cfNA fragments are analyzed using a nucleic acid-based detection assay. In someembodiments, the eluted cfNA fragments are analyzed. In some embodiments, the cfNA fragments are analyzed using a nucleic acid-based detection assay. In some embodiments, the nucleic acid-based detection assay comprises qPCR, gel electrophoresis (including for e.g., Northern or Southern blot), immunochemistry, in situ hybridization such as fluorescent in situ hybridization (FISH), cytochemistry, or sequencing. In some embodiments, the sequencing technique comprises next generation sequencing. In some embodiments, the methods involve a hybridization assay such as Anorogenic qPCR (e.g., TaqManTM or SYBR green), which involves a nucleic acid amplification reaction with a specific primer pair, and hybridization of the amplified nucleic acid probes comprising a detectable moiety or molecule that is specific to a predetermined nucleic acid sequence. In some embodiments, the electrophoresis is automated. In some embodiments, the electrophoresis utilizes a TapeStation system.

[0089] In some cases, the methods disclosed herein may further comprise performing a next generation sequencing (NGS) reaction (e.g. sequencing using reversible terminators, bridge amplification, DNA nanoballs, or any combination thereof) on the size selected cfNA fragments to obtain the sequences of a plurality of non-canonical cell-free nucleic acid (cfNA) fragments corresponding to plurality of genomic regions of the subject. Next generation sequencing (NGS) is applied in the field of genomics to enable rapid and cost-effective sequencing of large amounts of DNA or RNA, to analyze entire genomes or transcriptomes in a single experiment. It may apply any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing. NGS parallelization of the sequencing reactions generates hundreds of megabases to gigabases of nucleotide sequence reads in a single instrument run. This has enabled a drastic increase in available sequence data and fundamentally changed genome sequencing approaches in the biomedical sciences.

[0090] In some embodiments, NGS allows sequencing of entire genomes for studying genetic variations, mutations, and structural changes related to various diseases and traits. In some embodiments, NGS enables transcriptome analysis for studying gene expression patterns, alternative splicing events, and non-coding RNA molecules in various tissues and under different conditions. In some embodiments, NGS may be applied to investigate epigenetic modifications, such as DNA methylation and histone modifications, which play a critical role in gene regulation and disease development. In some embodiments, NGS may be applied to analyze complex microbial communities found in environmental samples, the human microbiome, or clinical samples. In some embodiments, NGS has been instrumental in identifying genomic alterations driving cancer development, enabling the development of personalized cancer therapies.

[0091] In some cases, the methods disclosed herein the size selecting comprises an electrophoretic separation procedure or an anionic capture procedure. The principle of electrophoretic separation is based on the fact that charged particles migrate when placed in an electric field. Electrophoretic separation is used to separate charged particles, such as proteins or nucleic acids, based on their size and charge. Electric field is applied causing the charged particles move through a medium, such as a gel or a capillary, at different rates based on their size and charge-to-mass ratio. This results in the separation of the particles based on their mobility, with smaller, more negatively charged particles moving faster than larger, less charged ones. In some cases, electrophoretic separation procedure comprises gel electrophoresis, Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE), Isoelectric Focusing (IEF), or Capillary Electrophoresis.

[0092] Anion capture procedure is used to focus and separate molecules based on their charge and size. Anion capture can be used in protein analysis. In some cases, anion capture procedure is a variation of capillary electrophoresis (CE). The principle of anion capture procedure involves the use of a negatively charged chemical additive, called an anionic detergent or additive, to interact with and modify the charge of the target molecules. In this procedure, the capillary or separation column used for CE is filled with a buffer solution containing the anionic additive. In some embodiments, anion capture procedure may comprise sample preparation, sample injection, electrophoretic separation, anion capture, focusing and separation, detection or any combination.

[0093] In some cases, the methods described herein comprise contacting a composition comprising cfNA from the subject with an anionic solid surface to isolate cfNA fragments of non-canonical length from the composition comprising cfNA. In some embodiments, the methods described herein comprise eluting cfNA bound to the anionic solid surface. An anion solid surface refers to a solid material or substrate that has a net negative charge. In some embodiments, the negative charge is due to the presence of an excess of electrons or functional groups with negative charges on the surface of the material.

