HERNANDEZ STEPHANI D (US)
KOTTWITZ DENISE (DE)
LEWIN JÖRN (DE)
STAUB UWE (DE)
WO2021122799A1 | 2021-06-24 | |||
WO2020225426A1 | 2020-11-12 | |||
WO2018140781A1 | 2018-08-02 |
US20180245157A1 | 2018-08-30 |
FARAHJ NASSAR ET AL: "Methylated circulating tumor DNA as a biomarker for colorectal cancer diagnosis, prognosis, and prediction", CLINICAL EPIGENETICS, BIOMED CENTRAL LTD, LONDON, UK, vol. 13, no. 1, 17 May 2021 (2021-05-17), pages 1 - 25, XP021290901, ISSN: 1868-7075, DOI: 10.1186/S13148-021-01095-5
MA ZHI YAO ET AL: "Methylated Septin 9 and Carcinoembryonic Antigen for Serological Diagnosis and Monitoring of Patients with Colorectal Cancer After Surgery", SCIENTIFIC REPORTS, vol. 9, no. 1, 17 July 2019 (2019-07-17), US, XP093118906, ISSN: 2045-2322, Retrieved from the Internet
BERGHEIM JULIA ET AL: "Potential of quantitativeSEPT9andSHOX2methylation in plasmatic circulating cell-free DNA as auxiliary staging parameter in colorectal cancer: a prospective observational cohort study", BRITISH JOURNAL OF CANCER, NATURE PUBLISHING GROUP UK, LONDON, vol. 118, no. 9, 3 April 2018 (2018-04-03), pages 1217 - 1228, XP036815831, ISSN: 0007-0920, [retrieved on 20180403], DOI: 10.1038/S41416-018-0035-8
HIDEKAZU KURAMOCHI ET AL: "Amphiregulin and Epiregulin mRNA expression in primary colorectal cancer and corresponding liver metastases", BMC CANCER, BIOMED CENTRAL, LONDON, GB, vol. 12, no. 1, 13 March 2012 (2012-03-13), pages 88, XP021123548, ISSN: 1471-2407, DOI: 10.1186/1471-2407-12-88
THE GREAT LAKES-NEW ENGLAND CLINICAL AND EPIDEMIOLOGY CENTER OF THE EARLY DETECTION RESEARCH NETWORK BRESALIER ET AL: "A circulating ligand for galectin-3 is a haptoglobin-related glycoprotein elevated in individuals with colon cancer", GASTROENTEROLOGY, ELSEVIER INC, US, vol. 127, no. 3, 1 September 2004 (2004-09-01), pages 741 - 748, XP005313960, ISSN: 0016-5085, DOI: 10.1053/J.GASTRO.2004.06.016
CLAIMS 1. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples from a subject, comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5- position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise carcinoembryonic antigen (CEA) and/or amphiregulin. 2. The method of claim 1, wherein the proliferative disease is a cancer. 3. The method of claim 1, wherein the proliferative disease is a colorectal cancer or a colorectal cell proliferative disease. 4. The method of claim 3, wherein the one or more methylated genomic DNA sequences associated with a proliferative disease is methylated Septin-9 (mSEPT9). 5. The method of claim 4, wherein mSEPT9 comprises one or more CpG dinucleotides within the sequence set forth in SEQ ID NO: 31. 6. The method of claim 5, wherein the synthetic DNA is generated using at least one nucleic acid molecule comprising a contiguous sequence at least 9 nucleotides in length that is complementary to, or hybridizes to, SEQ ID NO: 31. 7. The method of claim 6, wherein the nucleic acid molecule is a methylation-specific oligonucleotide. 8. The method of any one of claims 3-7, wherein the one or more methylated genomic DNA sequences associated with a proliferative disease is methylated ANKRD13B (mANKRD13B). 9. The method of claim 8, wherein mANKRD13B comprises one or more CpG dinucleotides within the sequence set forth in SEQ ID NO: 6 or 11. 10. The method of claim 9, wherein the synthetic DNA is generated using at least one nucleic acid molecule comprising a contiguous sequence at least 9 nucleotides in length that is complementary to, or hybridizes to, SEQ ID NO: 6 or 11. 11. The method of claim 10, wherein the nucleic acid molecule is a methylation-specific oligonucleotide. 12. The method of any one of claims 1-11, wherein synthetic DNA is generated by treating the genomic DNA with bisulfite to produce sulfonated DNA. 13. The method of any one of claims 1-12, wherein the one or more protein biomarkers comprise CEA. 14. The method of any one of claims 1-12, wherein the one or more protein biomarkers comprise amphiregulin. 15. The method of any one of claims 1-12, wherein the one or more protein biomarkers comprise CEA and amphiregulin. 16. The method of any one of claims 1-15, wherein the one or more protein biomarkers further comprise CYFRA21-1. 17. The method of any one of claims 1-16, wherein the one or more protein biomarkers further comprise a galectin-3 ligand. 18. The method of claim 17, wherein the galectin-3 ligand is haptoglobin. 19. The method of any one of claims 1-18, wherein detecting the presence or amount of the one or more protein biomarkers comprises contacting the one or more biological samples with an antibody specific for the one or more protein biomarkers, and detecting the antibody. 20. The method of any one of claims 1-18, wherein the presence or amount of the one or more protein biomarkers is detecting by western blot, enzyme-linked immunosorbent assay (ELISA), immunobead-based format, proximity extension assay (PEA) or mass- spectrometry. 21. The method of any one of claims 1-20, wherein the biological sample comprises genomic DNA from a circulating cancer cell. 22. The method of any one of claims 1-21, wherein the one or more biological samples is a blood sample, a serum sample, a plasma sample, a urine sample, a saliva sample, a stool sample, or a combination thereof. 23. The method of any one of claims 1-22, wherein the one or more biological samples is a blood sample, a serum sample, a plasma sample, or a combination thereof. 24. The method of any one of claims 1-23, wherein the one or more biological samples are the same biological sample. 25. The method of any one of claims 1-23, wherein the one or more biological samples are different biological samples. 26. The method of any one of claims 1-25, further comprising diagnosing the subject as having a proliferative disease. 27. The method of any one of claims 1-26, wherein the presence of one or more methylated genomic DNA sequences and one or more protein biomarkers is indicative of the presence of a proliferative disease in a subject, or indicative of the presence of a risk of a subject having a proliferative disease. 28. The method of any one of claims 1-27, wherein the method detects proliferative disease in a subject with a sensitivity of at least 0.65 and/or a specificity of at least 0.8. 29. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. 30. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising: (i) detecting DNA methylation within SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b) in the one or more biological samples, wherein cytosine unmethylated in the 5-position is converted to uracil or another base that does not hybridize to guanine, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. 31. The method of claim 29 or 30, wherein the biological sample is from a subject at risk or suspected of being at risk for having or developing colorectal cancer or a colorectal cell proliferative disease. 32. The method of any one of claims 29-31, wherein the one or more protein biomarkers comprise CEA. 33. The method of any one of claims 29-32, wherein the one or more protein biomarkers comprise amphiregulin. 34. The method of any one of claims 29-32, wherein the one or more protein biomarkers comprise CEA and amphiregulin. 35. The method of any one of claims 29-34, wherein the one or more protein biomarkers further comprise CYFRA21-1. 36. The method of any one of claims 29-35, wherein the one or more protein biomarkers further comprise a galectin-3 ligand. 37. The method of claim 36, wherein the galectin-3 ligand is haptoglobin. 38. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand. 39. The method of claim 38, wherein the one or more protein biomarkers comprise (i) CEA and the galectin-3 ligand, (ii) amphiregulin and the galectin-3 ligand, or (iii) CEA, amphiregulin and the galectin-3 ligand. 40. The method of claim 38 or 39, wherein the galectin-3 ligand is haptoglobin. 41. The method of claim 39 or 40, wherein the method detects colorectal cancer or a colorectal cell proliferative disease in a subject with a sensitivity of at least 0.7 and/or a specificity of at least 0.8. 42. The method of any one of claims 29-41, wherein detecting the presence or amount of the one or more protein biomarkers comprises contacting the one or more biological samples with an antibody specific for the one or more protein biomarkers, and detecting the antibody. 43. The method of any one of claims 29-41, wherein the presence or amount of the one or more protein biomarkers is detecting by western blot, enzyme-linked immunosorbent assay (ELISA), immunobead-based format, proximity extension assay (PEA) or mass- spectrometry. 44. The method of any one of claims 29-43, wherein the one or more biological samples is a blood sample, a serum sample, a plasma sample, a urine sample, a saliva sample, a stool sample, or a combination thereof. 45. The method of any one of claims 29-44, wherein the one or more biological samples is a blood sample, a serum sample, a plasma sample, or a combination thereof. 46. The method of any one of claims 29-45, wherein the method detects colorectal cancer or a colorectal cell proliferative disease in a subject with a sensitivity of at least 0.65 and/or a specificity of at least 0.8. 47. The method of any one of claims 1-46, wherein the one or more protein biomarkers are detected by a manual, semi-automated, or fully automated system. 48. The method of any one of claims 1-47, wherein the methylated genomic DNA is detected by a manual, semi-automated, or fully automated system. 49. The method of any one of claims 1-48, wherein the one or more protein biomarkers are detected by a monoplex or multiplex system. 50. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples from a subject, comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. 51. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. 52. A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising: (i) detecting DNA methylation within SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b) in the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. 53. A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. 