# US 2017/0285033 A1 · Method for evaluation of presence of or risk of colon tumors

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- Number: US 2017/0285033 A1
- Document ID: US20170285033A1
- Status: Published application
- Kind: A1
- Application number: 15/622,340
- Filed: 2017-06-14
- Published: 2017-10-05
- Earliest claimed: 2012-11-30
- Assignees: Applied Proteomics, Inc.
- Applicants: Applied Proteomics, Inc.
- Inventors: John Blume; Ryan Benz; Lisa Croner; Roslyn Dillon; Arlo Z. Randall; Jeffrey Jones; Heather Skor; Tom Stockfisch; Bruce Wilcox; Daniel Ruderman
- Web page: https://patentgrep.com/patent/US20170285033A1

## CPC

- G01N 33/57535: of the large intestine, e.g. colon, rectum or anus
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 40/20: Supervised data analysis
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- G01N 2800/60: Complex ways of combining multiple protein biomarkers for diagnosis
- G01N 2800/7028: Cancer
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

The disclosed methods are used to predict or assess colon tumor status in a patient. They can be used to determine nature of tumor, recurrence, or patient response to treatments. Some embodiments of the methods include generating a report for clinical management. The methodology provided herein is intended to detect technical variations and to allow for data normalization and enhance signal detection and build predictive proteins profiles of disease status and response.

## Claims

### Claim 1

A method of detecting the presence of an adenoma or polyp of the colon in a subject with a sensitivity of greater than 70% or a selectivity of greater than 70%; said method comprising the steps of:
(a) obtaining a blood sample from a subject;
(b) cleaving proteins in said blood sample to provide a sample comprising peptides;
(c) analyzing said sample for the presence of at least ten peptides;
(d) comparing the results of analyzing said sample with control reference values to determine a positive or negative score for the presence of an adenoma or polyp of the colon with a sensitivity of greater than 70% or a selectivity of greater than 70%.

### Claim 2 (depends on 1)

The method of claim 1, wherein said sensitivity is selected from greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 3 (depends on 1)

The method of claim 1, wherein said selectivity is selected from greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 4 (depends on 1)

The method of claim 1, wherein said selectivity and said sensitivity are greater than 90%.

### Claim 5 (depends on 1)

The method of claim 1, wherein said subject is asymptomatic.

### Claim 6 (depends on 1)

The method of claim 1, wherein said subject has previously received treatment for colon polyps.

### Claim 7 (depends on 1)

The method of claim 1, wherein said analyzing step comprises spectroscopic analysis, mass spectrometry, immunological analysis, enzymatic reactivity analysis, and combinations thereof.

### Claim 8 (depends on 1)

The method of claim 1, wherein said analyzing comprises mass spectrometry.

### Claim 9 (depends on 1)

The method of claim 1, wherein said at least ten peptides are selected from the neutral mass classifiers of FIG. 8.

### Claim 10 (depends on 1)

A method of treating an adenoma or polyp of the colon in a subject comprising
(a) performing the method of claim 1 to yield a subject with a positive score for the presence of an adenoma or polyp; and
(b) performing a procedure for removal of adenoma or polyp tissue in said subject.

### Claim 11

A method of detecting the presence or absence of an adenoma or polyp of the colon in a subject, wherein said subject has no symptoms or family history of adenoma or polyps of the colon, said method comprising the steps of:
(a) obtaining a biological sample from said subject;
(b) performing an analysis of the biological sample for the presence and amount of one or more proteins and/or peptides;
(c) comparing the presence and amount of one or more proteins and/or peptides from said biological sample to a control reference value; and
(d) correlating the presence and amount of one or more proteins and/or peptides with the subject's adenoma or polyp status.

### Claim 12 (depends on 11)

The method of claim 11, wherein said method achieves a sensitivity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 13 (depends on 11)

The method of claim 11, wherein said method achieves a specificity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 14 (depends on 11)

The method of claim 11, wherein said method achieves sensitivity and specificity each individually selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 15 (depends on 11)

The method of claim 11, further comprising preparing a report for said subject, wherein said report indicates the presence or absence of an adenoma or polyp.

### Claim 16 (depends on 15)

The method of claim 15, wherein said report indicates a predisposition or risk for polyp development, a degree of cell dysplasia, a subtype of adenomatous polyp, or a subtype of benign colon tumor disease.

