Genetic dissection methods: Designs used for tests of gene-environment interaction

Current Opinion in Genetics and Development

Volumn 14, Issue 3, 2004, Pages 241-245

  Liu, Xin ^a   Fallin, M Daniele ^b   Kao, W H Linda ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

false positive rate; FPR; gene by environment; G E; odds ratio; OR

Indexed keywords

ALLELE; ANALYTIC METHOD; CORRELATION ANALYSIS; ENVIRONMENT; ENVIRONMENTAL FACTOR; GENE INTERACTION; GENETIC ANALYSIS; GENETIC EPIDEMIOLOGY; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOTYPE; HEREDITY; HETEROZYGOTE; HOMOZYGOTE; HUMAN; HYPOTHESIS; METHODOLOGY; MOLECULAR GENETICS; PARENT; POPULATION GENETICS; POPULATION RESEARCH; PRIORITY JOURNAL; REVIEW; SAMPLING; SIBLING; SMOKING; STATISTICAL ANALYSIS; VALIDATION PROCESS;

EID: 2542483575     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2004.04.011     Document Type: Note

References (38)

1. Winslow R.L., Boguski M.S. Genome informatics: current status and future prospects. Circ Res. 92:2003;953-961
2. Yoon Y., Song J., Hong S.H., Kim J.Q. Analysis of multiple single nucleotide polymorphisms of candidate genes related to coronary heart disease susceptibility by using support vector machines. Clin Chem Lab Med. 41:2003;529-534
3. Hahn L.W., Ritchie M.D., Moore J.H. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics. 19:2003;376-382
4. Goldstein A.M., Andrieu N. Detection of interaction involving identified genes: available study designs. J Natl Cancer Inst Monogr. 26:1999;49-54
5. Khoury M.J., Flanders W.D. Nontraditional epidemiologic approaches in the analysis of gene-environment interaction: case-control studies with no controls! Am J Epidemiol. 144:1996;207-213
6. Maestri N.E., Beaty T.H., Hetmanski J., Smith E.A., McIntosh I., Wyszynski D.F., Liang K.Y., Duffy D.L., VanderKolk C. Application of transmission disequilibrium tests to nonsyndromic oral clefts: including candidate genes and environmental exposures in the models. Am J Med Genet. 73:1997;337-344
7. Piegorsch W.W., Weinberg C.R., Taylor J.A. Non-hierarchical logistic models and case-only designs for assessing susceptibility in population-based case-control studies. Stat Med. 13:1994;153-162
8. Schaid D.J. Case-parents design for gene-environment interaction. Genet Epidemiol. 16:1999;261-273
9. Umbach D.M., Weinberg C.R. The use of case-parent triads to study joint effects of genotype and exposure. Am J Hum Genet. 66:2000;251-261
10. Weinberg C.R., Umbach D.M. Choosing a retrospective design to assess joint genetic and environmental contributions to risk. Am J Epidemiol. 152:2000;197-203
11. Witte J.S., Gauderman W.J., Thomas D.C. Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: basic family designs. Am J Epidemiol. 149:1999;693-705
12. Umbach D.M., Weinberg C.R. Designing and analysing case-control studies to exploit independence of genotype and exposure. Stat Med. 16:1997;1731-1743
13. Hwang S.J., Beaty T.H., Liang K.Y., Coresh J., Khoury M.J. Minimum sample size estimation to detect gene-environment interaction in case-control designs. Am J Epidemiol. 140:1994;1029-1037
14. Thomas D.C. Case-parents design for gene-environment interaction by Schaid. Genet Epidemiol. 19:2000;461-463
15. Thomas D.C., Witte J.S. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 11:2002;505-512
16. Wacholder S., Rothman N., Caporaso N. Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst. 92:2000;1151-1158
17. Gauderman W.J. Sample size requirements for matched case-control studies of gene-environment interaction. Stat Med. 21:2002;35-50
18. Albert P.S., Ratnasinghe D., Tangrea J., Wacholder S. Limitations of the case-only design for identifying gene-environment interactions. Am J Epidemiol. 154:2001;687-693
19. Spitz M.R., Shi H., Yang F., Hudmon K.S., Jiang H., Chamberlain R.M., Amos C.I., Wan Y., Cinciripini P., Hong W.K., Wu X. Case-control study of the D2 dopamin receptor gene and smoking status in lung cancer patients. J Natl Cancer Inst. 90:1998;358-363