[0094] In some cases, the methods disclosed herein comprise detecting a relative abundance of nucleic acid fragments indicative of a first fragmentation pattern. In some embodiments, the first fragmentation pattern comprise a predominance of fragments less than about 500 bp, less than about 450 bp less than about 400 bp less than about 350 bp less than about 300 bp, less than about 250 bp less than about 200 bp, less than about 180 bp, less than about 160 bp, less than about 140 bp, less than about 120 bp, less than about 100 bp, less than about 80 bp less than about 60 bp less than about 50 bp less than about 40 bp or less than about 30 bp in length.

[0095] In some cases, the methods disclosed herein comprise detecting a relative abundance of nucleic acid fragments indicative of a first fragmentation pattern. In some embodiments, the first fragmentation pattern comprise a predominance of fragments greater than about 30 bp, greater than about 40 bp, great then about 50 bp, greater than about 60 bp, greater than about 80 bp, greater than about 100 bp, greater than about 120 bp, greater than about 150 bp, greater than about 200 bp, greater than about 250 bp, greater than about 300 bp, greater than about 350 bp, greater than about 400 bp, greater than about 450 bp, greater than about 500 bp, greater than about 600 bp, greater than about 700 bp, greater than about 800 bp, greater than about 900 bp, greater than about 1000 bp, greater than about 1200 bp, greater than about 1400 bp, greater than about 1600 bp, greater than about 1800 bp, or greater than about 2000 bp in length.

[0096] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%, 72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%, 92.5%, 95%, 97.5%, 100%, or any range between these values, of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 25% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, themethods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed hereincomprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about55%, or from about 45% to about 50% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the genes in cfDNA associated with a colon neoplasm listedin Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 5%, or from about 85% to about 90% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table 1A.

[0097] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermalamplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 900, at least about 950, at least about 1000, at least about 1050, at least about 1100, at least about 1200, or any range between these values of the genes in cfDNA associated with a colon neoplasm listed in Table 1A.Table 1A: Genes (provided as gene symbols) in cfDNA associated with a colon neoplasm(e.g. colorectal cancer, advanced adenoma) in cfDNA.

[0098] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%, 72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%, 92.5%, 95%, 97.5%, 100%, or any range between these values, of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25%to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the genes in cfDNA associated with a colon neoplasm listed inTable IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about40% to about 50%, or from about 40% to about 45% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the genes in cfDNA associated with a colon neoplasm listed in Table IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table IB.

[0099] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermal amplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, atleast about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 854, or any range between these values of the genes in cfDNA associated with a colon neoplasm listed in Table IB.Table IB: Genes (provided as gene symbols) in cfDNA associated with a colon neoplasm(e.g. colorectal cancer, advanced adenoma) in cfDNA

[0100] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in asubject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%, 72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%, 92.5%, 95%, 97.5%, 100%, or any range between these values, of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of the a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level about 25% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the genes in cfDNA associated with a colon neoplasm listed inTable 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g.colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the genes incfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C. In some embodiments, themethods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the genes in cfDNA associated with a colon neoplasm listed in Table 1C.

[0101] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermal amplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 196 or any range between these values of the genes in cfDNA associated with a colon neoplasm listed in Table 1A.Table 1C: Genes (provided as gene symbols) in cfDNA associated with a colon neoplasm(e.g. colorectal cancer, advanced adenoma) in cfDNA

[0102] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the loci in cfDNA associated with a colon neoplasm listed in Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% ofthe loci in cfDNA associated with a colon neoplasm listed in Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the loci in cfDNA associated with a colon neoplasm listed in Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%,72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%, 92.5%, 95%, 97.5%, 100%, or any range between these values, of the loci in cfDNA associated with a colon neoplasm listed in Table 2A. In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed hereincomprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm listed fromTable 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level offrom about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, themethods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm listed from Table 2A.

