Genetic association studies in cancer: Good, bad or no longer ugly?

Human Genomics

Volumn 2, Issue 6, 2006, Pages 415-421

  Savage, Sharon A ^a   Chanock, Stephen J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Association study; Cancer risk; Genome wide scan; Haplotype; Linkage disequilibrium; Single nucleotide polymorphism

Indexed keywords

ACYLTRANSFERASE; APOLIPOPROTEIN E; BRCA1 PROTEIN; BRCA2 PROTEIN; CYTOCHROME P450 1A1; DOPAMINE 2 RECEPTOR; INTERLEUKIN 1 RECEPTOR BLOCKING AGENT; INTERLEUKIN 10; PROTEIN MDM2; PROTEIN P53; TUMOR NECROSIS FACTOR;

ADRENAL CORTEX CARCINOMA; BLADDER CANCER; BRAIN TUMOR; BREAST CANCER; CANCER GENETICS; CANCER RISK; CARCINOGENESIS; CHILDHOOD CANCER; ENVIRONMENTAL FACTOR; ESOPHAGUS CANCER; FAMILIAL CANCER; GENE INTERACTION; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC RISK; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; LEUKEMIA; LUNG CANCER; MEDICAL DECISION MAKING; NONHODGKIN LYMPHOMA; OVARY CANCER; PROGNOSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RETINOBLASTOMA; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STOMACH CANCER; SYSTEMATIC REVIEW; VALIDATION PROCESS;

EID: 33746368733     PISSN: 14797364     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/1479-7364-2-6-415     Document Type: Review

References (80)