### Claim 17 (depends on 11)

The method of claim 11, wherein said method detects the presence or absence of an adenoma.

### Claim 18 (depends on 17)

The method of claim 17, wherein said adenoma is an adenomatous polyp or polypoid adenoma.

### Claim 19 (depends on 18)

The method of claim 18, wherein said adenomatous polyp or polypoid adenoma is selected from the group of pedunculated polyps and sessile polyps.

### Claim 20 (depends on 18)

The method of claim 18, wherein said adenomatous polyp or polypoid adenoma is characterized according to a degree of cell dysplasia or pre-malignancy.

### Claim 21 (depends on 11)

The method of claim 11, wherein said method further detects the presence or absence of colorectal carcinoma.

### Claim 22 (depends on 11)

The method of claim 11, wherein said method does not detect the presence or absence of colorectal carcinoma.

### Claim 23 (depends on 11)

The method of claim 11, wherein the presence or absence of colorectal carcinoma is not determined.

### Claim 24 (depends on 11)

The method of claim 11, wherein said presence or absence is confirmed by colonoscopy, imaging, and/or surgery.

### Claim 25 (depends on 11)

The method of claim 11, wherein said biological sample is selected from the group consisting of whole blood, serum, plasma, blood constituent, bone marrow, saliva, cheek swab, urine, stool, lymph fluid, CNS fluid, and lesion exudate.

### Claim 26 (depends on 25)

The method of claim 25, wherein said biological sample is selected from the group consisting of whole blood, serum, and plasma.

### Claim 27 (depends on 11)

The method of claim 11, wherein said subject is asymptomatic.

### Claim 28 (depends on 11)

The method of claim 11, wherein said subject is from 18 to 49 years old.

### Claim 29 (depends on 11)

The method of claim 11, wherein said subject has not previously received a colonoscopy.

### Claim 30 (depends on 11)

The method of claim 11, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma.

### Claim 31 (depends on 11)

The method of claim 11, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma other than age.

### Claim 32 (depends on 11)

The method of claim 11, wherein said analysis of step (b) includes a method selected from the group consisting of spectroscopic analysis, mass spectrometry, immunological analysis, and enzymatic reactivity.

### Claim 33 (depends on 32)

The method of claim 32, wherein said analysis is mass spectrometry.

### Claim 34 (depends on 32)

The method of claim 32, wherein said immunological analysis includes an enzyme-linked immunosorbent assay or radioimmunoassay.

### Claim 35 (depends on 32)

The method of claim 32, wherein said immunological analysis includes immunoblotting, immunodiffusion, immunoelectrophoresis, or immunoprecipitation.

### Claim 36 (depends on 32)

The method of claim 32, wherein said immunological analysis includes immunostaining and/or flow cytometry analysis.

### Claim 37 (depends on 11)

The method of claim 11, wherein said control reference is the presence and amount of a set of one or more non-overlapping proteins and/or peptides in the same biological sample.

### Claim 38 (depends on 11)

The method of claim 11, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is present.

### Claim 39 (depends on 11)

The method of claim 11, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is not present.

### Claim 40 (depends on 11)

The method of claim 11, wherein said analysis detects the presence and amount of a number of proteins or polypeptides, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, and at least 1000.

### Claim 41 (depends on 11)

The method of claim 11, wherein said analysis detects the presence and amount of one or more of the following sets:
i) one or more proteins selected from SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
ii) one or more peptide fragments of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
iii) one or more peptides with a sequence homology to SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof, wherein said sequence homology is selected from the group of greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%; and
iv) one or more binding partners of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof.

### Claim 42 (depends on 11)

The method of claim 11, wherein said analysis detects the presence and/or amount of one or more neutral mass clusters from FIG. 7 or FIG. 8.

### Claim 43 (depends on 42)

The method of claim 42, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, at least 200, at least 500, and at least 1000.

### Claim 44 (depends on 42)

The method of claim 42, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is at least one, and is selected from less than 5, less than 10, less than 50, less than 100, less than 200, less than 500, and less than 1000.

### Claim 45 (depends on 42)

The method of claim 42, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from the group consisting of 10 to 50, 60 to 100, 150-300, 400-600, and 800-1000, inclusive.

### Claim 46 (depends on 42)

The method of claim 42, wherein said neutral mass cluster has a classifier frequency when tested according to a 70/30 training/test for split classifiers, wherein said classifier frequency is selected from at least 3 out of 50, at least 10 out of 50, at least 20 out of 50, at least 30 out of 50, and at least 40 out of 50.