54. A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma or serum samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma or serum samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more plasma or serum samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. 55. A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. 56. The method of claim 55, wherein the galectin-3 ligand is haptoglobin. 57. The method of any one of claims 54-56, wherein colorectal cancer or the colorectal cell proliferative disease is detected in the subject with a sensitivity of at least 0.65 and/or a specificity of at least 0.8. 58. A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. 59. A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma or serum samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma or serum samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. 60. A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand; and (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more plasma samples. 61. The method of claim 60, wherein the galectin-3 ligand is haptoglobin. 62. The method of any one of claims 53-61, further comprising performing a colonoscopy on the subject to confirm the presence of colorectal cancer or the colorectal cell proliferative disease. 63. The method of claim 62, further comprising treating the subject after confirmation of the presence of colorectal cancer or the colorectal cell proliferative disease in the subject. 64. The method of claim 63, wherein treating the subject comprises surgery, radiation therapy, chemotherapy, or immunotherapy. 65. A kit suitable for performing the method of any one of claims 1-54, comprising (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; and (iii) instructions for detecting methylation of genomic DNA in one or more biological samples in combination with instructions for detecting the one or more protein biomarkers, wherein the one or more protein biomarkers is CEA and/or amphiregulin in the one or more biological samples. 66. A kit suitable for performing the method of any one of claims 1-54, comprising (i) one or more reagents for detecting the one or more protein biomarkers, wherein the one or more protein biomarkers is CEA and/or amphiregulin; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more biological samples in combination with instructions for detecting methylated genomic DNA. 67. A kit suitable for performing the method of any one of claims 1-54, comprising (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers, wherein the one or more protein biomarkers is CEA and/or amphiregulin; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more biological samples. 68. The kit of any one of claims 65-67, wherein the instructions comprise steps for diagnosing, prognosing, or classifying colorectal cancer or a colorectal cell proliferative disease based on the detection of methylated genomic DNA and the one or more protein biomarkers. 69. The kit of any one of claims 65-68, wherein the one or more biological samples is a blood sample, a serum sample, a plasma sample, a urine sample, a saliva sample, or a stool sample. 70. The kit of any one of claims 65-69, wherein the one or more biological samples is a blood sample, a serum sample, or a plasma sample. 71. The kit of any one of claims 65-70, wherein the one or more biological samples is obtained from a subject at risk or suspected of being at risk for having or developing colorectal cancer or a colorectal cell proliferative disease. 72. The kit of any one of claims 65-71, wherein the one or more protein biomarkers comprises a galectin-3 ligand, optionally wherein the galectin-3 ligand is haptoglobin. |
rc = reverse complement; C to G or G to A means converted by bisulfite conversion of cytosines outside of CpG context into uracil and replaced by thymidine in subsequent amplification. Bis1 refers to the bisulfite converted forward strand (as recited in the SEQ ID of the respective genomic DNA) and bis2 refers to the bisulfite converted reverse complement strand of the forward strand (reverse complement of the SEQ ID of the respective genomic DNA), whereby the direction of the strand is defined by the direction of the genomic reference sequence as e.g., obtained from the genome build (GRCh38). Biological Samples The methods, assays and kits described herein are useful for detecting one or more methylated genomic DNA and one or more protein biomarkers in a biological sample obtained from a subject. Exemplary biological samples include, but are not limited to, plasma, urine, saliva, whole blood, dried blood spot, serum, dried serum spot, stool, and/or hair. In some embodiments, the biological sample is derived from blood. In some embodiments, the biological sample is serum. In some embodiments, the biological is plasma. In some embodiments, the biological sample is whole blood, serum or plasma. In some embodiments, a processed biological sample, e.g., blood plasma or serum, is frozen for transport and/or long-term storage. In some embodiments, the methods, assays and kits described herein detect one or more methylated genomic DNA and one or more protein biomarkers in one or more biological samples. In some embodiments, one or more methylated genomic DNA and one or more protein biomarkers are detected in different biological samples obtained from the same patient. For example, methylated genomic DNA may be detected in plasma and a protein biomarker is detected in stool, or vice versa. In some embodiments, one or more methylated genomic DNA and one or more protein biomarkers are detected in the same biological obtained from the same patient. In some embodiments, the biological sample is processed to allow for detecting of the target of interest, i.e., methylated genomic DNA or protein biomarker. In some embodiments, a biological sample is desialylated. Desialylation is a part of sialic acid metabolism, which removes the terminal sialic acid residue on glycans to modulate the structure and function of glycans, glycoproteins or glycolipids. In some embodiments, desialylation of a sample is needed to identify a target of interest, e.g., glycoform of haptoglobin as described herein. In some embodiments, a serum sample is desialylated. In some embodiments, a plasma sample is desialylated. In some embodiments, a blood sample is desialylated. In some embodiments, desialylating a sample comprises treating the sample with a mild acid. In some embodiments, desialylating a sample comprises treating the sample with a neuraminidase. In some embodiments, a biological sample is processed in a manner consistent with methods for detecting protein or DNA methylation. In some embodiments, a sample is processed to isolate the proteins for detection. Methods for isolating proteins are known to those of skill in the art. In some embodiments, a sample is processed to isolate genomic DNA for methylation detection. Methods for isolating genomic DNA are known to those of skill in the art. Subject Screening Eligibility In some aspects, the methods, assays and kits described herein are useful for screening a subject for a proliferative disease. A subject eligible for screening can be identified by a clinician. In some embodiments, a subject eligible for screening is based on criteria defined by the American Cancer Society for cancer generally or for colorectal cancer. Exemplary criteria for identifying a subject eligible for screening includes, but is not limited to: age, gender, proliferative disease status, treatment of proliferative disease status, family medical history, lifestyle, and weight. In some embodiments, a subject eligible for screening is suspected of having a proliferative disease. In some embodiments, a subject eligible for screening is suspected of being at risk for having a proliferative disease. In some embodiments, a subject eligible for screening has not been previously diagnosed with a proliferative disease. In some embodiments, a subject eligible for screening has been previously diagnosed with a proliferative disease but is suspected of having or being at risk for having a different proliferative disease. In some embodiments, a subject eligible for screening has not received treatment for a proliferative disease. In some embodiments, a subject eligible for screening has not been subject to surgical treatment for a proliferative disease. In some embodiments, a subject eligible for screening is suspected of having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening is suspected of having a pre-cancerous lesion (e.g., advanced adenoma). In some embodiments, a subject eligible for screening is suspected of being at risk for having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening is suspected of being at risk for having a pre-cancerous lesion (e.g., advanced adenoma). In some embodiments, a subject eligible for screening has not been previously diagnosed with colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening has not been previously diagnosed with a pre-cancerous lesion (e.g., advanced adenoma). In some embodiments, a subject eligible for screening has been previously diagnosed with a pre-cancerous lesion (e.g., advanced adenoma). In some embodiments, a subject eligible for screening has been previously diagnosed with a proliferative disease but is suspected of having or being at risk for having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening has not received treatment for colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening is suspected of having a recurrence of colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening has not been subject to surgical treatment for colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening has not received a colonoscopy. In some embodiments, a subject eligible for screening has not receive a recent colonoscopy for diagnosing colorectal cancer or a colorectal cell proliferative disease. In some embodiments, a subject eligible for screening for a proliferative disease is at least 45 years of age. In some embodiments, a subject