Genome-wide association studies in cancer-current and future directions

Carcinogenesis

Volumn 31, Issue 1, 2009, Pages 111-120

  Chung, Charles C ^a   Magalhaes, Wagner C S ^a,b   Gonzalez Bosquet, Jesus ^a   Chanock, Stephen J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BLADDER CANCER; BREAST CANCER; CANCER CLASSIFICATION; CANCER GENETICS; CANCER RISK; CHROMOSOME 5P; COLORECTAL CANCER; FOLLOW UP; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN GENOME; LUNG CANCER; MALIGNANT NEOPLASTIC DISEASE; PHARMACOGENOMICS; PRIORITY JOURNAL; PROSTATE CANCER; SINGLE NUCLEOTIDE POLYMORPHISM; GENETICS; NEOPLASM;

GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 74049103101     PISSN: 01433334     EISSN: 14602180     Source Type: Journal    
DOI: 10.1093/carcin/bgp273     Document Type: Article

References (151)

1. The International HapMap Consortium. (2003) The International HapMap Project. Nature, 426, 789-796.
2. Collins, F.S. et al. (2003) A vision for the future of genomics research. Nature, 422, 835-847.
3. Lander, E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
4. Venter, J.C. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
5. The International HapMap Consortium. (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
6. Sachidanandam, R. et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928-933.
7. Chanock, S. (2001) Candidate genes and single nucleotide polymorphisms (SNPs) in the study of human disease. Dis. Markers, 17, 89-98.
8. Miki, Y. et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science, 266, 66-71.
9. NIH/CEPH Collaborative Mapping Group. (1992) A comprehensive genetic linkage map of the human genome. NIH/CEPH Collaborative Mapping Group. Science, 258, 67-86.
10. Elston, R.C. et al. (2001) Overview of model-free methods for linkage analysis. Adv. Genet., 42, 135-150.
11. Malkin, D. et al. (1990) Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science, 250, 1233-1238.
12. Hussussian, C.J. et al. (1994) Germline p16 mutations in familial melanoma. Nat. Genet., 8, 15-21.
13. Kamb, A. et al. (1994) Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. Nat. Genet., 8, 23-26.
14. Wooster, R. et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature, 378, 789-792.
15. Risch, N.J. (2000) Searching for genetic determinants in the new millennium. Nature, 405, 847-856.
16. Garcia-Closas, M. et al. (2005) NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Lancet, 366, 649-659.
17. Rothman, N. et al. (2006) Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: a report from the InterLymph Consortium. Lancet Oncol., 7, 27-38.
18. Cox, A. et al. (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nat. Genet., 39, 352-358.
19. Garcia-Closas, M. et al. (2007) Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. PLoS Genet., 3, e29.
20. Dunning, A.M. et al. (2009) Association of ESR1 gene tagging SNPs with breast cancer risk. Hum. Mol. Genet., 18, 1131-1139.
21. Risch, N. (2001) The genetic epidemiology of cancer: interpreting family and twin studies and their implications for molecular genetic approaches. Cancer Epidemiol. Biomarkers Prev., 10, 733-741.
22. Risch, N. et al. (1996) The future of genetic studies of complex human diseases. Science, 273, 1516-1517.
23. The Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature, 447, 661-678.
24. Barrett, J.C. et al. (2006) Evaluating coverage of genome-wide association studies. Nat. Genet., 38, 659-662.
25. O'Berg, M.T. (1980) Epidemiologic study of workers exposed to acrylonitrile. J. Occup. Med., 22, 245-252.
26. Wolff, M.S. et al. (1993) Blood levels of organochlorine residues and risk of breast cancer. J. Natl. Cancer Inst., 85, 648-652.
27. Erichsen, H.C. et al. (2004) SNPs in cancer research and treatment. Br. J. Cancer, 90, 747-751.
28. Frazer, K.A. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
29. Kidd, J.M. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
30. Levy, S. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
31. Ng, S.B. et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272-276.
32. Wang, J. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
33. Wheeler, D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
34. Kim, J.I. et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature, 460, 1011-1015.
35. Harismendy, O. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32.
36. Yeager, M. et al. (2008) Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum. Genet., 124, 161-170.
37. Hinds, D.A. et al. (2005) Whole-genome patterns of common DNA variation in three human populations. Science, 307, 1072-1079.