### Claim 47 (depends on 42)

The method of claim 42, wherein said analysis detects the presence and/or amount of a protein or peptide from which one or more neutral mass clusters from FIG. 7 or FIG. 8 is derived.

### Claim 48 (depends on 11)

The method of claim 11, further comprising
(e) performing an analysis of the biological sample for the presence and amount of one or more analytes selected from the groups consisting of metabolites, DNA sequences, RNA sequences, and combinations thereof; and
(f) comparing the presence and amount of said analytes to a control reference value; and
(g) correlating the presence and amount of said analytes with the subject's adenoma or polyp status.

### Claim 49

A method of detecting the presence or absence of an adenoma or polyp of the colon in a subject in whom a colonoscopy yielded a negative result comprising the steps of:
(a) obtaining a biological sample from a subject with a negative diagnosis of adenoma or polyps based on colonoscopy;
(b) performing an analysis of the biological sample for the presence and amount of one or more proteins and/or peptides;
(c) comparing the presence and amount of one or more proteins and/or peptides from said biological sample to a control reference value; and
(d) correlating the presence and amount of one or more proteins and/or peptides with the subject's adenoma or polyp status.

### Claim 50 (depends on 49)

The method of claim 49, wherein said method achieves a sensitivity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 51 (depends on 49)

The method of claim 49, wherein said method achieves a specificity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 52 (depends on 49)

The method of claim 49, wherein said method achieves sensitivity and specificity each individually selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 53 (depends on 49)

The method of claim 49, further comprising preparing a report for said subject, wherein said report indicates the presence or absence of an adenoma or polyp.

### Claim 54 (depends on 53)

The method of claim 53, wherein said report indicates a predisposition or risk for polyp development, a degree of cell dysplasia, a subtype of adenomatous polyp, or a subtype of benign colon tumor disease.

### Claim 55 (depends on 49)

The method of claim 49, wherein said method detects the presence or absence of an adenoma.

### Claim 56 (depends on 55)

The method of claim 55, wherein said adenoma is an adenomatous polyp or polypoid adenoma.

### Claim 57 (depends on 56)

The method of claim 56, wherein said adenomatous polyp or polypoid adenoma is selected from the group of pedunculated polyps and sessile polyps.

### Claim 58 (depends on 56)

The method of claim 56, wherein said adenomatous polyp or polypoid adenoma is characterized according to a degree of cell dysplasia or pre-malignancy.

### Claim 59 (depends on 49)

The method of claim 49, wherein said method further detects the presence or absence of colorectal carcinoma.

### Claim 60 (depends on 49)

The method of claim 49, wherein said method does not detect the presence or absence of colorectal carcinoma.

### Claim 61 (depends on 49)

The method of claim 49, wherein the presence or absence of colorectal carcinoma is not determined.

### Claim 62 (depends on 49)

The method of claim 49, wherein said presence or absence is confirmed by colonoscopy, imaging, and/or surgery.

### Claim 63 (depends on 49)

The method of claim 49, wherein said biological sample is selected from the group consisting of whole blood, serum, plasma, blood constituent, bone marrow, saliva, cheek swab, urine, stool, lymph fluid, CNS fluid, and lesion exudate.

### Claim 64 (depends on 63)

The method of claim 63, wherein said biological sample is selected from the group consisting of whole blood, serum, and plasma.

### Claim 65 (depends on 49)

The method of claim 49, wherein said subject is asymptomatic.

### Claim 66 (depends on 49)

The method of claim 49, wherein said subject is from 18 to 49 years old.

### Claim 67 (depends on 49)

The method of claim 49, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma.

### Claim 68 (depends on 49)

The method of claim 49, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma other than age.

### Claim 69 (depends on 49)

The method of claim 49, wherein said analysis of step (b) includes a method selected from the group consisting of spectroscopic analysis, mass spectrometry, immunological analysis, and enzymatic reactivity.

### Claim 70 (depends on 69)

The method of claim 69, wherein said analysis is mass spectrometry.

### Claim 71 (depends on 69)

The method of claim 69, wherein said immunological analysis includes an enzyme-linked immunosorbent assay or radioimmunoassay.

### Claim 72 (depends on 69)

The method of claim 69, wherein said immunological analysis includes immunoblotting, immunodiffusion, immunoelectrophoresis, or immunoprecipitation.

