Genome-wide association studies of cancer

Future Oncology

Volumn 3, Issue 4, 2007, Pages 419-427

  Jorgenson, Eric ^a,b   Witte, John S ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Institute for Human Genetics   (United States)

Author keywords

Cancer; Copy number variant; Gene expression; Genome wide association; Linkage disequilibrium; Race ethnicity; Single nucleotide polymorphism; Whole genome

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN;

ARTICLE; BREAST CANCER; CANCER; CANCER GENETICS; CANCER RISK; CANCER SUSCEPTIBILITY; CARCINOGENESIS; DNA MICROARRAY; ETHNIC DIFFERENCE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC RISK; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; INHERITANCE; LINKAGE ANALYSIS; PRIORITY JOURNAL; PROSTATE CANCER; RACE DIFFERENCE; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM;

CHRONIC DISEASE; EPIDEMIOLOGIC STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; NEOPLASMS;

EID: 34547894717     PISSN: 14796694     EISSN: 17448301     Source Type: Journal    
DOI: 10.2217/14796694.3.4.419     Document Type: Article

References (56)

1. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 273(5281), 1516-1517 (1996).
2. Crawford DC, Carlson CS, Rieder MJ et al.: Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism and blood pressure regulation in two populations. Am. J. Hum. Genet. 74(4), 610-622 (2004).
3. Leabman MK, Huang CC, DeYoung J et al.: Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc. Natl Acad. Sci. USA 100(10), 5896-5901 (2003).
4. Hinds DA, Stuve LL, Nilsen GB et al.: Whole-genome patterns of common DNA variation in three human populations Science 307(5712), 1072-1079 (2005).
5. Feuk L, Marshall CR, Wintle RF, Scherer SW: Structural variants: changing the landscape of chromosomes and design of disease studies. Hum. Mol. Genet. 15 Spec No 1, R57-R66 (2006).
6. Redon R, Ishikawa S, Fitch KR et al.: Global variation in copy number in the human genome. Nature 444(7118), 444-454 (2006).
7. Hinds DA, Klock AP, Jen M, Chen X, Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet. 38(1), 82-85 (2006).
8. Pritchard JK, Cox NJ: The allelic architecture of human disease genes: common disease-common variant or not? Hum. Mol. Genet. 11(20), 2417-2423 (2002).
9. Wang WY, Barratt BJ, Clayton DG, Todd JA: Genome-wide association studies: theoretical and practical concerns. Nat. Rev. Genet. 6(2), 109-118 (2005).
10. Jorgenson E, Witte JS: Coverage and power in genome-wide association studies. Am. J. Hume. Genet. 78(5), 884-888 (2006).
11. Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Trends in Genetics 18(1), 19-24 (2002).
12. Jorgenson E, Witte JS: A gene-centric appoach to genome-wide association studies. Nat. Rev. Genet. 7(11), 885-891 (2006).
13. Jorgenson E, Tang H, Gadde M et al.: Ethnicity and human genetic linkage maps. Am. J. Hum. Genet. 76(2), 276-290 (2005).
14. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat. Rev. Genet. 7(2), 85-97 (2006).
15. Ke X, Hunt S, Tapper W et al.: The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum. Mol. Genet. 13(6), 577-588 (2004).
16. Stephens JC, Schneider JA, Tanguay DA et al.: Haplotype variation and linkage disequilibrium in 313 human genes. Science 293(5529), 489-493 (2001).
17. Pritchard JK, Rosenberg NA: Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65(1), 220-228 (1999).
18. Devlin B, Rooder K, Wasserman L: Genomic control, a new approach to genetic-based association studies. Theor. Popul. Biol. 60(3), 155-166 (2001).
19. Price AL, Patterson NJ, Plenge RM, Weinblart ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38(8), 904-909 (2006).
20. Freedman ML, Haiman CA, Patterson N et al.: Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl Acad. Sci. USA 103(38), 14068-14073 (2006).
21. Witte JS: Multiple prostate cancer risk variants on 8q24. Nat. Genet. 39(5), 579-580 (2007).
22. Yeager M, Orr N, Hayes RB et al.: Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet. 39(5), 645-649 (2007).
23. Gudmundsson J, Sulem P, Manolescu A et al.: Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet. 39(5), 631-637 (2007).
24. Easton DF, Pooley KA, Dunning AM et al.: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447(7148), 1087-1093 (2007).
25. Hunter DJ, Kraft P, Jacobs KB et al.: A genome-wide association study indentifies alleles in FGFR2 associated with risk of sporadic post-menopausal breast cancer. Nat. Genet. 39(7), 870-874 (2007).
26. Stacey SN, Manolescu A. Sulem P et al.: Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer Nat. Genet. 39(7), 865-869 (2007).
