Biomarker panel for colorectal cancer

1 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising at least two polynucleotides selected from SEQ ID NOs 1-5.

2 . The panel of claim 1 , where the panel is selected for analysis of polynucleotide expression levels for colorectal cancer and colorectal polyps.

3 . The panel of claim 2 , where the polynucleotide expression levels are mRNAs.

4 . The panel of claim 2 , where the polynucleotide expression levels are cDNAs.

5 . The panel of claim 1 , where at least one of the polynucleotides is a fragment.

6 . The panel of claim 1 , where at least one of the polynucleotides is a variant.

7 . The panel of claim 1 , where the panel is used for the management of patient care in colorectal cancer and colorectal polyps.

8 . The panel of claim 7 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

9 . The panel of claim 1 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

10 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising:

at least two polynucleotides selected from SEQ ID NOs 1-5; and

at least one polynucleotide selected from SEQ ID NOs 6-14.

11 . The panel of claim 10 , where the panel is selected for analysis of polynucleotide expression levels for colorectal cancer and colorectal polyps.

12 . The panel of claim 11 , where the polynucleotide expression levels are mRNAs.

13 . The panel of claim 11 , where the polynucleotide expression levels are cDNAs.

14 . The panel of claim 10 , where at least one of the polynucleotides is a fragment.

15 . The panel of claim 10 , where at least one of the polynucleotides is a variant.

16 . The panel of claim 10 , where the panel is used in the management of patient care for colorectal cancer and colorectal polyps.

17 . The panel of claim 16 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

18 . The panel of claim 10 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

19 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising:

at least two polynucleotides selected from SEQ ID NOs 1-5;

at least one polynucleotide selected from SEQ ID NOs 6-14; and

at least one polynucleotide selected from SEQ ID NOs 15-22.

20 . The panel of claim 19 , where the panel is selected for analysis of polynucleotide expression levels for colorectal cancer and colorectal polyps.

21 . The panel of claim 20 , where the polynucleotide expression levels are mRNAs.

22 . The panel of claim 20 , where the polynucleotide expression levels are cDNAs.

23 . The panel of claim 19 , where at least one of the polynucleotides is a fragment.

24 . The panel of claim 19 , where at least one of the polynucleotides is a variant.

25 . The panel of claim 25 , where the panel is the basis for management of patient care in colorectal cancer and colorectal polyps.

26 . The panel of claim 19 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

27 . The panel of claim 25 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

28 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising at least two polypeptides selected from SEQ ID NOs 23-27.

29 . The panel of claim 28 , where the panel is selected for analysis of polypeptide expression levels for colorectal cancer and colorectal polyps.

30 . The panel of claim 28 , where at least one of the polypeptides is a fragment.

31 . The panel of claim 28 , where at least one of the polypeptides is a variant.

32 . The panel of claim 28 , where the panel is used in the management of patient care in colorectal cancer and colorectal polyps.

33 . The panel of claim 32 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

34 . The panel of claim 28 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

35 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising:

at least two polypeptides selected from SEQ ID NOs 23-27; and

at least one polypeptide selected from SEQ ID NOs 28-36.

36 . The panel of claim 35 , where the panel is selected for analysis of polypeptide expression levels for colorectal cancer and colorectal polyps.

37 . The panel of claim 35 , where at least one of the polypeptides is a fragment.

38 . The panel of claim 35 , where at least one of the polypeptides is a variant.

39 . The panel of claim 35 , where the panel is used in the management of patient care in colorectal cancer and colorectal polyps.

40 . The panel of claim 39 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

41 . The panel of claim 35 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

42 . A panel of biomarkers for colorectal cancer and colorectal polyps comprising:

at least two polypeptides selected from SEQ ID NOs 23-27;

at least one polypeptide selected from SEQ ID NOs 28-36; and

at least one polypeptide selected from SEQ ID NOs 37-44.

43 . The panel of claim 42 , where the panel is selected for analysis of polypeptide expression levels for colorectal cancer and colorectal polyps.

44 . The panel of claim 42 , where at least one of the polypeptides is a fragment.

45 . The panel of claim 42 , where at least one of the polypeptides is a variant.

46 . The panel of claim 42 , where the panel is used in the management of patient care in colorectal cancer and colorectal polyps.

47 . The panel of claim 46 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

48 . The panel of claim 42 , where the panel is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

49 . A method for measuring expression levels of polynucleotides from biomarkers for colorectal cancer and colorectal polyps, comprising:

selecting a panel of biomarkers comprising at least two polynucleotides from SEQ ID NOs 1-5;

obtaining a biological sample;

isolating cellular RNA from the sample;

amplifying copies of cDNA from the sample for each biomarker in the panel; and

quantifying levels of cDNA amplified from the sample.

50 . The method of claim 49 , where the step of selecting a panel of biomarkers further comprises at least one polynucleotide from SEQ ID NOs 6-14.

51 . The method of claim 49 , where the step of selecting a panel of biomarkers further comprises:

at least one polynucleotide from SEQ ID NOs 6-14; and

at least one polynucleotide from SEQ ID NOs 15-22.

52 . The method of claim 49 , where the step of amplifying copies of cDNA further comprises at least two sets of primers chosen from SEQ. ID NOs 45-50.

