Variants at chr8q24.21 confer risk of cancer
A locus on chromosome 8q24.21 has been demonstrated to play a major role in particular forms of cancer. It has been discovered that certain markers and haplotypes are indicative of a susceptibility to particular cancers. Diagnostic applications for identifying susceptibilty to cancer are described.
1 . A method of diagnosing a susceptibility to a cancer in a subject, comprising detecting a marker or haplotype associated with LD Block A, wherein the presence of the marker or haplotype is indicative of a susceptibility to cancer.
2 . The method of claim 1 wherein the marker or haplotype is a marker selected from the group consisting of the markers in Table 13.
3 . The method of claim 2 wherein the marker is the rs1447295 A allele or the DG8S737 −8 allele.
4 . The method of claim 1 wherein the marker or at risk haplotype is an at risk haplotype comprising a haplotype selected from the group consisting of: haplotype 1 and haplotype 1a.
5 . The method of claim 1 wherein the marker or haplotype is a haplotype that comprises one or more markers selected from the group consisting of the markers in Table 13.
6 . The method of claim 5 wherein the haplotype comprises the rs1447295 A allele or the DG8S737 −8 allele.
7 . The method of claim 1 wherein the cancer is selected from the group consisting of prostate cancer, breast cancer, lung cancer and melanoma.
8 . The method of claim 7 wherein cancer is prostate cancer, and the marker or haplotype has a relative risk of at least 1.5.
9 . The method of claim 8 wherein the prostate cancer is an aggressive prostate cancer as defined by a combined Gleason score of 7(4+3)-10.
10 . The method of claim 8 wherein the prostate cancer is a less aggressive prostate cancer as defined by a combined Gleason score of 2-7(3+4).
11 . The method of claim 8 wherein the presence of the marker or haplotype is indicative of a more aggressive prostate cancer and/or a worse prognosis.
12 . The method of claim 7 wherein the cancer is breast cancer, and the marker or haplotype has a relative risk of at least 1.3.
13 . The method of claim 7 wherein the cancer is lung cancer, and the marker or haplotype has a relative risk of at least 1.3.
14 . The method of claim 7 wherein the cancer is melanoma, and the marker or haplotype has a relative risk of at least 1.5.
15 . The method of claim 7 wherein the melanoma is malignant cutaneous melanoma.
16 . The method of claim 1 wherein the presence of the marker or haplotype is indicative of a different response rate of the subject to a particular treatment modality.
17 . The method of claim 1 , wherein the presence of the marker or haplotype is indicative of a predisposition to a somatic rearrangement of Chr8q24.21 in a tumor or its precursor.
18 . The method of claim 17 wherein the somatic rearrangement is selected from the group consisting of an amplification, a translocation, an insertion and a deletion.
19 . The method of claim 1 , wherein the marker or haplotype comprises one or more markers associated with Chr8q24.21 in strong linkage disequilibrium, as defined by (|D′|>0.8) and/or r 2 >0.2, with one or more markers selected from the group consisting of the markers in Table 13.
20 . The method of claim 19 , wherein the one or more marker comprises the rs1447295 A allele or the DG8S737 −8 allele.
21 . A method of diagnosing a susceptibility to a cancer comprising detecting a marker or haplotype associated with Chr8q24.21, wherein the presence of the marker or haplotype is indicative of a susceptibility to cancer.
22 . (canceled)
23 . A method of predicting an increased risk for aggressive prostate cancer in a subject comprising detecting a marker or haplotype associated with LD Block A, wherein the presence of the marker or haplotype is indicative of an increased risk for aggressive prostate cancer.
24 . (canceled)
25 . A kit for assaying a sample from a subject to detect a susceptibility to a cancer, wherein the kit comprises one or more reagents for detecting a marker or haplotype associated with LD Block A.
26 - 28 . (canceled)
29 . A method for diagnosing an increased risk of cancer in a subject, comprising screening for a marker or haplotype associated with LD Block A, wherein the marker or haplotype is more frequently present in a subject having the cancer than in a subject not having the cancer, and wherein the presence of the marker or haplotype increases the risk of the subject having the cancer.
30 . (canceled)
31 . A method for diagnosing a susceptibility to cancer in a subject, comprising:
i) obtaining a nucleic acid sample from the subject; and
ii) analyzing the nucleic acid sample for the presence or absence of at least one marker or haplotype associated with LD Block A, wherein the presence of the marker or haplotype is indicative of a susceptibility to the cancer.
32 - 34 . (canceled)
35 . A method of diagnosing a Chr8q24.21-associated cancer in a subject, comprising detecting the presence of a marker or haplotype associated with Chr8q24.21, wherein the presence of the marker or haplotype is indicative of the Chr8q24.21-associated cancer.
36 - 38 . (canceled)
39 . A method of diagnosing a susceptibility to prostate cancer in an individual, comprising:
1) detecting marker DG8S737, wherein the presence of a −8 allele in DG8S737 is indicative of a susceptibility to prostate cancer; and/or
2) detecting marker rs1447295, wherein the presence of an A allele in rs1447295 is indicative of a susceptibility to prostate cancer.
40 - 43 . (canceled)
44 . A method of diagnosing an increased risk of prostate cancer in an individual, comprising:
1) detecting marker DG8S737, wherein the presence of a −8 allele in DG8S737 is indicative of an increased risk of prostate cancer; and/or
2) detecting marker rs1447295, wherein the presence of an A allele in rs1447295 is indicative of a susceptibility to prostate cancer.
45 . A method of predicting an increased risk for prostate cancer in a subject comprising:
1) detecting marker DG8S737, wherein the presence of a −8 allele in DG8S737 is indicative of an increased risk for prostate cancer; and/or
2) detecting marker rs1447295, wherein the presence of an A allele in rs1447295 is indicative of a susceptibility to prostate cancer.
46 . A method of predicting an increased risk for aggressive prostate cancer in a subject comprising:
1) detecting marker DG8S737, wherein the presence of a −8 allele in DG8S737 is indicative of an increased risk for aggressive prostate cancer; and/or
2) detecting marker rs1447295, wherein the presence of an A allele in rs1447295 is indicative of a susceptibility to prostate cancer.
47 . A method of diagnosing a susceptibility to prostate cancer in a human having ancestry that includes African ancestry, comprising:
1) detecting marker DG8S737, wherein the presence of a −8 allele in DG8S737 is indicative of a susceptibility to prostate cancer; and/or
2) detecting marker rs1447295, wherein the presence of an A allele in rs1447295 is indicative of a susceptibility to prostate cancer.
48 - 55 . (canceled)
56 . A method of diagnosing a decreased susceptibility to prostate cancer in an individual, comprising detecting the haplotype shown in Table 22, wherein the presence of the haplotype is indicative of a decreased susceptibility to prostate cancer.
57 . A method of diagnosing a decreased susceptibility to prostate cancer in an individual, comprising detecting a marker shown in Table 13 having a relative risk of less than one, wherein the presence of the marker is indicative of a decreased susceptibility to prostate cancer.
58 . A method of diagnosing an increased susceptibility to prostate cancer in an individual, comprising detecting a marker shown in Table 13 having a relative risk of greater than one, wherein the presence of the marker is indicative of an increased susceptibility to prostate cancer.
59 . A method for diagnosing a susceptibility to cancer in a subject, comprising analyzing a nucleic acid sample obtained from the subject for the presence of at least one marker or haplotype associated with LD Block A, wherein the presence of the marker or haplotype is indicative of increased susceptibility to the cancer.
60 - 84 . (canceled)