eligible for screening for a proliferative disease is 45-85 years of age. In some embodiments, a subject eligible for screening for a proliferative disease is 45-75 years of age. In some embodiments, a subject eligible for screening for colorectal cancer or a colorectal cell proliferative disease is at least 45 years of age. In some embodiments, a subject eligible for screening for colorectal cancer or a colorectal cell proliferative disease is 45-85 years of age. In some embodiments, a subject eligible for screening for colorectal cancer or a colorectal cell proliferative disease is 45-75 years of age. In some embodiments, a subject eligible for screening exhibits at least one risk factor associated with a proliferative disease. In some embodiments, a subject eligible for screening exhibits at least one risk factor associated with colorectal cancer or a colorectal cell proliferative disease. Risk factors can include, but are not limited to, family history of cancer, obesity, alcohol consumption, exposure to chemicals, exposure to radiation, tobacco use, age, lack of physical activity, and poor diet. Discriminatory Ability In some embodiments, the methods, assays and kits described herein have discriminatory ability for detecting a proliferative disease in a subject. In some embodiments, the methods, assays and kits described herein having enhanced discriminatory ability for detecting a proliferative disease in a subject relative to a method, assay or kit that does not include detecting one or more protein biomarkers. In some embodiments, the methods, assays and kits described herein have discriminatory ability for detecting colorectal cancer or a colorectal cell proliferative disease in a subject. In some embodiments, the methods, assays and kits described herein having enhanced discriminatory ability for detecting colorectal cancer or a colorectal cell proliferative disease in a subject relative to a method, assay or kit that does not include detecting one or more protein biomarkers. The discriminatory ability of biomarkers, such as the presence of methylated genomic DNA and proteins associated with a proliferative disease, is an evaluation of whether the biomarker can accurately identify subjects with and without the proliferative disease. Failure of a biomarker to have sufficient discriminatory ability can lead to false negatives and false positives, each having detrimental impacts on a subject. Discriminatory ability is determined based on sensitivity, specificity and receiver-operating characteristics (ROC) probability curves. Sensitivity is the ability to detect a disease in patients in whom the disease is truly present (i.e., a true positive), and specificity is the ability to rule out the disease in patients whom the disease is truly absent (i.e., a true negative). To plot ROC probability curves, the false positive rate is plotted on the x-axis against the true positive rate on the y-axis. The area under the ROC curve (AUC, or AUROC) ranges from 0.5, indicating no power to separate cases from non-cases, to 1, indicating perfect discrimination. To be clinically meaningful, biomarkers should have an AUC value as close to 1 as possible. In some embodiments, the methods, assays and kits described herein have a pre- determined sensitivity and/or specificity for determining the presence or absence of colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the pre-determined sensitivity and/or specificity is determined by a state or country regulatory body. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.65 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.66 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.67 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.68 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.69 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.70 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.71 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.72 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.73 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.74 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.75 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.76 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.77 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.78 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.79 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.80 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.81 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.82 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.83 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.84 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.85 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.86 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.87 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.88 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.89 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.90 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.91 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.92 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.93 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.94 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.95 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.96 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.97 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.98 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.99 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of 1.00 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.80 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.81 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.82 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.83 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.84 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.85 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.86 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.87 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.88 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.89 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.90 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.91 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.92 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.93 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.94 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.95 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.96 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.97 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.98 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.99 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of 1.00 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.65 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.65 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.70 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.70 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.71 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.71 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.72 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.72 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.73 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.73 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.74 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.74 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.75 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect a proliferative disease with a sensitivity of at least 0.75 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.65 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.66 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.67 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.68 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.69 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.70 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.71 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.72 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.73 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.74 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.75 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.76 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.77 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.78 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.79 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.80 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.81 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.82 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.83 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.84 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.85 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.86 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.87 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.88 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.89 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.90 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.91 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.92 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.93 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.94 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.95 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.96 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.97 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.98 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of at least 0.99 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a sensitivity of 1.00 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.80 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.81 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.82 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.83 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.84 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.85 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.86 