Candidate gene case-control studies

Pharmacogenomics

Volumn 4, Issue 2, 2003, Pages 127-139

  Daly, Ann K ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Cancer; Candidate gene; DNA repair; Single nucleotide polymorphism; Xenobiotic metabolism

Indexed keywords

DNA;

ALZHEIMER DISEASE; CANCER DIAGNOSIS; CANCER RISK; CANCER SUSCEPTIBILITY; CARCINOGENESIS; CASE CONTROL STUDY; CROHN DISEASE; DISEASE ASSOCIATION; DNA POLYMORPHISM; ENVIRONMENTAL FACTOR; EXPERIMENTAL DESIGN; FAMILY STUDY; FEASIBILITY STUDY; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC LINKAGE; GENETIC SUSCEPTIBILITY; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; NON INSULIN DEPENDENT DIABETES MELLITUS; POPULATION RESEARCH; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

CASE-CONTROL STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; GENOTYPE; HUMANS; MULTIFACTORIAL INHERITANCE; NEOPLASMS; POLYMORPHISM, GENETIC; RESEARCH DESIGN; RISK FACTORS;

EID: 0037342213     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/phgs.4.2.127.22629     Document Type: Review

References (108)

1. Roses AD: Pharmacogenetics and the practise of medicine. Nature 405, 857-865 (2000).
2. Risch NJ: Searching for genetic determinants in the new millenium. Nature 405, 847-856 (2000).
3. Weiss KM, Terwilliger JD: How many diseases does it take to map a gene with SNPs? Nat. Genet. 26, 151-157 (2000).
4. Judson R, Salisbury B, Schneider J, Windemuth A, Stephens JC: How many SNPs does a genome-wide haplotype map require? Pharmacogenomics 3, 279-391 (2002).
5. Speilman RS, Ewens WJ: The TDT and other family-based tests for linkage disequiLibrium. Am. J. Hum. Genet. 59, 983-989 (1996).
6. Speilman RS, Ewens WJ: A sibship test for linkage in the presence of association: the sib transmission/disequiLibrium test. Am. J. Hum. Genet. 62, 450-458 (1998).
7. Witte JS, Gauderman WJ, Thomas DC: Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: basic family designs. Am. J. Epidemiol 148, 693-705 (1999).
8. Alfie ME, Sigmon DH, Pomposiello SI, Carretero OA: Effect of high salt intake in mutant mice lacking bradykinin-B2 receptors. Hypertension 29, 483-487 (1997).
9. Ogura Y, Bonen DK, Inohara N et al.: A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411, 603-606 (2001).
10. Hayes JD, Pulford DJ: The glutathione S-Transferase supergene family: regulation of GST and the contribution of the isoenzymes to cancer chemoprotection and drug resistance. Crit. Rev. Biochem. Mol. Biol. 30, 445-600 (1995).
11. Dunning AM, Healey CS, Pharoah PDP, Teare MD, Ponder BAJ, Easton DF: A systematic review of genetic polymorphisms and breast cancer risk. Cancer Epidemiol. Biomarkers Prev. 8, 843-854 (1999).
12. Gu CC, Rao DC, Stormo G, Hicks C, Province MA: Role of gene expression microarray analysis in finding complex disease genes. Genet. Epidemiol. 23, 37-56 (2002).
13. Kwok PY, Gu ZJ: Single nucleotide polymorphism libraries: why and how are we building them? Mol. Med. Today 5, 538-543 (1999).
14. Perneger TV: What's wrong with Bonferroni adjustments? Br. Med. J. 316, 1235-1237 (1998).
15. Hemminki K, Forsti A: Proper controls for SNP studies. Carcinogenesis 23, 1405 (2002).
16. Thomas DC, Witte JS: Point: Population stratification: a problem for case-control studies of candidate-gene associations. Cancer Epidemiol. Biomark. Prev. 11, 505-512 (2002).