38. Yeager, M. et al. (2009) Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer. Hum. Genet., 126, 743-750.
39. Parikh, H. et al. (2009) A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33. Hum. Genet., in press.
40. Kruglyak, L. et al. (2001) Variation is the spice of life. Nat. Genet., 27, 234-236.
41. Reich, D.E. et al. (2001) Linkage disequilibrium in the human genome. Nature, 411, 199-204.
42. Reich, D.E. et al. (2003) Quality and completeness of SNP databases. Nat. Genet., 33, 457-458.
43. Hayden, E.C. (2008) International genome project launched. Nature, 451, 378-379.
44. Hudson, T.J. (2003) Wanted: regulatory SNPs. Nat. Genet., 33, 439-440.
45. Packer, B.R. et al. (2006) SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res., 34, D617-D621.
46. Stephens, M. et al. (2006) Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat. Genet., 38, 375-381.
47. Marth, G. et al. (2003) Sequence variations in the public human genome data reflect a bottlenecked population history. Proc. Natl Acad. Sci. USA, 100, 376-381.
48. Marth, G.T. et al. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet., 23, 452-456.
49. McCarroll, S.A. et al. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 39, S37-S42.
50. Scherer, S.W. et al. (2007) Challenges and standards in integrating surveys of structural variation. Nat. Genet., 39, S7-S15.
51. Sebat, J. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525-528.
52. Bailey, J.A. et al. (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res., 11, 1005-1017.
53. Bailey, J.A. et al. (2002) Recent segmental duplications in the human genome. Science, 297, 1003-1007.
54. Buckley, P.G. et al. (2005) Copy-number polymorphisms: mining the tip of an iceberg. Trends Genet., 21, 315-317.
55. McCarroll, S.A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
56. Bonnen, P.E. et al. (2002) Haplotype and linkage disequilibrium architecture for human cancer-associated genes. Genome Res., 12, 1846-1853.
57. Sabeti, P.C. et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
58. Slatkin, M. (2008) Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat. Rev. Genet., 9, 477-485.
59. Orr, N. et al. (2008) Common genetic variation and human disease. Adv. Genet., 62, 1-32.
60. Carlson, C.S. et al. (2004) Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet., 74, 106-120.
61. Cardon, L.R. et al. (2003) Using haplotype blocks to map human complex trait loci. Trends Genet., 19, 135-140.
62. Johnson, G.C. et al. (2001) Haplotype tagging for the identification of common disease genes. Nat. Genet., 29, 233-237.
63. Chanock, S.J. et al. (2007) Replicating genotype-phenotype associations. Nature, 447, 655-660.
64. Thomas, G. et al. (2009) A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat. Genet., 41, 579-584.
65. Thomas, G. et al. (2008) Multiple loci identified in a genome-wide association study of prostate cancer. Nat. Genet., 40, 310-315.
66. Yeager, M. et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet., 39, 645-649.
67. Yu, K. et al. (2008) Population substructure and control selection in genome-wide association studies. PLoS One, 3, e2551.
68. Patterson, N. et al. (2006) Population structure and eigenanalysis. PLoS Genet., 2, e190.
69. Price, A.L. et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
70. Ryckman, K. et al. (2008) Calculation and use of the Hardy-Weinbergmodel in association studies. Curr. Protoc. Hum. Genet., 57, 1.18.1-1.18.11.
71. Falush, D. et al. (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
72. Devlin, B. et al. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
73. Pritchard, J.K. et al. (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet., 65, 220-228.
74. Feigelson, H.S. et al. (2007) Successful genome-wide scan in paired blood and buccal samples. Cancer Epidemiol. Biomarkers Prev., 16, 1023-1025.
75. Easton, D.F. et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature, 447, 1087-1093.
76. Hindorff, L.A. et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
77. Manolio, T.A. et al. (2008) A HapMap harvest of insights into the genetics of common disease. J. Clin. Invest., 118, 1590-1605.