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.87 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.88 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.89 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.90 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.91 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.92 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.93 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.94 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.95 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.96 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.97 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.98 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of at least 0.99 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein have a specificity of 1.00 for detecting colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.65 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.65 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.70 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.70 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.71 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.71 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.72 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.72 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.73 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.73 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.74 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.74 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.75 and a specificity of at least 0.8. In some embodiments, the methods, assays and kits described herein detect colorectal cancer or a colorectal cell proliferative disease with a sensitivity of at least 0.75 and a specificity of at least 0.9. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.70 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.71 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.72 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.73 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.74 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.75 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.76 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.77 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.78 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.79 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.80 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.81 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.82 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.83 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.84 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.85 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.86 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.87 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.88 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.89 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.90 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.91 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.92 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.93 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.94 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.95 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.96 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.97 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.98 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of at least 0.99 for detecting a proliferative disease. In some embodiments, the methods, assays and kits described herein have an AUC of 1.0 for detecting a proliferative disease. Exemplary Multi-Analyte Embodiments In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more biological samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more biological samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more serum or plasma samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting methylated genomic DNA and protein in one or more serum or plasma samples comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in the one or more serum or plasma samples, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; and (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin, wherein the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject with a sensitivity of at least 0.70-0.75 and/or a specificity of at least 0.85-0.9. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b); (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more biological samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some embodiments, the disclosure provides a method for prognosing a subject with colorectal cancer or a colorectal cell proliferative disease comprising: (i) detecting DNA methylation within one or more genomic DNA polynucleotide in one or more serum or plasma samples from the subject, wherein the one or more genomic DNA polynucleotides comprise SEQ ID NO: 31 (mSEPT9) and SEQ ID NOs: 6 and 11 (mANKDRD13b), wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected; (ii) detecting the presence or amount of one or more protein biomarkers in the one or more serum or plasma samples, wherein the one or more protein biomarkers comprise CEA and amphiregulin; and, (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples. In some or embodiments, detection of mSEPT9 is carried out using the Epi proColon assay kit (epiprocoln.com; accessdata.fda.gov/cdrh_docs/pdf13/p13001c.pdf). In some embodiments, In some embodiments, a method or assay described herein comprises: (i) detecting DNA methylation of mSEPT9 in one or more biological samples comprising analyzing the one or more biological samples using an Epi proColon assay kit; (ii) detecting DNA methylation of mANKRD13B in the one or more biological samples; and (iii) detecting the presence or amount of one or more protein biomarkers in the biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin. In some or any of the foregoing embodiments, the one or more protein biomarkers comprises haptoglobin. In some embodiments, the one or more protein biomarkers comprises CEA and haptoglobin. In some embodiments, the one or more protein biomarkers comprises amphiregulin and haptoglobin. In some embodiments, the one or more protein biomarkers comprises CEA, amphiregulin and haptoglobin. In some embodiments, including haptoglobin increases sensitivity for detecting colorectal cancer, advanced adenoma, or a colorectal cell proliferative disease compared to a method or assay that does not detect haptoglobin. Methods of Treating Proliferative Disease In some aspects, the disclosure provides methods of treating a proliferative disease detected by any one of the methods, assays or kits described herein. In some aspects, the disclosure provides methods of treating colorectal cancer or a colorectal cell proliferative disease detected by any one of the methods, assays or kits described herein. In some embodiments, the methods, assays or kits described here predict whether a subject has a proliferative disease such as colorectal cancer. Accordingly, in some embodiments, prior to treatment, confirmation of the proliferative disease is needed. For example, in some embodiments, wherein a method, assay or kit described herein detects colorectal cancer in a subject, a colonoscopy is administered to confirm the subject has colorectal cancer. Upon confirmation of the presence of a proliferative disorder, treatment may be administered as determined by a clinician. The proliferative disease can be classified into subtypes (as defined by the corresponding TNM classification(s) in brackets) of the cancer and each of its subtypes: stage 0 (T0, N0, M0), stage I (Tl, NO, M0), stage II (T2, NO, M0), stage III (T3, NO, M0; or T1 to T3, N1, MO), stage IVA (T4a, NO or N1, MO; or T1 to T4a, N2, M0), stage IVB (T4b, any N, MO or any T, N3, MO), and stage IVC (any T, any N, M1). The TNM classification is a staging system for malignant cancer. As used herein the term “TNM classification” refers to the 6 th edition of the TNM stage grouping as defined in Sobin et al. (International Union Against Cancer (UICC), TNM Classification of Malignant tumors, 6 th ed. New York; Springer, 2002, pp.191-203). The goal of cancer treatment is to completely remove tumors, cancers, and adenomas from the body or kill all the cancer cells in the body. Cancer treatments may involve the use of surgery, radiation, medications, and other therapies to cure a cancer, reduce the size of a tumor or cancer, or stop the progression or growth of a tumor or cancer. Cancer treatments can typically be broken down into three stages. In a first stage, a primary treatment is applied to remove the cancer or kill all the cancer cells. In a second stage, an adjuvant treatment may be applied to kill any cancer cells that remain after the primary treatment. In some cases, the adjuvant treatment may be applied prior to or concurrently with the primary treatment to reduce the size of the cancer or tumor and to make the primary treatment easier or more effective. In a third stage, palliative treatments may be applied to relieve the side effects of the primary and palliative treatments as well as the symptoms caused by the cancer itself. In some cases, the palliative treatment may occur prior to or concurrently with the primary and/or adjuvant treatments. In some embodiments, a method for treating cancer comprises surgery. Several types of surgery are employed in the identification, characterization, and removal of tumors, cancers, and adenomas from the body. These surgeries may be carried out using a variety of surgical techniques including, but not limited to, microscopically controlled surgery, laser surgery, cryosurgery, and electrosurgery. In some embodiments, a diagnostic surgery is used to identify the presence of a cancer within a mass of cells. A tissue sample is collected from the subject wherein said tissue sample is then evaluated to determine the presence or absence of cancer, to identify the type of cancer if cancer is present, and