17. Schaid DJ, Rowland C: Use of parents, sibs and unrelated controls for detection of associations between genetic markers and disease. Am. J. Hum. Genet. 63, 1492-1506 (1998).
18. Bacanu S-A, Devlin B, Roeder K: The power of genomic control. Am. J. Hum. Genet. 66, 1933-1944 (2000).
19. Pritchard JK, Rosenberg NA: Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65, 220-228 (1999).
20. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P: Association mapping in structured populations. Am. J. Hum. Genet. 67, 170-181 (2000).
21. Wacholder S, Rothman N, Caparaso N: Population stratification in epidemiological studies of common genetic variants and cancer: quantification of bias. J. Natl. Cancer Inst. 92, 1151-1158 (2000).
22. Vyse TJ, Todd JA: Genetic analysis of autoimmune disease. Cell 85, 311-318 (1996).
23. Bell GI, Horita S, Karam JH: A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus. Diabetes 33, 176-183 (1984).
24. Todd JA. From genome to aetiology in a multifactorial disease, Type I diabetes. Bioessays 21, 164-174 (1999).
25. Saunders A, Strittmatter W, Schmechel D et al.: Association of apolipoprotein-E allele epsilon-4 with late- onset familial and sporadic Alzheimer's disease. Neurology 43, 1467-1472 (1993).
26. Altshuler D, Hirschhorn J, Klannemark M et al.: The common PPAR gamma Pro12Ala polymorphism is associated with decreased risk of Type 2 diabetes. Nat. Genet. 26, 76-80 (2000).
27. Ring HZ, Kroetz DL: Candidate gene approach for pharmacogenetic studies. Pharmacogenomics 3, 47-56 (2002).
28. Risch N: The genetic epidemiology of cancer: Interpreting family and twin studies and their implications for molecular genetic approaches. Cancer Epidemiol. Biomarkers Prev. 10, 733-741 (2001).
29. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K: A comprehensive review of genetic association studies. Genet. Med. 4, 45-61 (2002).
30. Brockmoller J, Cascorbi I, Henning S, Meisel C, Roots I: Molecular genetics of cancer susceptibility. Pharmacology 61, 212-227 (2000).
31. Kouri RE, McKinney CE, Slomiany DJ, Snodgrass DR, Wray NP, McLemore TL: Positive correlation between high aryl hydrocarbon hydroxylase activity and primary lung cancer as analysed in cryopreserved lymphocytes. Cancer Res. 42, 5030-5037 (1982).
32. Ayesh R, Idle JR, Ritchie JC, Crothers MJ, Hetzel MR: Metabolic oxidation phenotypes as markers for susceptibility to lung cancer. Nature 311, 169-170 (1984).
33. Seidegard J, Pero RW, Miller DG, Beattie EJ: A glutathione transferase in human leukocytes as a marker for the susceptibility to lung cancer. Carcinogenesis 7, 751-753 (1986).
34. Smart J, Daly AK: Variation in induced CYP1A1 levels: relationship to CYP1A1, Ah receptor and GSTM1 polymorphisms. Pharmacogenetics 10, 11-24 (2000).
35. Cauchi S, Stucker I, Solas C et al.: Polymorphisms of human aryl hydrocarbon receptor (AhR) gene in a French population: relationship with CYP1A1 inducibility and lung cancer. Carcinogenesis 22, 1819-1824 (2001).
36. Kawajiri K, Nakachi K, Imai K, Yoshii A, Shinoda N, Watanabe J: Identification of genetically high risk individuals to lung cancer by DNA polymorphisms of the cytochrome P450IA1 gene. FEBS Lett. 263, 131-133 (1990).
37. Hayashi S, Watanabe J, Nakachi K, Kawajiri K: Genetic linkage of lung cancer-associated MspI polymorphisms with amino acid replacement in the heme binding region of the human cytochrome P450IA1 gene. J. Biochem. 110, 407-411 (1991).