[0103] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermal amplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 900, at least about 950, at least about 1000, at least about 1050, at least about 1100, at least about 1200,, at least about 1250, at least about 1300, at least about 1350, at least about 1400, at least about 1450, at least about 1500, at least about 1550, at least about 1600, at least about 1650, at least about 1700, at least about 1750, at least about 1800, at least about 1900, at least about 1950, or at least about 1997, or any range between these values of the loci in cfDNA associated with a colon neoplasm listed from Table 2A.Table 2A. Loci corresponding to TFBSs, enhancers, gene bodies, and promoters associated with a colon neoplasm in cfDNA.

[0104] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the loci in cfDNA associated with a colon neoplasm listed in Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% of the loci in cfDNA associated with a colon neoplasm listed in Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the loci in cfDNA associated with a colon neoplasm listed in Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%, 72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%, 92.5%, 95%, 97.5%, 100%, or any range between these values, of the loci in cfDNA associated with a colon neoplasm listed in Table 2B. In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the lociin cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In someembodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In someembodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B.

[0105] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, orlevel of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about40% to about 50%, or from about 40% to about 45% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of aspecific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B. In some embodiments, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in the subject based on the presence, absence, or level of from about 95% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2B.

[0106] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermal amplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 876, or any range between these values of the loci in cfDNA associated with a colon neoplasm listed in Table 2B.Table 2B. Loci corresponding to TFBSs, enhancers, gene bodies, and promoters associated with a colon neoplasm in cfDNA.

[0107] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 5% of the loci in cfDNA associated with a colon neoplasm listed in Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 10% of the loci in cfDNA associated with a colon neoplasm listed in Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5% to about 25% of the loci in cfDNA associated with a colon neoplasm listed in Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of about 2.5%, 5%, 7.5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, 32.5%, 35%, 37.5%, 40%, 52.5%, 55%, 57.5%, 60%, 62.5%, 65%, 67.5%, 70%, 72.5%, 75%, 77.5%, 80%, 82.5%, 85%, 87.5%, 90%. 92.5%, 95%, 97.5%, 100%, or any range between these values, of the loci in cfDNA associated with a colon neoplasm listed in Table 2C. In some cases, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in the subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, fromabout 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of theloci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with an a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) (e.g. RA) or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C.

[0108] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments,the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about45%, or from about 35% to about 40% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the unique genes in cfDNAassociated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of fromabout 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of aspecific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C.

[0109] In some cases, the methods disclosed herein comprise performing a sequencing or an amplification reaction (e.g. a PCR, qPCR, rtPCR, or ddPCR reaction, an isothermal amplification, or any combination thereof) to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150, at least about 160, at least about 170, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 450, at least about 500, at least about 550, at least about 600, at least about 650, at least about 700, at least about 750, at least about 800, at least about 850, at least about 900, at least about 950, at least about 1000, at least about 1050, at least about 1100, at least about 1200, or any range between these values of the loci in cfDNA associated with a colon neoplasm listed in Table 2CTable 2C. Loci corresponding to TFBSs, enhancers, gene bodies, and promoters associated with a colon neoplasm in cfDNA.

[0110] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of aspecific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci incfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm in the subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm (e.g. colorectal cancer generally, a specific stage of colorectal cancer, or advanced adenoma) or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm in the subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detector identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C.

[0111] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about30% to about 35% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of theunique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, oradvanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. Insome embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Table 2C.

[0112] In some cases, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm in the subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence,absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%,from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identifypresence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2B.

[0113] In some cases, the methods disclosed herein comprise identifying presence or absence of a colon neoplasm in the subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the lociin cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identifypresence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on thepresence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2A and 2C.

[0114] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about25% to about 30% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advancedadenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about35% to about 40% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence,absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about60% to about 65% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectalcancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and IB.

[0115] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% toabout 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about 40% to about 50%, or from about 40% to about 45% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed fromTables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectalcancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the loci in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB.