to determine the stage of said cancer. In some embodiments, a staging surgery is employed after a positive diagnosis of cancer. Staging surgery may be prescribed after a positive confirmation of cancer following a diagnostic surgery. Staging surgery serves to uncover the extent of the cancer or size of the tumor in the body. During a laproscopy, a surgical staging procedure, a camera is inserted through a small incision to examine the tumors or cancers and, in some cases, to also remove tissue samples. In some cases, staging surgery may be combined with a diagnostic surgery. Upon a positive diagnosis of cancer, a patient may be treated with curative, debulking, palliative, preventive, and/or supportive surgery to aid in the treatment or removal of said cancer, to ease discomfort due to cancer symptoms and/or treatments, and/or to aid in the efficacy of cancer treatment. When the cancer is localized to a specific area of the body, curative surgery can be used to remove the cancerous growth from the body. In cases where removal of the entire tumor mass is deemed too dangerous for the patient, debulking surgery may be employed to partially, but not completely, remove the tumor or cancer. In some embodiments, a method for treating cancer comprises chemotherapy and/or radiation therapy. Chemotherapy is a drug treatment in which one or more anti-cancer drugs, chemicals, or poisons are delivered to the patient, often intravenously, to kill fast-growing cells in the body. Chemotherapy is often employed during cancer treatments because cancer cells grow and multiply much more quickly than most other cells in the body. Chemotherapy may be employed as a primary, adjuvant, and/or palliative treatment. Many different chemotherapy drugs are available. Chemotherapy drugs can be used alone or in combination to treat a wide variety of cancers. Chemotherapy drugs can be administered in a variety of formats which included, but are not limited to, intravenous infusions, shots, pills, creams, or via methods of direct application. Chemotherapy treatment carries a risk of side effects. Some side effects of chemotherapy are mild and treatable, while others can cause serious complications. Common side effects of chemotherapy drugs include nausea, vomiting, diarrhea, hair loss, fatigue, loss of appetite, bruising and bleeding, oral sores, pain, fever, and constipation. Though many of these symptoms recede following the conclusion of treatment, additional palliative treatment may be prescribed to relieve the side effects of chemotherapy. Chemotherapy drugs also carry the risk for chronic complications including, but not limited to, heart and lung problems, infertility, kidney failure, nerve damage, and the risk of a second cancer. Radiation therapy is a therapy in which ionizing radiation is applied to the body to control or kill tumors or cancerous cells. Radiation therapy damages the DNA within tissues subjected to the radiation and leads to cellular death. As the ionizing radiation can damage normal, healthy cells similarly to tumor or cancer cells, treatment plans seek to optimally target the tumor or cancer site and reduce the exposure of healthy tissues to the ionizing radiation. In external beam radiation, ionizing radiation beams are aimed to intersect at the cancer or tumor site and provide a much larger dose of radiation within the cancer or tumor site than in the surrounding healthy tissue. Brachytherapy is a form of therapy in which a solid source of radiation is place internally near the cancer or tumor site to locally apply radiation to the cancer or tumor site and reduce exposure of other non-cancerous tissues to the radiation source. Systemic radiation therapy involves the introduction of a liquid radiation source to the subject’s circulatory system and/or gastric system. Radiation therapy is typically combined with other forms of therapy as a primary, adjuvant, and/or palliative treatment. Some cancer types are promoted by specific hormones, wherein the removal of said hormones or blockage of their effects may reduce or stop growth of the tumor or cancer. Hormone therapy involved the manipulation of the endocrine system through exogenous administration of specific hormones, usually steroid hormones, that either inhibit the production of tumor- or cancer- growth-promoting hormones or blocks the activity of said hormones. In some cases, hormone therapy also involves surgical removal of the endocrine organs. Hormonal therapy is used for several types of cancers derived from hormonally responsive tissues, including the breast, prostate, endometrium, and adrenal cortex. Cancer immunotherapy involves the treatment of disease by activating or suppressing the immune system to promote anti-tumor and anti-cancer activities within the subject’s immune system. Cancer immunotherapy exploits the fact that cancer cells often have tumor-specific antigens present on their surfaces by introducing or promoting the activity of immune cells in the subject. Cell-based immunotherapies mediated by immune effector cells such as natural killer (NK) cells, lymphokine-activated killer cells, cytotoxic T cells and dendritic cells promote anti- tumor and anti-cancer activities within the immune system by targeting abnormal antigens expressed on the surface of tumor cells. Activation immunotherapies are designed to activate or elicit an immune response to target cancer and tumor cells for destruction. Suppression immunotherapies are designed to inhibit or suppress an immune response to prohibit the growth of cancers and tumors. Targeted therapy is a type of cancer treatment that targets proteins that control the growth, division, and spread of tumor and cancer cells. Targeted therapies can block or turn off signals that control cancer and tumor cell growth, prevents cancer and tumor cells from living longer than normal, and destroys cancer and tumor cells. Targeted therapy blocks the growth of cancer and tumor cells by interfering with the activity of specific target molecules needed for carcinogenesis and tumor growth, rather than by simply interfering with all rapidly dividing cells (e.g., with traditional chemotherapy). As such, targeted cancer therapies may be more effective and less harmful to normal cells than alternative forms of treatment like radiation therapy and chemotherapy. The most successful targeted therapies involve entities that specifically or preferentially target a protein or enzyme that carries a mutation or genetic alteration that is associated with cancer cells and not found or less frequently found in normal host tissues. As targeted therapies require the targeting of specific cancer- and tumor-associated factors, most targeted therapies require the use of biomarkers to aid in the selection of patients who will respond to a specific targeted therapy. There are targeted therapies for lung cancer, colorectal cancer, head and neck cancer, breast cancer, multiple myeloma, lymphoma, prostate cancer, melanoma and other cancers. Targeted therapies may also be combined with other forms of cancer treatment. Cancer care typically requires a multi-faceted approach in which several of the techniques described above are employed together to create a plan to cure the patient’s cancer. Colorectal cancer treatment plans typically involve surgery, radiation therapy, chemotherapy, targeted therapy, and immunotherapy. Surgical resection is the most common treatment for colorectal cancer in which the tumor and some of the healthy surrounding tissue from the colon or rectum and nearby lymph nodes is removed. In some cases, radiation therapies and/or chemotherapies are employed prior to surgery to reduce tumor or cancer cell size to aid in tumor removal. In some cases, radiation therapy and/or chemotherapy is employed after surgery to destroy any remaining cancer or tumor cells. Colorectal cancers are also susceptible to targeted therapies. Colorectal cancer often overproduction of epidermal growth factor receptor (EGFR). Drugs that block EGFR may help stop or slow cancer growth. Other options include drugs that inhibit vascular endothelial growth factor (VEGF), tumor-agnostic treatment focusing on an NTRK fusion, and anti-angiogenesis therapy. In some embodiments, a cancer therapy is selected from the group consisting of antibodies (e.g. antibodies stimulating an immune response destroying cancer cells such as retuximab or alemtuzubab, antibodies stimulating an immune response by binding to receptors of immune cells an inhibiting signals that prevent the immune cell to attack "own" cells, such as ipilimumab, antibodies interfering with the action of proteins necessary for tumor growth such as bevacizumab, cetuximab or panitumumab, or antibodies conjugated to a drug, preferably a cell- killing substance like a toxin, chemotherapeutic or radioactive molecule, such as Y-ibritumomab tiuxetan, I-tositumomab or ado-trastuzumab emtansine), cytokines (e.g. interferons or interleukins such as INF-alpha and IL-2), vaccines (e.g. vaccines comprising cancer-associated antigens, such as sipuleucel-T), oncolytic viruses (e.g. naturally oncolytic viruses such as reovirus, Newcastle disease virus or mumps virus, or viruses genetically engineered viruses such as measles virus, adenovirus, vaccinia virus or herpes virus preferentially targeting cells carrying cancer-associated antigens), gene therapy agents (e.g. DNA or RNA replacing an altered tumor suppressor, blocking the expression of an oncogene, improving a subject's immune system, making cancer cells more sensitive to chemotherapy, radiotherapy or other treatments, inducing cellular suicide or conferring an anti-angiogenic effect) and adoptive T cells (e.g. subject- harvested tumor-invading T-cells selected for antitumor activity, or subject-harvested T-cells genetically modified to recognize a cancer-associated antigen). In some embodiments, the one or more cancer therapies selected from the group consisting of Abiraterone Acetate, ABVD, ABVE, ABVE-PC, AC, AC-T, ADE, Ado- Trastuzumab Emtansine, Afatinib Dimaleate, Aldesleukin, Alemtuzumab, Aminolevulinic