1. Brookes, A.J. (1999), 'The essence of SNPs', Gene Vol. 234, pp. 177-186.
2. Kong, A., Gudbjartsson, D.F., Sainz, J. et al. (2002), 'A high-resolution recombination map of the human genome', Nat. Genet. Vol. 31, pp. 241-247.
3. Collins, A., Lonjou, C. and Morton, N.E. (1999), 'Genetic epidemiology of single-nucleotide polymorphisms', Proc. Natl. Acad. Sci. USA Vol. 96, pp. 15173-15177.
4. Cardon, L.R. and Abecasis, G.R. (2003), 'Using haplotype blocks to map human complex trait loci', Trends Genet. Vol. 19, pp. 135-140.
5. Martin, E.R., Lai, E.H., Gilbert, J.R. et al. (2000), 'SNPing away at complex diseases: Analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease', Am. J. Hum. Genet. Vol. 67, pp. 383-394.
6. Altshuler, D., Brooks, L.D., Chakravarti, A. et al. (2005), 'A Haplotype map of the human genome', Nature Vol. 437, pp. 1299-1320.
7. Packer, B.R., Yeager, M., Burdett, L. et al. (2006), 'SNP500Cancer: A public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes', Nucleic Acids Res. Vol. 34, pp. D617-D621.
8. Kwok, P.Y. and Chen, X. (2003), 'Detection of single nucleotide polymorphisms', Cur. Issues Mol. Biol. Vol. 5, pp. 43-60.
9. Steemers, F.J., Chang, W., Lee, G. et al. (2006), 'Whole-genome genotyping with the single-base extension assay', Nat. Methods Vol. 3, pp. 31-33.
10. de Bakker, P.I., Yelensky, R., Pe'er, I. et al. (2005), 'Efficiency and power in genetic association studies', Nat. Genet. Vol. 37, pp. 1217-1223.
11. Carlson, C.S., Eberle, M.A., Rieder, M.J. et al. (2004), 'Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium', Am. J. Hum. Genet. Vol. 74, pp. 106-120.
12. Balmain, A., Gray, J. and Ponder, B. (2003), 'The genetics and genomics of cancer', Nat. Genet. Vol. 33(Suppl.), pp. 238-244.
13. Chen, Y.C. and Hunter, D.J. (2005), 'Molecular epidemiology of cancer', CA Cancer J. Clin. Vol. 55, pp. 45-54.
14. Knudson Jr., A.G. (1971), 'Mutation and cancer: Statistical study of retinoblastoma', Proc. Natl. Acad. Sci. USA Vol. 68, pp. 820-823.
15. Zhu, L. (2005), 'Tumour suppressor retinoblastoma protein Rb: A transcriptional regulator', Eur. J. Cancer Vol. 41, pp. 2415-2427.
16. Li, F. and Fraumeni Jr., J.F. (1969), 'Soft-tissue sarcomas, breast cancer, and other neoplasms. A familial syndrome?, Ann. Intern. Med. Vol. 71, pp. 747-752.
17. Li, F.P., Fraumeni Jr., J.F., Mulvihill, J.J. et al. (1988), 'A cancer family syndrome in twenty-four kindreds', Cancer Res. Vol. 48, pp. 5358-5362.
18. Sengupta, S. and Harris, C.C. (2005), 'p53: Traffic cop at the crossroads of DNA repair and recombination', Nat. Rev. Mol. Cell Biol. Vol. 6, pp. 44-55.
19. Artandi, S.E. and Attardi, L.D. (2005), 'Pathways connecting telomeres and p53 in senescence, apoptosis, and cancer', Biochem. Biophys. Res. Commun. Vol. 331, pp. 881-890.
20. Vogelstein, B. and Kinzler, K.W (2004), 'Cancer genes and the Pathways they control', Nat. Med. Vol. 10, pp. 789-799.
21. Hopper, J.L. (2001), 'Genetic epidemiology of feniale breast cancer', Semin. Cancer Biol. Vol. 11, pp. 367-374.
22. Yoshida, K. and Miki, Y (2004), 'Role of BRCA1 and BRCA2 as regulators of DNA repair, transcription, and cell cycle in response to DNA damage', Cancer Sci. Vol. 95, pp. 866-871.
23. Freedman, M.L., Penney, K.L., Stram, D.O. et al. (2004), 'Common variation in BRCA2 and breast cancer risk: A haplotype-based analysis in the Multiethnic Cohort', Hum. Mol. Genet. Vol. 13, pp. 2431-2441.
24. Chanock, S. (2001), 'Candidate genes and single nucleotide polymorphisms (SNPs) in the study of human disease', Dis. Markers Vol. 17, pp. 89-98.
25. Tabor, H.K., Risch, N.J. and Myers, R.M. (2002), 'Opinion: Candidate gene approaches for studying complex genetic traits: Practical considerations', Nat. Rep. Genet. Vol. 3, pp. 391-397.
26. Hughes, A.L., Packer, B., Welch, R. et al. (2005), 'High level of functional polymorphism indicates a unique role of natural selection at human immune system loci', Immunogenetics Vol. 57, pp. 821-827.
27. Fredman, D., Sawyer, S.L., Stromqvist, L. et al. (2006), 'Nonsynonymous SNPs: Validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection', Hum. Mutat. Vol. 27, pp. 173-186.
28. Johnson, M.M., Houck, J. and Chen, C. (2005), 'Screening for deleterious nonsynonymous; single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response', Cancer Epidemiol. Biomarkers Prev. Vol. 14, pp. 1326-1329.
29. Bond, G.L., Hu, W., Bond, E.E. et al. (2004), 'A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans', Cell Vol. 119, pp. 591-602.
30. Duan, J., Wainwright, M.S., Comeron, J.M. et al. (2003), 'Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor', Hum. Mol. Genet. Vol. 12, pp. 205-216.