### Claim 73 (depends on 69)

The method of claim 69, wherein said immunological analysis includes immunostaining and/or flow cytometry analysis.

### Claim 74 (depends on 49)

The method of claim 49, wherein said control reference is the presence and amount of a set of one or more non-overlapping proteins and/or peptides in the same biological sample.

### Claim 75 (depends on 49)

The method of claim 49, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is present.

### Claim 76 (depends on 49)

The method of claim 49, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is not present.

### Claim 77 (depends on 49)

The method of claim 49, wherein said analysis detects the presence and amount of a number of proteins or polypeptides, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, and at least 1000.

### Claim 78 (depends on 49)

The method of claim 49, wherein said analysis detects the presence and amount of one or more of the following sets:
i) one or more proteins selected from SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
ii) one or more peptide fragments of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
iii) one or more peptides with a sequence homology to SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof, wherein said sequence homology is selected from the group of greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%; and
iv) one or more binding partners of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof.

### Claim 79 (depends on 49)

The method of claim 49, wherein said analysis detects the presence and/or amount of one or more neutral mass clusters from FIG. 7 or FIG. 8.

### Claim 80 (depends on 79)

The method of claim 79, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, at least 200, at least 500, and at least 1000.

### Claim 81 (depends on 79)

The method of claim 79, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is at least one, and is selected from less than 5, less than 10, less than 50, less than 100, less than 200, less than 500, and less than 1000.

### Claim 82 (depends on 79)

The method of claim 79, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from the group consisting of 10 to 50, 60 to 100, 150-300, 400-600, and 800-1000, inclusive.

### Claim 83 (depends on 79)

The method of claim 79, wherein said neutral mass cluster has a classifier frequency when tested according to a 70/30 training/test for split classifiers, wherein said classifier frequency is selected from at least 3 out of 50, at least 10 out of 50, at least 20 out of 50, at least 30 out of 50, and at least 40 out of 50.

### Claim 84 (depends on 79)

The method of claim 79, wherein said analysis detects the presence and/or amount of a protein or peptide from which one or more neutral mass clusters from FIG. 7 or FIG. 8 is derived.

### Claim 85 (depends on 79)

The method of claim 79, further comprising
(e) performing an analysis of the biological sample for the presence and amount of one or more analytes selected from the groups consisting of metabolites, DNA sequences, RNA sequences, and combinations thereof; and
(f) comparing the presence and amount of said analytes to a control reference value; and
(g) correlating the presence and amount of said analytes with the subject's adenoma or polyp status.

### Claim 86

A method of detecting recurrence or absence of an adenoma or polyp of the colon in a subject previously treated for adenoma or polyps of the colon comprising the steps of:
(a) obtaining a biological sample from a subject previously treated for adenoma or polyps of the colon;
(b) performing an analysis of the biological sample for the presence and amount of one or more proteins and/or peptides;
(c) comparing the presence and amount of one or more proteins and/or peptides from said biological sample to a control reference value; and
(d) correlating the presence and amount of one or more proteins and/or peptides with the subject's adenoma or polyp status.

### Claim 87 (depends on 86)

The method of claim 86, wherein said method achieves a sensitivity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 88 (depends on 86)

The method of claim 86, wherein said method achieves a specificity selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 89 (depends on 86)

The method of claim 86, wherein said method achieves sensitivity and specificity each individually selected from greater than 70%, greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%.

### Claim 90 (depends on 86)

The method of claim 86, further comprising preparing a report for said subject, wherein said report indicates the presence or absence of an adenoma or polyp.

### Claim 91 (depends on 90)

The method of claim 90, wherein said report indicates a predisposition or risk for polyp development, a degree of cell dysplasia, a subtype of adenomatous polyp, or a subtype of benign colon tumor disease.

### Claim 92 (depends on 86)

The method of claim 86, wherein said method detects the presence or absence of an adenoma.

### Claim 93 (depends on 92)

The method of claim 92, wherein said adenoma is an adenomatous polyp or polypoid adenoma.

### Claim 94 (depends on 93)

The method of claim 93, wherein said adenomatous polyp or polypoid adenoma is selected from the group of pedunculated polyps and sessile polyps.

### Claim 95 (depends on 93)

The method of claim 93, wherein said adenomatous polyp or polypoid adenoma is characterized according to a degree of cell dysplasia or pre-malignancy.