38. Persson I, Johansson I, IngelmanSundberg M: In vitro kinetics of two human CYP1A1 variant enzymes suggested to be associated with interindividual differences in cancer susceptibility. Biochem. Biophys. Res. Commun. 231, 227-230 (1997).
39. Zhang ZY, Fasco MJ, Huang LL, Guengerich FP, Kaminsky LS: Characterization of purified human recombinant cytochrome P4501A1-Ile(462) and -Val(462): Assessment of a role for the rare allele in carcinogenesis. Cancer Res. 56, 3926-3933 (1996).
40. Schwarz D, Kisselev P, Cascorbi I, Schunck W-H, Roots I: Differential metabolism of benzo[a]pyrene and benzo[alpyrene-7,8-dihydrodiol by human CYP1A1 variants. Carcinogenesis 22, 453-459 (2001).
41. Caporaso NE, Tucker MA, Hoover RN et al.: Lung cancer and the debrisoquine metabolic phenotype. J. Natl. Cancer Inst. 82, 1264-1272 (1990).
42. Wolf CR, Smith CAD, Gough AC et al.: Relationship between the debrisoquine hydroxylase polymorphism and cancer susceptibility. Carcinogenesis 13, 1035-1038 (1992).
43. Stucker I, Cosme J, Laurent P et al.: CYP2D6 genotype and lung cancer risk according to histologic type and tobacco exposure. Carcinogenesis 16, 2759-2764. (1995).
44. London SJ, Daly AK, Leathart JBS, Navidi WC, Carpenter CC, Idle JR: Genetic polymorphism of CYP2D6 and lung cancer risk in African-Americans and Caucasians in Los Angeles county. Carcinogenesis 18, 1203-1214 (1997).
45. Rostami-Hodjegan A, Lennard MS, Woods HE, Tucker GT: Meta-analysis of studies of the CYP2D6 polymorphism in relation to lung cancer and Parkinson's disease. Pharmacogenetics 8, 227-238 (1998).
46. Patten CJ, Smith TJ, Murphy SE et al.: CYP2D6 and NNK Kinetic analysis of the activation of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone by heterologously expressed human P450 enzymes and the effect of P450-specific chemical inhibitors on this activation in human liver microsomes. Arch. Biochem. Biophys. 333, 127-138 (1996).
47. Kivisto KT, Griese E-U, Stuven T et al.: Analysis of CYP2D6 expression in human lung: implications for the association between CYP2D6 activity and susceptibility to lung cancer. Pharmacogenetics 7, 295-302. (1997).
48. McWilliams JE, Sanderson BJS, Harris EL, Richertboe KE, Henner WD: Glutathione-S-Transferase M1 (Gstm 1) Deficiency and Lung-Cancer Risk. Cancer Epidemiol. Biomarkers Prev. 4, 589-594 (1995).
49. d'Errico A, Malats N, Vineis P, Boffetta P: Review of studies of selected polymorphisms and cancer. In: Metabolic Polymorphisms and Susceptibility to Cancer. Vineis P et al. (Eds), IARC Scientific Publications, Lyon, France 323-393 (1999).
50. Houlston RS: Glutathione S-transferase M1 status and lung cancer risk: A meta-analysis. Cancer Epidemiol. Biomarkers Prev. 8, 675-682 (1999).
51. Benhamou S, Lee WJ, Alexandrie AK et al.: Meta- and pooled analyses of the effects of glutathione S- transferase M1 polymorphisms and smoking on lung cancer risk. Carcinogenesis 23, 1343-1350 (2002).
52. London SJ, Yuan JM, Chung FL et al.: Isothiocyanates, glutathione S-transferase M1 and T1 polymorphisms, and lung-cancer risk: a prospective study of men in Shanghai, China. Lancet 356, 724-729 (2000).
53. Pianezza ML, Sellers EM, Tyndale RF: Nicotine metabolism defect reduces smoking. Nature 393, 750-750 (1998).
54. London SJ, Idle JR, Daly AK, Coetzee GA: Genetic variation of CYP2A6, smoking, and risk of cancer. Lancet 353, 898-899 (1999).