78. Manolio, T.A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
79. Purcell, S. et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
80. Diskin, S.J. et al. (2009) Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 459, 987-991.
81. Gudmundsson, J. et al. (2009) Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat. Genet., 41, 1122-1126.
82. Gudmundsson, J. et al. (2007) Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet., 39, 631-637.
83. Gudmundsson, J. et al. (2008) Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat. Genet., 40, 281-283.
84. Yeager, M. et al. (2009) Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat. Genet., 41, 1055-1057.
85. Eeles, R.A. et al. (2009) Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat. Genet., 41, 1116-1121.
86. Houlston, R.S. et al. (2008) Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat. Genet, 40, 1426-1435.
87. Hunter, D.J. et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat. Genet., 39, 870-874.
88. Zanke, B.W. et al. (2007) Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat. Genet., 39, 989-994.
89. Eeles, R.A. et al. (2008) Multiple newly identified loci associated with prostate cancer susceptibility. Nat. Genet., 40, 316-321.
90. Haiman, C.A. et al. (2007) Multiple regions within 8q24 independently affect risk for prostate cancer. Nat. Genet., 39, 638-644.
91. Schumacher, F.R. et al. (2007) A common 8q24 variant in prostate and breast cancer from a large nested case-control study. Cancer Res., 67, 2951-2956.
92. Stacey, S.N. et al. (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat. Genet., 39, 865-869.
93. Zheng, W. et al. (2009) Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat. Genet., 41, 324-328.
94. Chanock, S.J. et al. (2008) Genomics: when the smoke clears. Nature, 452, 537-538.
95. Hung, R.J. et al. (2008) A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature, 452, 633-637.
96. McKay, J.D. et al. (2008) Lung cancer susceptibility locus at 5p15.33. Nat. Genet., 40, 1404-1406.
97. Wang, Y. et al. (2008) Common 5p15.33 and 6p21.33 variants influence lung cancer risk. Nat. Genet., 40, 1407-1409.
98. Bierut, L.J. et al. (2007) Novel genes identified in a high-density genomewide association study for nicotine dependence. Hum. Mol. Genet., 16, 24-35.
99. Caporaso, N. et al. (2009) Genome-wide and candidate gene association study of cigarette smoking behaviors. PLoS One, 4, e4653.
100. Easton, D.F. et al. (2008) Genome-wide association studies in cancer. Hum. Mol. Genet., 17, R109-R115.
101. Kanetsky, P.A. et al. (2009) Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. Nat. Genet., 41, 811-815.
102. Rapley, E.A. et al. (2009) A genome-wide association study of testicular germ cell tumor. Nat. Genet., 41, 807-810.
103. Skinner, D.G. (1983) Urological Cancer. Grune & Stratton, New York.
104. Swerdlow, A.J. et al. (1997) Risks of breast and testicular cancers in young adult twins in England and Wales: evidence on prenatal and genetic aetiology. Lancet, 350, 1723-1728.
105. Gudmundsson, J. et al. (2009) Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Nat. Genet., 41, 460-464.
106. Jemal, A. et al. (2008) Cancer statistics, 2008. CA Cancer J. Clin., 58, 71-96.
107. Amundadottir, L. et al. (2009) Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat. Genet., 41, 986-990.
108. Bodmer, W. et al. (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet., 40, 695-701.
109. Wolpin, B.M. et al. (2009) ABO blood group and the risk of pancreatic cancer. J. Natl Cancer Inst., 101, 424-431.
110. Chang, B.L. et al. (2009) Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum. Mol. Genet., 18, 1368-1375.
111. Liu, P. et al. (2008) Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. J. Natl Cancer Inst., 100, 1326-1330.
112. Capasso, M. et al. (2009) Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. Nat. Genet., 41, 718-723.
113. Maris, J.M. et al. (2008) Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N. Engl. J. Med., 358, 2585-2593.
114. Papaemmanuil, E. et al. (2009) Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nat. Genet., 41, 1006-1010.
115. Trevino, L.R. et al. (2009) Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nat. Genet., 41, 1001-1005.
116. Andriole, G.L. et al. (2009) Mortality results from a randomized prostatecancer screening trial. N. Engl. J. Med., 360, 1310-1319.
117. Schroder, F.H. et al. (2009) Screening and prostate-cancer mortality in a randomized European study. N. Engl. J. Med., 360, 1320-1328.
118. Ahn, J. et al. (2008) Variation in KLK genes, prostate-specific antigen and risk of prostate cancer. Nat. Genet., 40, 1032-1034; author reply 1035-1036.