### Claim 96 (depends on 86)

The method of claim 86, wherein said method further detects the presence or absence of colorectal carcinoma.

### Claim 97 (depends on 86)

The method of claim 86, wherein said method does not detect the presence or absence of colorectal carcinoma.

### Claim 98 (depends on 86)

The method of claim 86, wherein the presence or absence of colorectal carcinoma is not determined.

### Claim 99 (depends on 86)

The method of claim 86, wherein said presence or absence is confirmed by colonoscopy, imaging, and/or surgery.

### Claim 100 (depends on 86)

The method of claim 86, wherein said biological sample is selected from the group consisting of whole blood, serum, plasma, blood constituent, bone marrow, saliva, cheek swab, urine, stool, lymph fluid, CNS fluid, and lesion exudate.

### Claim 101 (depends on 100)

The method of claim 100, wherein said biological sample is selected from the group consisting of whole blood, serum, and plasma.

### Claim 102 (depends on 86)

The method of claim 86, wherein said subject is asymptomatic.

### Claim 103 (depends on 86)

The method of claim 86, wherein said subject is from 18 to 49 years old.

### Claim 104 (depends on 86)

The method of claim 86, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma.

### Claim 105 (depends on 86)

The method of claim 86, wherein said subject has no symptoms for colorectal carcinoma, no family history for colorectal carcinoma, and no recognized risk factors for colorectal carcinoma other than age.

### Claim 106 (depends on 86)

The method of claim 86, wherein said analysis of step (b) includes a method selected from the group consisting of spectroscopic analysis, mass spectrometry, immunological analysis, and enzymatic reactivity.

### Claim 107 (depends on 106)

The method of claim 106, wherein said analysis is mass spectrometry.

### Claim 108 (depends on 106)

The method of claim 106, wherein said immunological analysis includes an enzyme-linked immunosorbent assay or radioimmunoassay.

### Claim 109 (depends on 106)

The method of claim 106, wherein said immunological analysis includes immunoblotting, immunodiffusion, immunoelectrophoresis, or immunoprecipitation.

### Claim 110 (depends on 106)

The method of claim 106, wherein said immunological analysis includes immunostaining and/or flow cytometry analysis.

### Claim 111 (depends on 86)

The method of claim 86, wherein said control reference is the presence and amount of a set of one or more non-overlapping proteins and/or peptides in the same biological sample.

### Claim 112 (depends on 86)

The method of claim 86, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is present.

### Claim 113 (depends on 86)

The method of claim 86, wherein said control reference is the presence and amount of an overlapping set of proteins and/or peptides obtained from one or more subjects in which adenoma or polyp of the colon is not present.

### Claim 114 (depends on 86)

The method of claim 86, wherein said analysis detects the presence and amount of a number of proteins or polypeptides, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, and at least 1000.

### Claim 115 (depends on 86)

The method of claim 86, wherein said analysis detects the presence and amount of one or more of the following sets:
i) one or more proteins selected from SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
ii) one or more peptide fragments of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
iii) one or more peptides with a sequence homology to SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof, wherein said sequence homology is selected from the group of greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%; and
iv) one or more binding partners of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), and ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 combinations thereof.

### Claim 116 (depends on 86)

The method of claim 86, wherein said analysis detects the presence and/or amount of one or more neutral mass clusters from FIG. 7 or FIG. 8.

### Claim 117 (depends on 116)

The method of claim 116, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from at least 2, at least 5, at least 10, at least 50, at least 100, at least 200, at least 500, and at least 1000.

### Claim 118 (depends on 116)

The method of claim 116, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is at least one, and is selected from less than 5, less than 10, less than 50, less than 100, less than 200, less than 500, and less than 1000.

### Claim 119 (depends on 116)

The method of claim 116, wherein said analysis detects the presence and/or amount of a number of neutral mass clusters from FIG. 7 or FIG. 8, wherein said number is selected from the group consisting of 10 to 50, 60 to 100, 150-300, 400-600, and 800-1000, inclusive.

### Claim 120 (depends on 116)

The method of claim 116, wherein said neutral mass cluster has a classifier frequency when tested according to a 70/30 training/test for split classifiers, wherein said classifier frequency is selected from at least 3 out of 50, at least 10 out of 50, at least 20 out of 50, at least 30 out of 50, and at least 40 out of 50.