Acid, Anastrozole, Aprepitant, Arsenic Trioxide, Asparaginase Erwinia chrysanthemi, Axitinib, Azacitidine, BEACOPP, Belinostat, Bendamustine Hydrochloride, BEP, Bevacizumab, Bexarotene, Bicalutamide, Bleomycin, Bortezomib, Bosutinib, Brentuximab Vedotin, Busulfan, Cabazitaxel, Cabozantinib-S-Malate, CAFCapecitabine, CAPOX, Carboplatin, CARBOPLATIN-TAXOL, Carfilzomib, Carmustine, Carmustine Implant, Ceritinib, Cetuximab, Chlorambucil, CHLORAMBUCIL-PREDNISONE, CHOP, Cisplatin, Clofarabine, CMF, COPP, COPP-ABV, Crizotinib, CVP, Cyclophosphamide, Cytarabine, Cytarabine, Liposomal, Dabrafenib, Dacarbazine, Dactinomycin, Dasatinib, Daunorubicin Hydrochloride, Decitabine, Degarelix, Denileukin Diftitox, Denosumab, Dexrazoxane Hydrochloride, Docetaxel, Doxorubicin Hydrochloride, Doxorubicin Hydrochloride Liposome, Eltrombopag Olamine, Enzalutamide, Epirubicin Hydrochloride, EPOCH, Eribulin Mesylate, Erlotinib Hydrochloride, Etoposide Phosphate, Everolimus, Exemestane, FEC, Filgrastim, Fludarabine Phosphate, Fluorouracil, FU-LV, Fulvestrant, Gefitinib, Gemcitabine Hydrochloride, GEMCITABINE- CISPLATIN, GEMCITABINE-OXALIPLATIN, Gemtuzumab Ozogamicin, Glucarpidase, Goserelin Acetate, HPV Bivalent Vaccine, Recombinant HPV Quadrivalent Vaccine, Hyper- CVAD, Ibritumomab Tiuxetan, Ibrutinib, ICE, Idelalisib, Ifosfamide, Imatinib, Mesylate, Imiquimod, Iodine 131 Tositumomab and Tositumomab, Ipilimumab, Irinotecan Hydrochloride, Ixabepilone, Lapatinib Ditosylate, Lenalidomide, Letrozole, Leucovorin Calcium, Leuprolide Acetate, Liposomal Cytarabine, Lomustine, Mechlorethamine Hydrochloride, Megestrol Acetate, Mercaptopurine, Mesna, Methotrexate, Mitomycin C, Mitoxantrone Hydrochloride, MOPP, Nelarabine, Nilotinib, Obinutuzumab, Ofatumumab, Omacetaxine Mepesuccinate, OEPA, OFF, OPPA, Oxaliplatin, Paclitaxel, Paclitaxel Albumin-stabilized Nanoparticle Formulation, PAD, Palifermin, Pal onosetron Hydrochloride, Pamidronate Disodium, Panitumumab, Pazopanib Hydrochloride, Pegaspargase, Peginterferon Alfa-2b, Pembrolizumab, Pemetrexed Disodium, Pertuzumab, Plerixafor, Pomalidomide, Ponatinib Hydrochloride, Pralatrexate, Prednisone, Procarbazine Hydrochloride, Radium 223 Dichloride, Raloxifene Hydrochloride, Ramucirumab, Rasburicase, R-CHOP, R-CVP, Recombinant HPV Bivalent Vaccine, Recombinant HPV Quadrivalent Vaccine, Recombinant Interferon Alfa-2b, Regorafenib, Rituximab, Romidepsin, Romiplostim, Ruxolitinib Phosphate, Siltuximab, Sipuleucel-T, Sorafenib Tosylate, STANFORD V, Sunitinib Malate, TAC, Talc, Tamoxifen Citrate, Temozolomide, Temsirolimus, Thalidomide, Topotecan Hydrochloride, Toremifene, Tositumomab and I 131 Iodine Tositumomab, TPF, Trametinib, Trastuzumab, Vandetanib, VAMP, VelP, Vemurafenib, Vinblastine Sulfate, Vincristine Sulfate, Vincristine Sulfate Liposome, Vinorelbine Tartrate, Vismodegib, Vorinostat, XELOX, Ziv-Aflibercept, and Zoledronic Acid. Kits In some aspects, the disclosure provides a kit comprising reagents and instructions necessary for carrying out the methods described herein. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; and (iii) instructions for detecting methylation of genomic DNA in one or more biological samples in combination with instructions for detecting the one or more protein biomarkers in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more biological samples in combination with instructions for detecting methylated genomic DNA. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more biological samples. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; and (iii) instructions for detecting methylation of genomic DNA in one or more plasma or serum samples in combination with instructions for detecting the one or more protein biomarkers in the one or more plasma or serum samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples in combination with instructions for detecting methylated genomic DNA. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; and (iii) instructions for detecting methylation of genomic DNA in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting the one or more protein biomarkers in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting methylated genomic DNA. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; and (iii) instructions for detecting methylation of genomic DNA in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting the one or more protein biomarkers in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease in combination with instructions for detecting methylated genomic DNA. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; and (iii) instructions for detecting methylation of genomic DNA in one or more biological samples in combination with instructions for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more biological samples in combination with instructions for detecting methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; (iii) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more biological samples. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; and (iii) instructions for detecting methylation of genomic DNA in one or more plasma or serum samples in combination with instructions for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin in the one or more plasma or serum samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples in combination with instructions for detecting methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to the genomic DNA; (iii) one or more reagents for detecting the one or more protein biomarkers; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers comprising CEA and/or amphiregulin in one or more plasma or serum samples. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; and (iii) instructions for detecting methylation of genomic DNA in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; (iii) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphireguiln; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more biological samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; and (iii) instructions for detecting methylation of genomic DNA in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease, in combination with instructions for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin in the one or more biological samples. In some embodiments, the kit comprises (i) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (ii) instructions for detecting the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease in combination with instructions for detecting methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof. In some embodiments, the kit comprises (i) an agent for converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA; (ii) at least one set of oligonucleotides complementary to methylated genomic DNA selected from mSEPT9, mANKRD13B, and combinations thereof; (iii) one or more reagents for detecting the one or more protein biomarkers comprising CEA and/or amphiregulin; and (iv) instructions for detecting methylation of genomic DNA and the presence or amount of the one or more protein biomarkers in one or more plasma or serum samples obtained from a subject suspected of having colorectal cancer or a colorectal cell proliferative disease. In some embodiments, the one or more protein biomarkers of the kit comprises haptoglobin. In some embodiments, a kit described herein comprises instructions for detecting haptoglobin in a sample (e.g., plasma sample). In some embodiments, a kit described herein comprises reagents for detecting haptoglobin in a sample (e.g., plasma sample). EXAMPLES EXAMPLE 1 – Multi-Analyte Panel for Detecting Colorectal Carcinoma To determine whether the specificity and sensitivity of an assay for detecting colorectal carcinoma in a subject could be improved, presence of protein biomarkers were assessed in combination with DNA methylation markers in the blood of subjects diagnosed with colorectal carcinoma relative to expression in control subjects. Methods Colorectal carcinoma (CRC) biomarkers were measured in four aliquots of blood plasma collected from 70 individuals with CRC and 171 individuals without CRC as further described in Tables 1 and 2. Two DNA methylation markers were measured in three assays in one combined multiplex Real-time PCR. Three selected protein biomarkers were individually measured using ELISAs. Table 1: Number of samples by gender for colorectal cancer (CRC) and for controls. Table 2: Number of samples by gender for different colorectal cancer (CRC) stages, and for controls from individuals with no evidence of disease (NED) and with polyps. DNA methylation markers Blood plasma samples from colorectal carcinoma patients (CRC) and individuals with no cancer (controls) were processed with the Epi BiSKit (Epigenomics AG). Briefly, DNA extraction from 3.5 ml of blood-plasma per individual and subsequent bisulfite conversion of DNA is performed with the Epi BiSKit (Epigenomics AG) according to the workflow as defined in the instructions for use of the Epi BiSKit (Epigenomics AG), including a prior treatment of blood plasma with proteinase K. For each sample, 25 μl bisulfite-treated DNA were amplified in duplicate in 50 μl total volume Real-time PCR quadruplex containing three methylation sensitive (MSP) assays for one bisulfite specific and methylation unspecific ACTB control assay and the two DNA-methylation markers mSeptin9 and mANKRD13B, which is measured on two strands (FIGs.3A-3B). Table 3 lists the genomic reference sequences and derived bisulfite converted sequences. Table 4 lists sequence IDs of oligomers used for Real-time PCR assays. The assays were measured using an Applied BiosystemsTM Quant StudioTM 5 Dx Real-Time PCR Instrument, using 45 cycles, and interpreting basic results as cycle thresholds (Cts) of Realtime-PCR amplification curves. For numerical interpretation, data for un-amplified assays (no curve) were set to the maximum Ct of 45. Table 3: Sequence IDs, abbreviations, names and associated regions in the human genome (GRCh38 build): genomic reference sequences and derived bisulfite converted sequences.