[0116] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes incfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about25% to about 30% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 30% to about 100%, from about 30% to about 95%, from about 30% to about 90%, from about 30% to about 85%, from about 30% to about 80%, from about 30% to about 75%, from about 30% to about 70%, from about 30% to about 65%, from about 30% to about 60%, from about 30% to about 55%, from about 30% to about 50%, from about 30% to about 45%, from about 30% to about 40%, or from about 30% to about 35% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 35% to about 100%, from about 35% to about 95%, from about 35% to about 90%, from about 35% to about 85%, from about 35% to about 80%, from about 35% to about 75%, from about 35% to about 70%, from about 35% to about 65%, from about 35% to about 60%, from about 35% to about 55%, from about 35% to about 50%, from about 35% to about 45%, or from about 35% to about 40% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 40% to about 100%, from about 40% to about 95%, from about 40% to about 90%, from about 40% to about 85%, from about 40% to about 80%, from about 40% to about 75%, from about 40% to about 70%, from about 40% to about 65%, from about 40% to about 60%, from about 40% to about 55%, from about40% to about 50%, or from about 40% to about 45% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 45% to about 100%, from about 45% to about 95%, from about 45% to about 90%, from about 45% to about 85%, from about 45% to about 80%, from about 45% to about 75%, from about 45% to about 70%, from about 45% to about 65%, from about 45% to about 60%, from about 45% to about 55%, or from about 45% to about 50% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 50% to about 100%, from about 50% to about 95%, from about 50% to about 90%, from about 50% to about 85%, from about 50% to about 80%, from about 50% to about 75%, from about 50% to about 70%, from about 50% to about 65%, from about 50% to about 60%, or from about 50% to about 55% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 55% to about 100%, from about 55% to about 95%, from about 55% to about 90%, from about 55% to about 85%, from about 55% to about 80%, from about 55% to about 75%, from about 55% to about 70%, from about 55% to about 65%, or from about 55% to about 60% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 60% to about 100%, from about 60% to about 95%, from about 60% to about 90%, from about 60% to about 85%, from about 60% to about 80%, from about 60% to about 75%, from about 60% to about 70%, or from about 60% to about 65% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in asubject based on the presence, absence, or level of from about 65% to about 100%, from about 65% to about 95%, from about 65% to about 90%, from about 65% to about 85%, from about 65% to about 80%, from about 65% to about 75%, or from about 65% to about 70% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 70% to about 100%, from about 70% to about 95%, from about 70% to about 90%, from about 70% to about 85%, from about 70% to about 80%, or from about 70% to about 75% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 75% to about 100%, from about 75% to about 95%, from about 75% to about 90%, from about 75% to about 85%, or from about 75% to about 80% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 80% to about 100%, from about 80% to about 95%, from about 80% to about 90%, or from about 80% to about 85% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 85% to about 100%, from about 85% to about 95%, or from about 85% to about 90% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 90% to about 100%, or from about 90% to about 95% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB. In some embodiments, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectalcancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from about 95% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 1A and IB.

[0117] In some cases, the methods disclosed herein comprise performing a sequencing reaction to detect or identify presence or absence of a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in a subject based on the presence, absence, or level of from at least about 25% to about 100% of the unique genes in cfDNA associated with a colon neoplasm or absence thereof listed from Tables 2, 1A and 1C. In some embodiments, the methods disclosed herein comprise identifying presence or absence of the a colon neoplasm (e.g. colorectal cancer generally, colorectal cancer of a specific stage, or advanced adenoma) in the subject based on the presence, absence, or level of from about 25% to about 100%, from about 25% to about 95%, from about 25% to about 90%, from about 25% to about 85%, from about 25% to about 80%, from about 25% to about 75%, from about 25% to about 70%, from about 25% to about 65%, from about 25% to about 60%, from about 25% to about 55%, from about 25% to about 50%, from about 25% to about 45%, from about 25% to about 40%, from about 25% to about 35%, or from about 25% to about 30...

Claims

1. CLAIMSWHAT IS CLAIMED IS:

1. A method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising:(a) detecting a presence or an absence of a plurality of genomic regions associated with said colon neoplasm from cell-free nucleic acid (cfNA) fragments derived from active chromatin in a sample obtained from said subject to obtain presence or absence data for said plurality of genomic regions; and(b) applying a computer-implemented algorithm to said presence or said absence data, wherein said computer implemented algorithm has been trained on said presence or absence data for said plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer and advanced adenoma.