### Claim 121 (depends on 116)

The method of claim 116, wherein said analysis detects the presence and/or amount of a protein or peptide from which one or more neutral mass clusters from FIG. 7 or FIG. 8 is derived.

### Claim 122 (depends on 86)

The method of claim 86, further comprising:
(e) performing an analysis of the biological sample for the presence and amount of one or more analytes selected from the groups consisting of metabolites, DNA sequences, RNA sequences, and combinations thereof;
(f) comparing the presence and amount of said analytes to a control reference value; and
(g) correlating the presence and amount of said analytes with the subject's adenoma or polyp status.

### Claim 123 (depends on 86)

The method of claim 86, wherein said subject was previously treated for polyps of the colon by removal of the polyps.

### Claim 124 (depends on 86)

The method of claim 86, wherein said subject was previously treated by removal of at least one centimeter of tissue from the colon.

### Claim 125

A method of protein and/or peptide detection for diagnostic application comprising the steps of:
(a) obtaining a biological sample from a subject;
(b) performing an analysis of the biological sample for the presence and amount of one or more proteins and/or peptides;
(c) comparing the presence and amount of one or more proteins and/or peptides from said biological sample to a control reference value; and
(d) correlating the presence and amount of one or more proteins and/or peptides with a diagnosis for said subject;
wherein said analysis detects the presence and amount of one or more of the following sets:
i) one or more proteins selected from SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
ii) one or more peptide fragments of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), and ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 combinations thereof;
iii) one or more peptides with a sequence homology to SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof, wherein said sequence homology is selected from the group of greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%;
iv) one or more binding partners of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), and ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 combinations thereof; and
v) a protein or peptide from which one or more neutral mass clusters from FIG. 7 or FIG. 8 is derived.

### Claim 126 (depends on 125)

The method of claim 125, wherein said diagnosis is the presence or absence of a condition selected from the group consisting of adenoma, polyp of the colon, colorectal carcinoma, and combinations thereof.

### Claim 127 (depends on 125)

The method of claim 125, further comprising determining said amount in step (b) by:
(b1) contacting the biological sample or portion thereof with a first anti-peptide antibody specific for a first peptide;
(b2) contacting the biological sample or portion thereof with a second anti-peptide antibody specific for a second peptide, wherein said second anti-peptide antibody is different from said first anti-peptide antibody;
(b3) separating peptides bound by said first and second anti-peptide antibodies from unbound peptides;
(b4) detecting and/or measuring amounts of said peptides bound by said first and second anti-peptide antibodies using mass spectrometry, flow cytometry, non-overlapping excitation spectra, western analysis, enzyme-linked immunosorbent assay, densitometry, or combinations thereof.

### Claim 128 (depends on 127)

The method of claim 127, wherein said biological sample or portion thereof is a proteolytic digest of said biological sample.

### Claim 129 (depends on 127)

The method of claim 127, where step (b4) includes mass spectrometry.

### Claim 130 (depends on 1, 129)

A kit for performing a method according to any one of claims 1-129:
(a) a container for collecting a sample from a subject;
(b) means for detecting one or more proteins or peptides, or means for transferring said container to a test facility; and
(c) written instructions.

### Claim 131 (depends on 130)

The kit of claim 130, wherein said means for detecting one or more proteins or peptides comprises one or more antibodies that bind one or more of the following sets:
i) one or more proteins selected from SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
ii) one or more peptide fragments of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), and ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof;
iii) one or more peptides with a sequence homology to SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof, wherein said sequence homology is selected from the group of greater than 75%, greater than 80%, greater than 85%, greater than 90%, greater than 95%, and greater than 99%;
iv) one or more binding partners of SCDC26 (CD26), CEA molecule 5 (CEACAM5), CA195 (CCR5), CA19-9, M2PK (PKM2), TIMP1, P-selectin (SELPLG), VEGFA, HcGB (CGB), VILLIN, TATI (SPINK1), A-L-fucosidase (FUCA2), ANXA5, GAPDH, PKM2, ANXA4, GARS, RRBP1, KRT8, SYNCRIP, S100A9, ANXA3, CAPG, HNRNPF, PPA1, NME1, PSME3, AHCY, TPT1, HSPB1, and RPSA, and/or the proteins in FIG. 9 and combinations thereof; and
v) a protein or peptide from which one or more neutral mass clusters from FIG. 7 or FIG. 8 is derived.

### Claim 132 (depends on 131)

The kit of claim 131, wherein one or more antibodies are each tagged with a label.