55. Sabol SZ, Hamer DH: An improved assay shows no association between the CYP2A6 gene and cigarette smoking behavior. Behav. Genet. 29, 257-261 (1999).
56. Oscarson M, McLellan RA, Gullsten H et al.: Identification and characterisation of novel polymorphisms in the CYP2A locus: implications for nicotine metabolism. FEBS Lett. 460, 321-327 (1999).
57. Rao YS, Hoffmann E, Zia M et al.: Duplications and defects in the CYP2A6 gene: Identification, genotyping, and in vivo effects on smoking. Mol. Pharmacol, 58, 747-755 (2000).
58. Ariyoshi N, Miyamoto M, Umetsu Y et al.: Genetic polymorphism of CYP2A6 gene and tobacco-induced lung cancer risk in male smokers. Cancer Epidemiol. Biomarkers Prev. 11, 890-894 (2002).
59. Welfare MR, Cooper J, Bassendine MF, Daly AK: Relationship between acetylator status, smoking, diet and colorectal cancer risk in the north-east of England. Carcinogenesis 18, 1351-1354 (1997).
60. Hirvonen A: Polymorphic NATs and cancer predisposition, In: Metabolic Polymorphisms and Susceptibility to Cancer. Vineis P et al. (Eds), International Agency for Research on Cancer, Lyon, France (1999).
61. Yu Z, Chen J, Ford BN, Brackley ME, Glickman BW: Human DNA repair systems: an overview. Environ. Mol. Mutagen. 33, 3-20 (1999).
62. Goode EL, Ulrich CM, Potter JD: Polymorphisms in DNA repair genes and associations with cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 1513-1530 (2002).
63. Zhou W, Liu G, Miller DP et al.: Gene-environment interaction for the ERCC2 polymorphisms and cumulative cigarette smoking exposure in lung cancer. Cancer Res. 62, 1377-1381 (2002).
64. Ambrosone CB, Freudenheim JL, Thompson PA et al.: Manganese superoxide dismutase (MnSOD) genetic polymorphisms, dietary antioxidants, and risk of breast cancer. Cancer Res. 59, 602-606 (1999).
65. Mitrunen K, Sillanpaa P, Kataja V et al.: Association between manganese superoxide dismutase (MnSOD) gene polymorphism and breast cancer risk. Carcinogenesis 22, 827-829 (2001).
66. Caporaso NE: Why have we failed to find the low penetrance genetic constituents of common cancers? Cancer Epidemiol, Biomark. Prev. 11, 1544-1549 (2002).
67. Houlston RS: CYP1A1 polymorphisms and lung cancer risk: a meta-analysis. Pharmacogenetics 10, 105-114 (2000).
68. Le Marchand L, Hankin JH, Wilkens LR et al.: Combined effects of well-done red meat, smoking, and rapid N-acetyltransferase 2 and CYP1A2 phenotypes in increasing colorectal cancer risk. Cancer Epidemiol. Biomarkers Prev. 10, 1259-1266 (2001).
69. Watanabe J, Shimada T, Gillam EMJ et al.: Association of CYP1B1 genetic polymorphism with incidence to breast and lung cancer. Pharmacogenetics 10, 25-33 (2000).
70. De Vivo I, Hankinson SE, Li L, Colditz GA, Hunter DJ: Association of CYP1B1 polymorphisms and breast cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 489-492 (2002).
71. Loriot MA, Rebuissou S, Oscarson M et al.: Genetic polymorphisms of cytochrome P450 2A6 in a case-control study on lung cancer in a French population. Pharmacogenetics 11, 39-44 (2001).
72. London SJ, Daly AK, Cooper J et al.: Lung cancer risk in relation to the CYP2E1 Rsa I genetic polymorphism among African-Americans and Caucasians in Los Angeles County. Pharmacogenetics 6, 151-158 (1996).