2. The method of claim 1, wherein said sample is a plasma, serum, peripheral blood, or whole blood sample.

3. The method of claim 1 or 2, wherein said sample is not a stool sample or derived from a stool sample.

4. The method of any one of claims 1-3, wherein said sample is a blood sample, further comprising obtaining said blood sample from said subject prior to (a) by venipuncture, central line collection, or capillary collection.

5. The method of any one of claims 1-4, further comprising obtaining said cfNA fragments from said sample from said subject prior to (a).

6. The method of any one of claims 1-5, wherein (a) further comprises: (i) contacting cfNA fragments derived from said sample obtained from said subject to an anionic surface to enrich said active chromatin, or (ii) performing a size selection to enrich said active chromatin.

7. The method of claim 6, further comprising performing a sequencing reaction on said cfNA fragments that have been enriched to obtain said obtain sequences of a plurality cfNA fragments derived from active chromatin.

8. The method of any one of claims 1-7, wherein said cfNA derived from active chromatin is about 200 base pairs (bp) or greater in length.

9. The method of any one of claims 1-8, wherein said cfNA fragments derived from active chromatin comprise cfDNA fragments.

10. The method of any one of claims 1-9, wherein said colon neoplasm is a colorectal cancer (CRC).

11. The method of any one of claims 1-9, wherein said colon neoplasm is an advanced adenoma.

12. The method of any one of claims 1-11, wherein said plurality of genomic regions associated with said colon neoplasm comprise transcription factor binding sites, RNAP II pausing sites, DNAse I sensitive regions, exons, promoters, or enhancers.

13. The method of any one of claims 1-12, comprising performing a size selection to enrich said cfNA fragments derived from said active chromatin from cfNA fragments derived from said sample obtained from said subject, wherein said size selection selects for cfNA fragments about 200 bp or greater in length.

14. The method of any one of claims 1-13, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said colorectal cancer and said subject not having said colorectal cancer.

15. The method of any one of claims 1-14, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said colorectal cancer and said subject not having said colorectal cancer with at least 93% diagnostic sensitivity.

16. The method of any one of claims 1-14, wherein said computer-implemented algorithm is capable of performing a classification between said subject having stage I, II, or III of said colorectal cancer and said subject not having a colorectal cancer with at least 94% diagnostic sensitivity.

17. The method of any one of claims 1-16, wherein said computer-implemented algorithm is capable of performing a classification between said subject having a stage IV of said colorectal cancer and said subject not having a colorectal cancer with at least 91% diagnostic sensitivity.

18. The method of any one of claims 1-14, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said advanced adenoma and said subject not having said advanced adenoma.

19. The method of any one of claims 1-18, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said advanced adenoma and said subject not having said advanced adenoma with at least 64% diagnostic sensitivity.

20. The method of any one of claims 1-18, further comprising detecting said colon neoplasm in said subject via said computer-implemented algorithm and administering a chemotherapeutic agent to said subject, performing a surgical resection on said subject, or performing radiotherapy on said subject.

21. The method of claim 20, comprising administering a chemotherapeutic agent to said subject, wherein said chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent.

22. The method of claim 20 or 21, comprising administering a chemotherapeutic agent to said subject, wherein said chemotherapeutic agent comprises an adjuvant chemotherapeutic agent.

23. The method of any one of claims 20-22, further comprising reporting an identification of said subject as having said colon neoplasm to a physician, a caregiver, or said subject, wherein said identification is performed at least in part on said computer implemented-algorithm.

24. The method of any one of claims 20-23, further comprising recommending administration of a chemotherapeutic agent to a physician of said subject, recommending surgical resection of a colon of said subject to a physician of said subject, or recommending radiotherapy on said subject to a physician of said subject.

25. The method of any one of claims 1-24, wherein said detecting said presence or absence of said plurality of genomic regions comprises performing a next-generation sequencing procedure.