### Claim 133 (depends on 132)

The kit of claim 132, wherein the label is selected from the group consisting of a radioactive label, a fluorescent label, an enzyme, a chemiluminescent tag, and combinations thereof.

### Claim 134 (depends on 131)

The kit of claim 131, wherein the antibodies are packaged in an aqueous medium or in lyophilized form.

### Claim 135 (depends on 130)

The kit of claim 130, wherein said means for detecting one or more proteins or peptides comprises an enzyme-linked immunosorbent assay.

### Claim 136

A method for the diagnosis, prediction, prognosis and/or monitoring a colon disease in a subject comprising: measuring at least one biomarker selected from the group ACTB ACTH, ANGT, SAHH, ALDR, AKT1, ALBU, AL1A1, AL1B1, ALDOA, AMY2B, ANXA1, ANXA3, ANXA4, ANXA5, APC, APOA1, APOC1, APOH, GDIR1, ATPB, BANK1, MIC1, CA195, CO3, CO9, CAH1, CAH2, CALR, CAPG, CD24, CD63, CDD, CEAM3, CEAM5, CEAM6 CGHB, CH3L1, KCRB, CLC4D, CLUS, CNN1, COR1C, CRP, CSF1, CTNB1, CATD, CATS, CATZ, CUL1, SYDC, DEF1, DEF3, DESM, DPP4, DPYL2, DYHC1, ECH1, EF2, IF4A3, ENOA EZRI, NIBL2, SEPR, FBX4, FIBB, FIBG, FHL1, FLNA, FRMD3, FRIH, FRIL, FUCO, GBRA1, G3P, SYG, GDF15, GELS, GSTP1, HABP2, HGF, 1A68, HMGB1, ROA1, ROA2, HNRPF, HPT, HS90B, ENPL, GRP75, HSPB1, CH60, SIAL, IFT74, IGF1, IGHA2, IL2RB, IL8, IL9, RASK, K1C19, K2C8, LAMA2, LEGS, LMNB1, MARE1, MCM4, MIF, MMP7, MMP9, CD20, MYL6, MYL9, NDKA, NNMT, A1AG1, PCKGM, PDIA3, PDIA6, PDXK, PEBP1, PIPNA, KPYM, UROK, IPYR, PRDX1, KPCD1, PRL, TMG4, PSME3, PTEN, FAK1, FAK2, RBX1, REG4, RHOA, RHOB, RHOC, RSSA, RRBP1, S10AB, S10AC, S10A8, S109, SAA1, SAA2, SEGN, SDCG3, DHSA, SBP1, SELPL, SEP9, A1AT, AACT, ILEU, SPB6, SF3B3, SKP1, ADT2, ISK1, SPON2, OSTP, SRC, STK11, HNRPQ, TAL1, TRFE, TSP1, TIMP1, TKT, TSG6, TR10B, TNF6B, P53, TPM2, TCTP, TRAP1, THTR, TBB1, UGDH, UGPA, VEGFA, VILI, VIME, VNN1, 1433Z, CCR5, FUCO, and combinations thereof in a biological sample from the subject.

### Claim 137

A method for the diagnosis, prediction, prognosis and/or monitoring a colon disease in a subject comprising: measuring at least one biomarker selected from the group SPB6, FRIL, P53, 1A68, ENOA, TKT, and combinations thereof in a biological sample from the subject.

### Claim 138

A method for the diagnosis, prediction, prognosis and/or monitoring a colon disease in a subject comprising: measuring at least one biomarker selected from the group SPB6, FRIL, P53, 1A68, ENOA, TKT, TSG6, TPM2, ADT2, FHL1, CCR5, CEAM5, SPON2, 1A68, RBX1, COR1C, VIME, PSME3, and combinations thereof in a biological sample from the subject.

### Claim 139

A method for the diagnosis, prediction, prognosis and/or monitoring a colon disease in a subject comprising: measuring at least one biomarker selected from the group SPB6, FRIL, P53, 1A68, ENOA, TKT, TSG6, TPM2, ADT2, FHL1, CCR5, CEAM5, SPON2, 1A68, RBX1, COR1C, VIME, PSME3, MIC1, STK11, IPYR, SBP1, PEBP1, CATD, HPT, ANXA5, ALDOA, LAMA2, CATZ, ACTB, AACT, and combinations thereof in a biological sample from the subject.