Table 4: Sequence IDs of oligomers (primers, probes) used for Real-time PCR assays. Amphiregulin (AR) Concentrations [pg/mL] of the protein Amphiregulin in blood plasma samples were assessed using the Human Amphiregulin Quantikine ELISA Kit from R&D Systems according to manufacturer’s protocol. In brief, two aliquots of 50 μl of blood plasma were used without previous dilution from each individual. Standard curve is prepared in the range of 0 to 1000 pg/ml. Washing steps were done manually, and final measurement is done with Tecan Infinite F200 PRO microplate reader at absorption of 450 nm. For calculation, the average of the duplicate readings for each standard, control, and sample were subtracted by the average zero standard absorbance (0 pg /ml). For the standard curve the mean absorbance for each standard is plotted on the y-axis against the concentration on the x-axis. Protein concentration is calculated with the slope of best linear fit through the points by crossing the origin (0,0). CYFRA Concentrations [ng/mL] of the protein Human Cytokeratin Fragment Antigen 21-1 (CYFRA21-1) in blood plasma samples were assessed using the Human Cytokeratin Fragment Antigen 21-1 (CYFRA21-1) ELISA kit from Cusabio according to manufacturer’s protocol. In brief, two aliquots of 100 μl of blood plasma were used without previous dilution from each individual. Standard curve is prepared in the range of 0 to 20 ng/ml. Washing steps were done using the Biotek 405TS microplate washer, and final measurement is done with Biotek ELx808LBS plate reader at absorption of 450 nm. For calculation, the average of the duplicate readings for each standard, control, and sample were subtracted by the average zero standard absorbance (0 ng/ml). For the standard curve, the mean absorbance for each standard is plotted on the y-axis against the concentration on the x-axis. Protein concentration is calculated using the linear trendline with a log concentration axis. CEA Concentrations [ng/mL] of the protein carcinoembryonic antigen (CEA) in blood plasma samples were assessed using the Human CEA ELISA Kit (PN:EHCEA) from ThermoFisher according to manufacturer’s protocol. In brief, 2 aliquots of 50 μl of blood plasma were used without previous dilution from each individual. Standard curve is prepared in the range of 0 to 83.3 ng/ml. Washing steps were done using the Biotek 405TS microplate washer, and final measurement is done with Biotek ELx808LBS plate reader at absorption of 450 nm. For calculation, the average of the duplicate readings for each standard, control, and sample were subtracted by the average zero standard absorbance (0 ng/ml). For the standard curve, the mean absorbance for each standard is plotted on the y-axis against the concentration on the x-axis. Protein concentration is calculated using the linear trendline with a log concentration axis. The three minimum Cts for all three MSP assays over duplicates were used in logistic regression without or with the protein measurements of the individuals as up to three additional numeric variables. The areas under the curve (AUC) of Receiver operating characteristic (ROC) analysis and the Sensitivity at Specificity of 0.9 using the full data set were used to assess the discrimination of CRC vs. control in the different sets of variables. Results The individual DNA methylation marker measurements by Realtime-PCR as assessed by minimum Cts of duplicates for each of the three MSP marker assays lead to AUCs between 0.75 and 0.79 and to Sensitivities from 0.56 to 0.63 (see FIGS. 4 to 6 and Table 5). The combination of DNA methylation markers lead to an AUC of 0.84 and Sensitivity of 0.67 at Specificity of 0.9 (see FIG.10). The individual protein measurements lead to AUC of 0.77 for CEA (see FIG. 7), of 0.74 for Amphiregulin (see FIG.8), and of 0.538 for CYPHRA (see FIG.9). Combinations of data from the three DNA-methylation biomarker assays with protein data from the two proteins with a performance > AUC of 0.7 (CEA and Amphiregulin) lead to higher sensitivities at a Specificity of 0.9 than obtained with the DNA methylation markers alone (see FIGS.11 - 13 and Table 6) with a maximum Sensitivity of 0.77 for the combination with CEA and Amphiregulin. Further, data for the combined markers (SEPT9 + ANB1 + ANB2 + CEA + AREG) was compared with altered data sets to assess the stability of the performance as described as Sensitivity at Specificity of 0.9. The sensitivity remains at levels > 0.75 in altered patient data sets (see Table 7) restricted to age subsets (age 45-75) at core screening population without optionally screened older patients, with addition of overrepresented advanced adenomas, or with exclusion of stage IV CRC patients. Overall, these data indicate including the detection of protein biomarkers in combination with detection of methylation of genomic DNA improves the sensitivity for detecting subjects with CRC. Table 5: Measurements for all biomarkers in all 241 individuals. The first column contains the diagnostic group. Column 2-4 contain the three blood plasma derived Ct values of methylation specific Realtime PCR quadruplex assays: ANKRD13b assays on the bisulfite converted sense strand (ANB1), ANKRD13b assay on the reverse complement strand (ANB2), Septin9 assay on the reverse complement strand (S9B2). The columns 5-7 contain protein measurements in [pg/mL] for CEA, Amphiregulin (AR) and CYFRA21-1 (CYPHRA) – negative results as obtained by calculations with the calibration curve were set to 0 (zero). Table 6: Performance for single markers (row 1 to 6) and of different marker combinations by logistic regression analysis (row 7 to 10), characterized by Sensitivity at Specificity of 0.9 and by area under the curve (AUC) of receiver operating characteristic (ROC) analysis. Table 7: Performance for combined markers ANB1+ANB2+S9B2+CEA+AR for comparison of performance of the Example 1 data set from individuals in the age eligible for screening (row 2) with altered settings with a restriction to a younger age group (row 2), addition of data from individuals with advanced adenomas in the control group (row 3) and excluding stage IV CRC patients (row 4), characterized by Sensitivity at Specificity of 0.9 and by area under the curve (AUC) of receiver operating characteristic (ROC) analysis. EXAMPLE 2 – Expanded Multi-analyte Panel for Detecting Colorectal Cancer To determine whether the specificity and sensitivity of an assay for detecting colorectal carcinoma and/or pre-cancerous lesions (e.g., advanced adenoma) in a subject could be improved, presence of protein biomarkers are assessed in combination with DNA methylation markers in the blood of subjects diagnosed with colorectal carcinoma or pre-cancerous lesions relative to expression in control subjects. Methods Colorectal carcinoma (CRC) biomarkers are measured in aliquots of blood plasma collected from individuals with CRC or without CRC as controls. Two DNA methylation markers are measured in three assays in one combined multiplex Real-time PCR. Four selected protein biomarkers are individually measured using ELISAs. DNA methylation markers DNA methylation markers are assessed as described in Example 1. For each sample, bisulfite-treated DNA are amplified in duplicate in 50 μl total volume Real-time PCR quadruplex containing three methylation sensitive (MSP) assays for one bisulfite specific and methylation unspecific control (e.g., ACTB) assay and the two DNA-methylation markers mSeptin9 and mANKRD13B, which is measured on two strands. The assays are measured using an Applied BiosystemsTM Quant StudioTM 5 Dx Real-Time PCR Instrument, using 45 