53 . The method of claim 52 , where the step of amplifying copies of cDNA further comprises using enzymes and reagents for the preparation of cDNAs.

54 . The method of claim 49 , where the step of quantifying the levels of cDNA further comprises labeling cDNA.

55 . The method of claim 54 , where labeling cDNA includes at least one chromophore.

56 . The method of claim 49 , where the cDNA levels for the sample are compared to a control.

57 . The method of claim 56 , where the comparison is used in the management of patient care in colorectal cancer and colorectal polyps.

58 . The method of claim 57 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

59 . The method of claim 56 , where the comparison is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

60 . The method of claim 49 , where the step of obtaining a biological sample is by obtaining a sample of colorectal cells.

61 . The method of claim 60 , where the step of obtaining a sample of colorectal cells is minimally invasive.

62 . The method of claim 61 , where the minimally invasive step is by use of a swab.

63 . The method of claim 60 , where the step of obtaining a sample of colorectal cells is non-invasive.

64 . The method of claim 63 , where the non-invasive step is by collection of a stool sample.

65 . A method for measuring expression levels of polypeptides from biomarkers for colorectal cancer and colorectal cancer, comprising:

selecting a panel of biomarkers comprising at least two polypeptides from SEQ ID NOs 23-27;

obtaining a biological sample;

creating an antibody panel for each biomarker in the panel;

using the antibody panel to bind the polypeptides from the sample; and

quantifying levels of polypeptides bound from the sample to the antibody panel.

66 . The method of claim 65 , where the step of selecting a panel of biomarkers further comprises at least one polypeptide from SEQ ID NOs 28-36.

67 . The method of claim 65 , where the step of selecting a panel of biomarkers further comprises:

at least one polypeptide from SEQ ID NOs 28-36; and

gat least one polypeptide from SEQ ID NOs 37-44.

68 . The method of claim 65 , where the polypeptide levels for the sample are compared to a control.

69 . The method of claim 68 , where the comparison is used in the management of patient care in colorectal cancer and colorectal polyps.

70 . The method of claim 69 , where the management of patient care includes one or more of risk assessment, early diagnosis, establishing prognosis, monitoring patient treatment, and detecting relapse.

71 . The method of claim 68 , where the comparison is used in discovery of therapeutic intervention of colorectal cancer and colorectal polyps.

72 . The method of claim 65 , where the step of obtaining a biological sample is by obtaining a sample of colorectal cells.

73 . The method of claim 72 , where the step of obtaining a sample of colorectal cells is minimally invasive.

74 . The method of claim 73 , where the minimally invasive step is by use of a swab.

75 . The method of claim 72 , where the step of obtaining a sample of colorectal cells is non-invasive.

76 . The method of claim 75 , where the non-invasive step is by collection of a stool sample.

77 . The method of claim 65 , where the step of quantifying the bound polypeptides further comprises labeling the polypeptides.

78 . The method of claim 77 , where labeling the polypeptides comprises using a second antibody.

79 . A kit for the determination of colorectal cancer and colorectal polyps comprising:

at least one reagent that is used in analysis of polynucleotide expression levels for a panel of biomarkers for colorectal cancer and colorectal polyps, where the panel comprises at least two polynucleotides listed in SEQ ID NOs 1-5; and

instructions for using the kit for analyzing the expression levels.

80 . The kit of claim 79 , where the panel of biomarkers further comprises at least one polynucleotides listed in SEQ ID NOs 6-14.

81 . The kit of claim 79 , where the panel of biomarkers further comprises:

at least one polynucleotide selected from SEQ ID NOs 6-14; and

at least one polynucleotide selected from SEQ ID NOs 15-22.

82 . The kit of claim 79 , where the polynucleotide expression levels are mRNAs.

83 . The kit of claim 79 , where the polynucleotide expression levels are cDNAs.

84 . The kit of claim 83 , where the reagent comprises at least two sets of primers chosen from SEQ. ID NOs 45-50.

85 . The kit of claim 84 , further comprising reagents for the preparation of cDNA.

86 . The kit of claim 79 , comprising a reagent that is used for detection and quantitation of polynucleotides.

87 . The kit of claim 86 , where the reagent includes at least one chromophore.

88 . The kit of claim 79 , further comprising consumable labware for at least one of sample collection, sample preparation, and sample analysis.

89 . A kit for the determination of colorectal cancer and colorectal polyps comprising:

at least one reagent used in that analysis of polypeptide expression levels for a panel of biomarkers for colorectal cancer and colorectal polyps, where the panel comprises at least two polypeptides listed in SEQ. ID NOs 23-27; and

instructions for using the kit for analyzing the expression levels.

90 . The kit of claim 89 , where the panel of biomarkers further comprises at least one polynucleotides listed in SEQ ID NOs 28-36.

91 . The kit of claim 89 , where the panel of biomarkers further comprises:

at least one polynucleotide selected from SEQ ID NOs 28-36; and

at least one polynucleotide selected from SEQ ID NOs 37-44.

92 . The kit of claim 89 , where the reagent is an antibody reagent that binds a polypeptide selected in the panel.

93 . The kit of claim 89 , further comprising a reagent that is used for detection and quantitation of a bound polypeptide.

94 . The kit of claim 93 , where the reagent includes a second antibody.

95 . The kit of claim 89 , further comprising consumable labware for at least one of sample collection, sample preparation, and sample analysis.