73. Le Marchand L, Sivaraman L, Pierce L et al.: Associations of CYP1A1, GSTM1, and CYP2E1 polymorphisms with lung cancer suggest cell type specificities to tobacco carcinogens. Cancer Res. 58, 4858-4863 (1998).
74. Lee WJ, Brennan P, Boffetta P et al.: Microsomal epoxide hydrolase polymorphisms and lung cancer risk: a quantitative review. Biomarkers 7, 230-241 (2002).
75. London SJ, Smart J, Daly AK: Lung cancer risk in relation to genetic polymorphisms of microsomal epoxide hydrolase among African-Americans and Caucasians in Los Angeles County. Lung Cancer 28, 147-155 (2000).
76. Sachse C, Smith G, Wilkie MJV et al.: A pharmacogenetic study to investigate the role of dietary carcinogens in the etiology of colorectal cancer. Carcinogenesis 23, 1839-1849 (2002).
77. Rosvold EA, McGlynn KA, Lustbader ED, Buetow KH: Identification of an Nad(P)H-quinone oxidoreductase polymorphism and its association with lung-cancer and smoking. Pharmacogenetics 5, 199-206 (1995).
78. Sunaga N, Kohno T, Yanagitani N et al.: Contribution of the NQO1 and GSTT1 polymorphisms to lung adenocarcinoma susceptibility. Cancer Epidemiol. Biomarkers Prev. 11, 730-738 (2002).
79. London SJ, Lerman TA, Taylor JA: Myeloperoxidase genetic polymorphism and lung cancer risk. Cancer Res. 57, 5001-5003 (1997).
80. Le Marchand L, Seifried A, Lum A, Wilkens LR: Association of the myeloperoxidase (-463)G → A polymorphism with lung cancer risk. Cancer Epidemiol. Biomarkers Prev. 9, 181-184 (2000).
81. Feyler A, Voho A, Bouchardy C et al.: Point: Myeloperoxidase (-463)G → A polymorphism and lung cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 1550-1554 (2002).
82. Xu LL, Liu G, Miller DP et al.: Counterpoint: The myeloperoxidase (-463)G → A polymorphism does not decrease lung cancer susceptibility in Caucasians. Cancer Epidemiol. Biomarkers Prev. 11, 1555-1559 (2002).
83. Wikman H, Thiel S, Jager B et al.: Relevance of N-acetyltransferase 1 and 2 (NAT1, NAT2) genetic polymorphisms in non-small cell lung cancer susceptibility. Pharmacogenetics 11, 157-168 (2001).
84. Bouchardy C, Mitrunen K, Wikman H et al.: N-acetyltransferase NAT1 and NAT2 genotypes and lung cancer risk. Pharmacogenetics 8, 291-298 (1998).
85. Ambrosone CB, Freudenheim JL, Graham S et al.: Cigarette smoking, N-acetyl-transferase 2 genetic polymorphisms, and breast cancer risk. JAMA 276, 1494-1501 (1996).
86. Jourenkova-Mironova N, Wikman H, Bouchardy C et al.: Role of glutathione S-transferase GSTM1, GSTM3, GSTP1 and GSTT1 genotypes in modulating susceptibility to smoking-related lung cancer. Pharmacogenetics 8, 495-502 (1998).
87. Stucker I, Hirvonen A, de Waziers I et al.: Genetic polymorphisms of glutathione S-transferases as modulators of lung cancer susceptibility. Carcinogenesis 23, 1475-1481 (2002).
88. Zheng Z, Park JY, Guillemette C, Schantz SP, Lazarus P: Tobacco carcinogen-detoxifying enzyme UGT1A7 and its association with orolaryngeal cancer risk. J. Natl. Cancer Inst. 93, 1411-1418 (2001).
89. Bamber DE, Fryer AA, Strange RC et al.: Phenol sulphotransferase SULT1A1*1 genotype is associated with reduced risk of colorectal cancer. Pharmacogenetics 11, 679-685 (2001).