31. Watters, J.W. and McLeod, H.L. (2003), 'Cancer pharmacogenomics: Current and future applications', Biochim. Biophys. Acta Vol. 1603, pp. 99-111.
32. Reich, D. and Patterson, N. (2005), 'Will admixture mapping work to find disease genes?', Philos. Trans. R. Soc. Lond. B. Biol. Sci. Vol. 360, pp. 1605-1607.
33. Patterson, N., Hattangadi, N., Lane, B. et al. (2004), 'Methods for high-density admixture mapping of disease genes', Am. J. Hum. Genet. Vol. 74, pp. 979-1000.
34. Voight, B.F., Kudaravalli, S., Wen, X. and Pritchard, J.K. (2006), 'A map of recent positive selection in the human genome', PLoS Biol. Vol. 4, p. e72.
35. Akey, J.M., Eberle, M.A., Rieder, M.J. et al. (2004), 'Population history and natural selection shape patterns of genetic variation in 132 genes', pLoS Biol. Vol. 2, p. e286.
36. Ioannidis, J.P., Ntzani, E.E. and Trikalinos, T.A. (2004), "'Racial" differences in genetic effects for complex diseases', Nat. Genet. Vol. 36, pp. 1312-1318.
37. Cardon, L.R. and Palmer, L.J. (2003), 'Population stratification and spurious allelic association', Lancet Vol. 361, pp. 598-604.
38. Marchini, J., Cardon, L.R., Phillips, M.S. and Donnelly, P. (2004), 'The effects of human population structure on large genetic association studies', Nat. Genet. Vol. 36, pp. 512-517.
39. Rothman, N., Skibola, C.F., Wang, S.S. et al. (2006), 'Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: A report from the InterLymph Consortium', Lancet Oncol. Vol. 7, pp. 27-38.
40. El Omar, E.M., Rabkin, C.S., Gammon, M.D. et al. (2003), 'Increased risk of noncardia gastric cancer associated with proinflammatory cytokine gene polymorphisms', Gastroenterology Vol. 124, pp. 1193-1201.
41. Hein, D.W., Doll, M.A., Fretland, A.J. et al. (2000), 'Molecular genetics and epidemiology of the NAT1 and NAT2 acetylation polymorphisms', Cancer Epidemiol. Biomarkers Prev. Vol. 9, pp. 29-42.
42. Golka, K., Prior, V., Blaszkewicz, M. and Bolt, H.M. (2002), 'The enhanced bladder cancer susceptibility of NAT2 slow acetylators towards aromatic amines: A review considering ethnic differences', Toxicol. Lett. Vol. 128, pp. 229-241.
43. Hein, D.W. (2002), 'Molecular genetics and function of NAT1 and NAT2: Role in aromatic amine metabolism and carcinogenesis', Mutat. Res. Vol. 506-507, pp. 65-77.
44. Davey, S.G. and Ebrahim, S. (2003), '"Mendelian randomization": Can genetic epidemiology contribute to understanding environmental determinants of disease?', Int. J. Epidemiol. Vol. 32, pp. 1-22.
45. Davey, S.G., Ebrahim, S., Lewis, S. et al. (2005), 'Genetic epidemiology and public health: Hope, hype, and future prospects', Lancet Vol. 366, pp. 1484-1498.
46. Smith, G.D. and Ebrahim, S. (2004), 'Mendelian randomization: Prospects, potentials, and limitations', Int. J. Epidemiol. Vol. 33, pp. 30-42.
47. Katan, M.B. (1986), 'Apolipoprotein E isoforms, serum cholesterol, and cancer', Lancet Vol. 1(8479), pp. 507-508.
48. Lewis, S.J. and Smith, G.D. (2005), 'Alcohol, ALDH2, and esophageal cancer: A meta-analysis which illustrates the potentials and limitations of a Mendelian randomization approach', Cancer Epidemiol. Biomarkers Prev. Vol. 14, pp. 1967-1971.
49. Sorlie, T., Tibshirani, R., Parker, J. et al. (2003), 'Repeated observation of breast tumor subtypes in independent gene expression data sets', Proc. Natl. Acad. Sci. USA Vol. 100, pp. 8418-8423.
50. Staudt, L.M. (2003), 'Molecular diagnosis of the hematologic cancers', N. Engl. J. Med. Vol. 348, pp. 1777-1785.
51. Carlson, C.S., Eberle, M.A., Rieder, M.J. et al. (2003), 'Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans', Nat. Genet. Vol. 33, pp. 518-521.
52. Kolonel, L.N., Altshuler, D. and Henderson, B.E. (2004), 'The multi-ethnic cohort study: Exploring genes, lifestyle and cancer risk', Nat. Rev. Cancer Vol. 4, pp. 519-527.
53. Hunter, D.J., Riboli, E., Haiman, C.A. et al. (2005), 'A candidate gene approach to searching for low-penetrance breast and prostate cancer genes', Nat. Rev. Cancer Vol. 5, pp. 977-985.
54. Ioannidis, J.P., Gwinn, M., Little, J. et al. (2006), 'A road map for efficient and reliable human genome epidemiology', Nat. Genet. Vol. 38, pp. 3-5.
55. Benhamou, S. and Sarasin, A. (2005), 'ERCC2 /XPD gene polymorphisms and lung cancer: A HuGE review', Am. J. Epidemiol. Vol. 161, pp. 1-14.
56. Hung, R.J., Hall, J., Brennan, P. and Boffetta, P. (2005), 'Genetic polymorphisms in the base excision repair pathway and cancer risk: A HuGE review', Am. J. Epidemiol. Vol. 162, pp. 925-942.