26. The method of any one of claims 1-24, wherein said detecting said presence of absence of said plurality of genomic regions comprises performing a quantitative reverse polymerase chain reaction (qPCR), a reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof.

27. The method of any one of claims 1-26, further comprising detecting an abundance of said plurality of genomic regions associated with said colon neoplasm and applying said computer- implemented algorithm to said abundance of said plurality of genomic regions, wherein said computer-implemented algorithm has been trained on abundance data for said plurality of individuals having predetermined colon neoplasm statuses including said colorectal cancer and said advanced adenoma.

28. The method of any one of claims 1-27, wherein said computer-implemented algorithm comprises a logistic regression algorithm, a random forest algorithm, a lasso regression algorithm, a ridge regression algorithm, an elastic-net regression algorithm, a neural network algorithm, Naive Bayes algorithm, or any combination thereof.

29. The method of any one of claims 1-28, wherein said plurality of genomic regions comprise at least 10% of the genes listed in Table 1A, at least 10% of the genes listed in Table IB; or at least 10% of the genes listed in Table 1C.

30. The method of any one of claims 1-29, wherein said plurality of genomic regions are at least 5 in number.

31. The method of any one of claims 29 or 30, further comprising detecting a presence or absence of at least 5% of the loci listed in Table 2A, at least 5% of the loci listed in Table 2B, or at least 5% of the loci listed in Table 2C from said cfNA fragments and generating correspondingpresence or absence data, wherein said computer-implemented algorithm is trained on presence or absence data for said loci.

32. The method of any one of claims 29-30, wherein the method does not comprise obtaining presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters from said cfNA fragments, or the method does not comprise obtaining presence or absence data for any of the transcription factor binding sites (TFBSs), exons, enhancers, or promoters of the genes in Table 2D.

33. A method, comprising: detecting a presence or absence of: i) at least 10% of the unique genes listed in Table 1A; ii) at least 10% of the unique genes listed in Table IB; or iii) at least 10% of the unique genes in Table 1C from cfNA fragments obtained from a blood sample or a fraction thereof from a subject suspected of having a colon neoplasm to generate presence or absence data, wherein said method involves detecting fewer than about 10,000 genes but greater than 4 genes.

34. The method of claim 33, wherein said colon neoplasm comprises colorectal cancer.

35. The method of any one of claims 33 or 34, wherein said colon neoplasm comprises advanced adenoma.

36. The method of any one of claims 33-35, wherein said blood sample is a plasma, serum, peripheral blood, or whole blood sample.

37. The method of any one of claims 33-36, wherein said cfNA fragments are non-canonical or active chromatin fragments about 200 bp or greater in length.

38. The method of any one of claims 33-37, wherein said cfNA fragments are obtained by contacting said cfNA fragments obtained from said blood sample or said fraction thereof to an anionic surface or performing a size selection to enrich cfNA fragments derived from active chromatin.

39. The method of any one of claims 33-38, further comprising detecting a presence of at least 10% of the loci listed in Table 2A, 2B, or 2C from said cfNA.

40. The method of any one of claims 33-39, wherein the method does not comprise generating presence or absence data for KRAS, BMP3, NDRG, or ACTB transcription factor binding sites (TFBSs), exons, enhancers, or promoters; or the method does not comprise generating presence or absence data for any of the genes in Table 2D.

41. The method of any one of claims 33-40, wherein said cfNA fragments comprise cfDNA fragments.

42. The method of any one of claims 33-41, wherein said detecting comprises performing a next generation sequencing procedure.

43. The method of any one of claims 33-42, wherein said detecting comprises performing a quantitative reverse polymerase chain reaction (qPCR), reverse transcriptase polymerase chain reaction (rtPCR), a digital droplet polymerase chain reaction (ddPCR), an isothermal amplification reaction, or any combination thereof.

44. The method of any one of claims 33-43, wherein said plurality of genomic regions comprise transcription factor binding sites (TFBSs), exons, enhancers, promoters, RNAP II pausing sites, DNAse I sensitive regions, or any combination thereof .