119. Eeles, R. et al. (2008) Reply to "Variation in KLK genes, prostate-specific antigen and risk of prostate cancer". Nat. Genet., 40, 1035-1036.
120. Garcia-Closas, M. et al. (2008) Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics. PLoS Genet., 4, e1000054.
121. Broderick, P. et al. (2009) Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Cancer Res., 69, 6633-6641.
122. Landi, M.T. et al. (2009) A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am. J. Hum. Genet., 85, 679-691.
123. Skibola, C.F. et al. (2009) Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Nat. Genet., 41, 873-875.
124. Chanock, S. (2009) High marks for GWAS. Nat. Genet., 41, 765-766.
125. Amundadottir, L.T. et al. (2006) A common variant associated with prostate cancer in European and African populations. Nat. Genet., 38, 652-658
126. Sun, J. et al. (2008) Evidence for two independent prostate cancer riskassociated loci in the HNF1B gene at 17q12. Nat. Genet., 40, 1153-1155.
127. Zheng, S.L. et al. (2009) Two independent prostate cancer risk-associated loci at 11q13. Cancer Epidemiol. Biomarkers Prev., 18, 1815-1820.
128. DePinho, R.A. et al. (1991) myc family oncogenes in the development of normal and neoplastic cells. Adv. Cancer Res., 57, 1-46.
129. Mhawech-Fauceglia, P. et al. (2006) Genetic alterations in urothelial bladder carcinoma: an updated review. Cancer, 106, 1205-1216.
130. Kiemeney, L.A. et al. (2008) Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet., 40, 1307-1312.
131. Ghoussaini, M. et al. (2008) Multiple loci with different cancer specificities within the 8q24 gene desert. J. Natl Cancer Inst., 100, 962-966.
132. Tomlinson, I. et al. (2007) A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat. Genet., 39, 984-988.
133. Tomlinson, I.P. et al. (2008) A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat. Genet., 40, 623-630.
134. Tenesa, A. et al. (2008) Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat. Genet., 40, 631-637.
135. Freedman, M.L. et al. (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl Acad. Sci. USA, 103, 14068-14073.
136. Al Olama, A.A. et al. (2009) Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat. Genet., 41, 1058-1060.
137. Gruber, S.B. et al. (2007) Genetic variation in 8q24 associated with risk of colorectal cancer. Cancer Biol. Ther., 6, 1143-1147.
138. Tuupanen, S. et al. (2009) The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat. Genet., 41, 885-890.
139. Pomerantz, M.M. et al. (2009) The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat. Genet., 41, 882-884.
140. Wu, X. et al. (2009) Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer. Nat. Genet., 41, 991-995.
141. Wrensch, M. et al. (2009) Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nat. Genet., 41, 905-908.
142. Shete, S. et al. (2009) Genome-wide association study identifies five susceptibility loci for glioma. Nat. Genet., 41, 899-904.
143. Choi, J. et al. (2008) TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental program. PLoS Genet., 4, e10.
144. Sweet-Cordero, A. et al. (2006) Comparison of gene expression and DNA copy number changes in a murine model of lung cancer. Genes Chromosomes Cancer, 45, 338-348.
145. Rafnar, T. et al. (2009) Sequence variants at the TERT-CLPTM1L locus associate with many cancer types. Nat. Genet., 41, 221-227.
146. Calado, R.T. et al. (2009) Constitutional hypomorphic telomerase mutations in patients with acute myeloid leukemia. Proc. Natl Acad. Sci. USA, 106, 1187-1192.
147. Yamaguchi, H. et al. (2005) Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia. N. Engl. J. Med., 352, 1413-1424.
148. Tsakiri, K.D. et al. (2007) Adult-onset pulmonary fibrosis caused by mutations in telomerase. Proc. Natl Acad. Sci. USA, 104, 7552-7557.
149. Mushiroda, T. et al. (2008) A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis. J. Med. Genet., 45, 654-656.
150. Calado, R.T. et al. (2009) A spectrum of severe familial liver disorders associate with telomerase mutations. PLoS ONE, 4, e7926.
151. Armanios, M.Y. et al. (2007) Telomerase mutations in families with idiopathic pulmonary fibrosis. N. Engl. J. Med., 356, 1317-1326.