27. Amundadottir IT, Sulem P, Gudmundsson J et al.: A common vanant associated with prostate cancer in European and African populations. Nat. Genet. 38(6), 652-658 (2006).
28. Scott LJ, Mohlke KL, Bonnycastle LL et al.: A genome-wide association study of Type 2 diabetes in Finns detects multiple susceptibility variants. Science 316(5829), 1341-4345 (2007).
29. Zeggini E, Weedon MN, Lindgren CM et al.: Replication of genome-wide association signals in UK samples reveals risk loci for Type 2 diabetes. Science DOI:10.1126/science 1142364 (2007) (Epub ahead of print).
30. Saxena R, Voight BF, Lyssenko V et al.: Genome-wide association analysis identifies loci for Type 2 diabetes and triglyceride levels. Science 316(5829), 1331-1336 (2007).
31. Cho EK, Tchinda J, Freeman JL, Chung YJ, Cai WW, Lee C: Array-based comparative genomic hybridization and copy number variation in cancer research. Cytogenet. Genome Res. 115(3-4), 262-272 (2006).
32. Braude I, Vukovic B, Prasad M et al.: Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia. BMC Genomics 7, 138 (2006).
33. Frank B, Bermejo JL, Hemminki K et al.: Copy number variant in the candidate tumor suppressor gene MTUS1 and familial breast cancer risk. Carcinogenesis DOI:10.1093/carcin/bgm033 (2007) (Epub ahead of print).
34. Greenman C. Stephens P, Smith R et al.: Patterns of somatic mutation in human cancer genomes. Nature 446(7132), 153-158 (2007).
35. True L, Coleman I, Hawley S et al.: A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc. Natl Acad. Sci. USA 103(29), 10991-10996 (2006).
36. Lapointe J, Li C, Higgins JP et al.: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc. Natl Sci. USA 101(3), 811-816 (2004).
37. Yosef N, Kaufman A, Ruppin E: Inferring functional pathways from multi-perturbation data. Bioinformatics 22(14), E539-E546 (2006).
38. Cebrian A, Pharoah PD, Ahmed S et al.: Genetic variants in epigenetic genes and breast cancer risk. Carcinogenesis 27(8), 1661-1669 (2006).
39. Andre F, Pusztai L: Molecular classification of breast cancer: implications for selection of adjuvant chemotherapy. Nat. Clin. Pract. Oncol. 3(11), 621-632 (2006).
40. Couzin J: Diagnostics. Amid debate, gene-based cancer test approved. Science 315(5814), 924 (2007).
41. Ozaki K, Ohnishi Y, Iida A et al.: Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction. Nat. Genet. 32(4), 650-654 (2002).
42. Helgadottir A, Thorleifsson G, Manolescu A et al.: A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316(5830), 1491-1493 (2007).
43. McPherson R, Pertsemlidis A, Kavaslar N et al.: A common allele on chromosome 9 associated with coronary heart disease. Science 316(5830), 1488-1491 (2007).
44. Klein R, Zeiss C, Chew EY et al.: Complement factor H polymorphism in age-related macular degeneration. Science 308(5720), 385-389 (2005).
45. Dewan A, Liu M, Hartman S et al.: HTRAI promoter polymosphism in wet age-related macular degeneration. Science 314(5801), 989-992 (2006).
46. Sladck R, Rocheleau G, Rung J et al.: A genome-wide association study identifies novel risk loci for Type 2 diabetes. Nature 445(7130), 881-885 (2007).
47. Steinthorsdottir V, Thorleifsson G, Reynisdottir I et al.: A variant in CDKAL1 influences insulin ressponse and risk of Type 2 diabetes. Nat. Genet. 39(6), 770-775 (2007).
48. Duerr RH, Taylor KD, Brant SR et al.: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314(5804), 1461-1463 (2006).
49. Hampe J, Franke A, Rosenstiel P et al.: A genome-wide association scan of nonsynonymous SNPs identifies a suscepntibility variant for Crohn disease in ATG16L21. Nat. Genet. 39(2), 207-211 (2007).
50. Rioux JD, Xavier RJ, Taylor KD et al.: Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet. 39(5), 596-604 (2007).
51. Herbert A, Gerry NP, McQueen MB et al.: A common genetic variant is associated with adult and childhood obesity. Science 312(5771), 279-283 (2006).
52. Frayling TM, Timpson NJ, Weadon MN et al.: A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316(5826), 889-894 (2007).
53. Burdick JT, Chen WM, Abecasis GR, Cheung VG: In silico method for inferring genotypes in pedigrees. Nat. Genet. 38(9), 1002-1004 (2006).
54. Chen G, Witte JS: Enriching the analysis of genome-wide association studies with hierarchical modeling. Am. J. Hum. Genetics 81(2), 397-404 (2007).
55. Clayton D, McKeigue PM: Epidemiological methods for studying genes and environmental factors in complex diseases. Lancet 358(9290), 1356-4360 (2001).
56. Pennisi E: Genomics. On your mark. Get set. Sequence! Science 314(5797), 232 (2006).