45. The method of any one of claims 33-44, further comprising detecting a presence of at least 10% of the loci listed in Table 2A, Table 2B, or Table 2C from said cfNA and generating corresponding presence or absence data.

46. The method of any one of claims 33-45, wherein said method further comprises applying a computer-implemented algorithm to said presence or said absence data, wherein said computer implemented algorithm has been trained on said presence or absence data for said plurality of genomic regions or said loci from a plurality of individuals having predetermined colon neoplasm statuses including colorectal cancer and advanced adenoma.

47. The method of claim 46, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said colorectal cancer and said subject not having said colorectal cancer.

48. The method of any one of claims 46 or 47, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said colorectal cancer and said subject not having said colorectal cancer with at least 93% diagnostic sensitivity.

49. The method of any one of claims 46-48, wherein said computer-implemented algorithm is capable of performing a classification between said subject having stage I, II, or III of said colorectal cancer and said subject not having a colorectal cancer with at least 94% diagnostic sensitivity.

50. The method of any one of claims 46-49, wherein said computer-implemented algorithm is capable of performing a classification between said subject having a stage IV of said colorectal cancer and said subject not having a colorectal cancer with at least 91% diagnostic sensitivity.

51. The method of any one of claims 46-50, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said advanced adenoma and said subject not having said advanced adenoma.

52. The method of claim 51, wherein said computer-implemented algorithm is capable of performing a classification between said subject having said advanced adenoma and said subject not having said advanced adenoma with at least 64% diagnostic sensitivity.

53. The method of any one of claims 46-52, further comprising detecting said colorectal cancer in said subject via said computer-implemented algorithm and administering a chemotherapeutic agent to said subject, performing a surgical resection on said subject, or performing radiotherapy on said subject.

54. The method of claim 53, comprising administering a chemotherapeutic agent to said subject, wherein said chemotherapeutic agent comprises a neoadjuvant chemotherapeutic agent.

55. The method of claim 53 or 54, comprising administering a chemotherapeutic agent to said subject, wherein said chemotherapeutic agent comprises an adjuvant chemotherapeutic agent.

56. The method of any one of claims 53-55, further comprising reporting an identification of said subject as having said colon neoplasm to a physician, a caregiver, or said subject, wherein said identification is performed at least in part on said computer implemented-algorithm.

57. The method of any one of claims 53-56, further comprising recommending administration of a chemotherapeutic agent to a physician of said subject, recommending surgical resection of a colon of said subject to a physician of said subject, or recommending radiotherapy on said subject to a physician of said subject.

58. A method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising:(a) detecting a presence or an absence of a plurality of genomic regions associated with said colon neoplasm in cell-free nucleic acid (cfNA) fragments derived from a sample of said subject; and(b) determining said subject has said colon neoplasm with a diagnostic sensitivity of at least 93% based on said presence or said absence of said plurality of genomic regions.

59. A method of processing a sample of nucleic acids from a subject having or suspected of having an advanced adenoma, the method comprising:(a) detecting a presence or an absence of a plurality of genomic regions associated with said colon neoplasm in cell-free nucleic acid (cfNA) fragments derived from a sample of said subject; and(b) determining said subject has said advanced adenoma with a diagnostic sensitivity of at least 64% based on said presence or said absence of said plurality of genomic regions.

60. A method of processing a sample of nucleic acids from a subject having or suspected of having a colon neoplasm, the method comprising:(a) detecting a presence or an absence of a plurality of genomic regions associated with said colon neoplasm in cell-free nucleic acid (cfNA) fragments derived from a sample of said subject; and(b) determining said subject has said colon neoplasm with a diagnostic sensitivity of at least 60% based on said presence or said absence of said plurality of genomic regions, wherein said subject has an autoimmune disease.

61. The method of any one of claims 58-60, wherein said determining further comprises applying a computer-implemented algorithm to said presence or said absence of said plurality of genomic regions, wherein said computer implemented algorithm has been trained on presence or absence data for said plurality of genomic regions from a plurality of individuals having predetermined colon neoplasm statuses.

62. The method of any one of claims 58-61, wherein said sample is a plasma, serum, peripheral blood, or whole blood sample.

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