90. Ye Z, Parry JM: The CYP17 MspA1 polymorphism and breast cancer risk: a meta- analysis. Mutagenesis 17, 119-126 (2002).
91. Haiman CA, Hankinson SE, Spiegelman D et al.: A tetranucleotide repeat polymorphism in CYP19 and breast cancer risk. Int. J. Cancer 87, 204-210 (2000).
92. Chen J, Giovannucci E, Kelsey K et al.: A methylenetetrahydrofolate reductase polymorphism and the risk of colorectal cancer. Cancer Res. 56, 4862-4864 (1996).
93. Ulrich CM, Kampman E, Bigler J et al.: Colorectal adenomas and the C677T MTHFR polymorphism: Evidence for gene-environment interaction? Cancer Epidemiol. Biomarkers Prev. 8, 659-668 (1999).
94. Thompson PA, Shields PG, Freudenheim JL et al.: Genetic polymorphisms in catechol-O-methyltransferase, menopausal status, and breast cancer risk. Cancer Res. 58, 2107-2110 (1998).
95. Mitrunen K, Kataja V, Eskelinen M et al.: Combined COMT and GST genotypes and hormone replacement therapy associated breast cancer risk. Pharmacogenetics 12, 67-72 (2002).
96. Wang W, Xue S, Ingles SA et al.: An association between genetic polymorphisms in the ileal sodium-dependent bile acid transporter gene and the risk of colorectal adenomas. Cancer Epidemiol. Biomark. Prev. 10, 931-936 (2001).
97. Le Marchand L, Donlon T, Lum-Jones A, Seifried A. Wikens LR: Association of the hOGG1 Ser326Cys polymorphism with lung cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 409-412 (2002).
98. Elahi A, Zheng Z, Park J, Eyring K, McCaffrey T, Lazarus P: The human OGG1 DNA repair enzyme and its association with orolaryngeal cancer risk. Carcinogenesis 23, 1229-1234 (2002).
99. Xu JF, Zheng SL, Turner A et al.: Associations between hOGG1 sequence variants and prostate cancer susceptibility. Cancer Res. 62, 2253-2257 (2002).
100. David-Beabes GL, London SJ: Genetic polymorphism of XRCC1 and lung cancer risk among African-Americans and Caucasians. Lung Cancer 34, 333-339 (2001).
101. Chen SQ, Tang DL, Xue KX et al.: DNA repair gene XRCC1 and XPD polymorphisms and risk of lung cancer in a Chinese population. Carcinogenesis 23, 1321-1325 (2002).
102. Kim SU, Park SK, Yoo KY et al.: XRCC1 genetic polymorphism and breast cancer risk. Pharmacogenetics 12, 335-338 (2002).
103. Rafii S, O'Regan P, Xinarianos G et al.: A potential role for the XRCC2 R188H polymorphic site in DNA- damage repair and breast cancer. Hum. Mol. Genet. 11, 1433-1438 (2002).
104. Stern MC, Umbach DM, Lunn RM, Taylor JA: DNA repair gene XRCC3 codon 241 polymorphism, its interaction with smoking and XRCC1 polymorphisms, and bladder cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 939-943 (2002).
105. Kuschel B, Auranen A, McBride S et al.: Variants in DNA double-strand break repair genes and breast cancer susceptibility. Hum. Mol. Genet. 11, 1399-1407 (2002).
106. Butkiewicz D, Rusin M, Enewold L, Shields PG, Chorazy M, Harris CC: Genetic polymorphisms in DNA repair genes and risk of lung cancer. Carcinegenesis 22, 593-597 (2001).
107. Stern MC, Johnson LR, Bell DA, Taylor JA: XPD codon 751 polymorphism, metabolism genes, smoking, and bladder cancer risk. Cancer Epidemiol. Biomarkers Prev. 11, 1004-1011 (2002).
108. Healey CS, Dunning AM, Teare MD et al.: A common variant in BRCA2 is associated with both breast cancer risk and prenatal viability. Nat. Genet. 26, 362-364 (2000).