cycles, and interpreting basic results as Cts of Realtime-PCR amplification curves. For numerical interpretation, data for un-amplified assays (no curve) are set to the maximum Ct of 45. Haptoglobin Serum or plasma specimens are thawed and samples are collected and diluted with water. NH 2 SO 4 is added and mixed with the diluted samples. Samples are heated at 80^ and then cooled on ice. PBS, NaOH, and water are added and mixed with the samples and the pH of the samples are checked and recorded. The resulting diluted desialylated serum samples are frozen and stored or used for ELISA. Microtiter plates are marked for serum specimens, PBST blanks, and normal asialohaptoglobin standards. An anti-haptoglobin antibody is diluted into PBS and added to each well of the microtiter plates. The plate is left overnight at 4^. Anti-haptoglobin is decanted and discarded and each well is washed with PBS.1% BSA in PBS (prepared fresh daily) is added to each well and incubated at room temp before the BSA/PBS is decanted and discarded. Appropriate dilutions, standards and controls are prepared. Desialyated serum is diluted in PBST. The plate is incubated at room temp. Each well is washed once with PBST. Biotinyl Erythrina cristagalli lectin in PBST is added to each well. The plate is incubated at room temp ande ach well is washed with PBST. A VECTASTAIN ABC Reagent Kit (Vector Elite PK-6100) is used for detection as described by the manufacturer’s protocol. Avidin-Biotin Complex is added and the plate is incubated at room temp. Each well is washed with PBST. ABTS reagent (0.03% H2O2, 1 mM 2,2-azino-di(3-ethylbenzthiazoline) sulfonate in 0.1 M citrate, pH 4.0) is added. The plate is incubated at room temp and read at A405 using an ELISA reader. Amphiregulin (AR) Concentrations [pg/mL] of the protein Amphiregulin in blood plasma samples are assessed using the Human Amphiregulin Quantikine ELISA Kit from R&D Systems according to manufacturer’s protocol and as described in Example 1. CYFRA Concentrations [ng/mL] of the protein Human Cytokeratin Fragment Antigen 21-1 (CYFRA21-1) in blood plasma samples are assessed using the Human Cytokeratin Fragment Antigen 21-1 (CYFRA21-1) ELISA kit from Cusabio according to manufacturer’s protocol and as described in Example 1. CEA Concentrations [ng/mL] of the protein carcinoembryonic antigen (CEA) in blood plasma samples are assessed using the Human CEA ELISA Kit (PN:EHCEA) from ThermoFisher according to manufacturer’s protocol and as described in Example 1. Analysis Protein biomarkers and DNA methylation markers are assessed alone and in combination. Sensitivity and specificity are determined as described in Example 1. EXAMPLE 3 – Detection of Haptoglobin Improves Sensitivity of Multi-Analyte Panel for Detecting Colorectal Cancer The presence of protein biomarkers was assessed in combination with DNA methylation markers in the blood of subjects diagnosed with colorectal carcinoma relative to expression in control subjects. Methods For each sample from Example 1, additional blood plasma aliquots were measured for detection of haptoglobin using an ELISA. The data was analyzed according to methods of Example 1 but included the measurement of haptoglobin. DNA methylation markers, CEA and amphiregulin were assessed as described in Example 1. Haptoglobin was detected as described below. For each individual two 400 μL of 1:80 dilutions of blood plasma in water were each mixed with 100μL of 0.5 N NH2SO4. Samples were heated at 80^ and then cooled to and stored at 4°C for 5 minutes. Each sample was mixed with 100μL PBS, 100 μL 0.5 N NaOH, and 300 μL of water, leading to 1 mL aliquots containing the plasma in a 1:200 dilution. The pH of the samples was checked to confirm a valid pH between 6.5 and 7.5, dropout samples were replaced by new preparations. Microtiter plates were marked for plasma specimens, PBST blanks, and normal asialohaptoglobin standards. Microtiter plates were coated by addition of 50 μl of 40 μg/mL Rabbit anti-Haptoglobin antibody in 1 x PBS and overnight storage at 4^. The antibody solution was discarded and each well was washed with 300 μl PBS.200 μL of 1% BSA in 1 x PBS was put to each well and incubated at room temp for one hour before the BSA/PBS was decanted and discarded. Quantification standards (Asialohaptoglobin in a 0.5 dilution series with 6 steps from 1 mg/mL down to 15.6 ng/mL) were prepared.20 μL of desialyated plasma per sample was diluted 1:100 in PBST using two 1:10 dilution steps, by first mixing with 180 μL PBST and then using 50 μL of that mix with 450 μL PBST, leading to a final 20,000 dilution of the blood plasma. Blocking solution was removed from the microtiter plates by discarding but without washing. The wells were filled with 50 μl/well by standards, diluted samples, and blanks in duplicate and the plate was sealed and incubated at 25°C for one hour. The plate was incubated at room temp. Each well was washed once with 300 μl PBST. 50 μl biotinyl Erythrina cristagalli lectin in1XPBST was added to each well and the plate was sealed and incubated at 25°C for one hour .The solution was removed and each well was washed with 300μl PBST three times. A VECTASTAIN ABC Reagent Kit (Vector Elite PK-6100) was used for detection as described by the manufacturer’s protocol.50 μl of Avidin-Biotin-HRT Complex was added per well and the plate was sealed and incubated 25°C for one hour. Each well was washed with 300 μL PBST three times. 100 μL of ABTS reagent (0.03% H2O2, 1 mM 2,2-azino-di(3- ethylbenzthiazoline) sulfonate in 0.1 M citrate, pH 4.0) was added. The plate was incubated at 25°C for exactly 30 minutes, shaken on an ELISA reader for 5 seconds and then read at A405. Median blank values were subtracted from A405 values for all samples, controls, and standards. Based on the dilution series, a linear function for calibration and quantification was calculated by linear regression for each plate to obtain ng/mL. To obtain final haptoglobin concentrations, results were multiplied by 20,000 and values were expressed as mg/mL. Results The individual protein measurement of Haptoglobin lead to an AUC of 0.37 (see FIG. 14). Protein measurements are provided in Table 8. The combination of DNA methylation markers with Haptoglobin lead to an AUC of 0.86 and Sensitivity of 0.69 at Specificity of 0.9, increasing both in comparison to methylation marker combinations without Haptoglobin (see FIG.15). Combinations of data from the three DNA-methylation biomarker assays with protein data from either or both of the two proteins CEA and Amphiregulin, as already described in Example 1, with data from the additional protein haptoglobin lead to higher Sensitivities at a Specificity of 0.9 and higher AUC than obtained with the corresponding marker combinations without haptoglobin (see FIGS.15 - 18 and Table 9) with a maximum Sensitivity of 0.81 for the combination of DNA methylation markers with CEA, Amphiregulin and Haptoglobin. Overall, these data indicate that including Haptoglobin into the combined detection of protein biomarkers and methylation of genomic DNA further improves the Sensitivity for detecting subjects with CRC. Table 8: Measurements for Haptoglobin in all 241 individuals as obtained in Example 3.
Table 9: Performance summary and comparison for the single marker Haptoglobin from Example 3 (row 1) and of different marker combinations from Example 1 (row 2,4,6,8) and Example 3 (row 3,5,7,9) by logistic regression analysis, characterized by Sensitivity (column 1) at Specificity of 0.9 and by area under the curve (AUC) (column 3) of receiver operating characteristic (ROC) analysis.
SEQUENCE LISTING