57. Masson, L.F., Sharp, L., Cotton, S.C. and Little, J. (2005), 'Cytochrome P-450 1A1 gene polymorphisms and risk of breast cancer: A HuGE review', Am. J. Epidemiol. Vol. 161, pp. 901-915.
58. Hu, Z., Wei, Q., Wang, X. and Shen, H. (2004), 'DNA repair gene XPD polymorphism and lung cancer risk: A meta-analysis', Lung Cancer Vol. 46, pp. 1-10.
59. Le Marchand, L., Guo, C., Benhamou, S. et al. (2003), 'Pooled analysis of the CYP1A1 exon 7 polymorphism and lung cancer (United States)', Cancer Causes Control Vol. 14, pp. 339-346.
60. Garcia-Closas, M., Egan, K.M., Newcomb, P.A. et al. (2006), 'Polymorphisms in DNA double-strand break repair genes and risk of breast cancer: Two population-based studies in USA and Poland, and meta-analyses', Hum. Genet. Vol. 119, pp. 376-388.
61. Savage, S.A., Abnet, C. C., Mark, S.D. et al. (2004), 'Variants of the IL8 and IL8RB genes and risk for gastric cardia adenocarcinoma and esophageal squamous cell carcinoma', Cancer Epidemiol. Biomarkers Prev. Vol. 13, pp. 2251-2257.
62. Taguchi, A., Ohmiya, N., Shirai, K. et al. (2005), 'Interleukin-8 promoter polymorphism increases the risk of atrophic gastritis and gastric cancer in Japan', Cancer Epidemiol. Biomarkers Prev. Vol. 14, pp. 2487-2493.
63. Ohyauchi, M., Imatani, A., Yonechi, M. et al. (2005), 'The polymorphism interleukin 8 -251 A/T influences the susceptibility of Helicobacter pylori related gastric diseases in the Japanese population', Gut Vol. 54, pp. 330-335.
64. Wacholder, S., Chanock, S., Garcia-Closas, M. et al. (2004), 'Assessing the probability that a positive report is false: An approach for molecular epiderniology studies', J. Natl. Cancer Inst. Vol. 96, pp. 434-442.
65. Sabatti, C., Service, S. and Freimer, N. (2003), 'False discovery rate in linkage and association genome screens for complex disorders', Genetics Vol. 164, pp. 829-833.
66. Weller, J.I., Song, J.Z., Heyen, D.W. et al. (1998), 'A new approach to the problem of multiple comparisons in the genetic dissection of complex traits', Genetics Vol. 150, pp. 1699-1706.
67. Lohmueller, K.E., Pearce, C.L., Pike, M. et al. (2003), 'Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease', Nat. Genet. Vol. 33, pp. 177-182.
68. Hirschhorn, J.N., Lohmueller, K., Byrne, E. and Hirschhorn, K. (2002), 'A comprehensive review of genetic association studies', Genet. Med. Vol. 4, pp. 45-61.
69. Egan, K.M., Cai, Q., Shu, X.O. et al. (2004), 'Genetic polymorphisms in GSTM1, GSTPI, and GSTT1 and the risk for breast cancer: Results from the Shanghai Breast Cancer Study and meta-analysis', Cancer Epidemiol. Biomarkers Prev. Vol. 13, pp. 197-204.
70. Sull, J.W., Ohrr, H., Kang, D.R. and Nam, C.M. (2004), 'Glutathione S-transferase M1 status and breast cancer risk: A meta-analysis', Yonsei Med. J. Vol. 45, pp. 683-689.
71. Vogl, F.D., Taioli, E., Maugard, C. et al. (2004), 'Glutathione S-transferases M1, T1, and P1 and breast cancer: A pooled analysis', Cancer Epidemiol. Biomarkers Prev. Vol. 13, pp. 1473-1479.
72. Ntais, C., Polycarpou, A. and Ioannidis, J.P. (2005), 'Association of GSTM1, GSTT1, and GSTP1 gene polymorphisms with the risk of prostate cancer: A meta-analysis', Cancer Epidemiol. Biomarkers Prev. Vol. 14, pp. 176-181.
73. Smit, K.M., Gaspari, L., Weijenberg, M.P. et al. (2003), 'Interaction between smoking, GSTM1 deletion and colorectal cancer: Results from the GSEC study', Biomarkers Vol. 8, pp. 299-310.
74. Ye, Z. and Song, H. (2005), 'Glutathione s-transferase polymorphisms (GSTM1, GSTP1 and GSTT1) and the risk of acute leukaemia: A systematic review and meta-analysis', Eur. J. Cancer Vol. 41, pp. 980-989.
75. Garcia-Closas, M., Malats, N., Silverman, D. 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 Vol. 366, pp. 649-659.
76. Wen, W., Gao, Y.T., Shu, X.O. et al. (2005), 'Insulin-like growth factor-I gene polymorphism and breast cancer risk in Chinese women', Int. J. Cancer Vol. 113, pp. 307-311.
77. Zhang, Y., Newcomb, P.A., Egan, K.M. et al. (2006), 'Genetic polymorphisms in base-excision repair pathway genes and risk of breast cancer', Cancer Epidemiol. Biomarkers Prev. Vol. 15, pp. 353-358.
78. Klein, R.J., Zeiss, C., Chew, E.Y. et al. (2005), 'Complement factor H polymorphism in age-related macular degeneration', Science Vol. 308, pp. 385-389.
79. Edwards, A.O., Ritter, III, R., Abel, K.J. et al. (2005), 'Complement factor H polymorphism and age-related macular degeneration', Science Vol. 308, pp. 421-424.
80. Haines, J.L., Hauser, M.A., Schmidt, S. et al. (2005), 'Complement factor H variant increases he risk of age-related macular degeneration', Science Vol. 308, pp. 419-421.