20. Miyasaka K., Yoshida Y., Matsushita S., Higuchi S., Maruyama K., Niino N., Ando F., Shimokata H., Ohta S., Funakoshi A. Association of cholesystokinin-a receptor gene polymorphism with alcohol dependence in a Japanese population. Alcohol Alcohol. 39:2004;25-28
21. Basham V.M., Pharoah P.D., Healey C.S., Luben R.N., Day N.E., Easton D.F., Ponder B.A., Dunning A.M. Polymorphisms in CYP1A1 and smoking: no association with breast cancer risk. Carcinogenesis. 22:2001;1797-1800
22. Bennett W.P., Alavanja M.C., Blomeke B., Vahakangas K.H., Castren K., Welsh J.A., Bowman E.D., Khan M.A., Flieder D.B., Harris C.C. Environmental tobacco smoke, genetic susceptibility, and risk of lung cancer in never-smoking women. J Natl Cancer Inst. 91:1999;2009-2014
23. Chang-Claude J., Dunning A., Schnitzbauer U., Galmbacher P., Tee L., Wjst M., Chalmers J., Zemzoum I., Harbeck N., Pharoah P.D., Hahn H. The patched polymorphism Pro1315Leu (C3944T) may modulate the association between use of oral contraceptives and breast cancer risk. Int J Cancer. 103:2003;779-783
24. Egan K.M., Newcomb P.A., Titus-Ernstoff L., Trentham-Dietz A., Mignone L.I., Farin F., Hunter D.J. Association of NAT2 and smoking in relation to breast cancer incidence in a population-based case-control study (United States). Cancer Causes Control. 14:2003;43-51
25. Infante-Rivard C., Amre D., Sinnett D. GSTT1 and CYP2E1 polymorphisms and trihalomethanes in drinking water: effect on childhood leukemia. Environ Health Perspect. 110:2002;591-593
26. Infante-Rivard C., Krajinovic M., Labuda D., Sinnett D. Childhood acute lymphoblastic leukemia associated with parental alcohol consumption and polymorphisms of carcinogen-metabolizing genes. Epidemiology. 13:2002;277-281
27. Saintot M., Malaveille C., Hautefeuille A., Gerber M. Interactions between genetic polymorphism of cytochrome P450-1B1, sulfotransferase 1A1, catechol-o-methyltransferase and tobacco exposure in breast cancer risk. Int J Cancer. 107:2003;652-657
28. Sturmer T., Wang-Gohrke S., Arndt V., Boeing H., Kong X., Kreienberg R., Brenner H. Interaction between alcohol dehydrogenase II gene, alcohol consumption, and risk for breast cancer. Br J Cancer. 87:2002;519-523
29. Tan Q., Yashin A.I., Bladbjerg E.M., de Maat M.P., Andersen-Ranberg K., Jeune B., Christensen K., Vaupel J.W. A case-only approach for assessing gene by sex interaction in human longevity. J Gerontol A Biol Sci Med Sci. 57:2002;129-133
30. Helzlsouer K.J., Selmin O., Huang H.Y., Strickland P.T., Hoffman S., Alberg A.J., Watson M., Comstock G.W., Bell D. Association between glutathione S-transferase M1, P1, and T1 genetic polymorphisms and development of breast cancer. J Natl Cancer Inst. 90:1998;512-518
31. Goodman J.E., Lavigne J.A., Wu K., Helzlsouer K.J., Strickland P.T., Selhub J., Yager J.D. COMT genotype, micronutrients in the folate metabolic pathway and breast cancer risk. Carcinogenesis. 22:2001;1661-1665
32. Visvanathan K., Helzlsouer K.J., Boorman D.W., Strickland P.T., Hoffman S.C., Comstock G.W., O'Brien T.G., Guo Y. Association among an ornithine decarboxylase polymorphism, androgen receptor gene (CAG) repeat length and prostate cancer risk. J Urol. 171:2004;652-655
33. Kao W., Coresh J., Shuldiner A.R., Boerwinkle E., Bray M.S., Brancati F.L. Pro12Ala of the peorxisome proliferators-activated receptor-2 gene is associated with lower serum insulin levels in nonobese African Americans. The Atherosclerosis Risk in Communities Study. Diabetes. 52:2003;1568-1572
34. Kao W., Coresh J., Shuldiner A.R., Boerwinkle E., Brancati F.L. Association between gene variants in the peroxisome proliferator activated receptor-gamma2 and the glycogen-targeting subunit of type 1 protein phosphatase and obesity, hyperinsulinemia, and type 2 diabetes mellitus in African Americans: The Atherosclerosis Risk in Communities (ARIC) Study [abstract]. Circulation. 101:1999;731
35. Beaty T.H., Wang H., Hetmanski J.B., Fan Y.T., Zeiger J.S., Liang K.Y., Chiu Y.F., Vanderkolk C.A., Seifert K.C., Wulfsberg E.A., Raymond G., Panny S.R., McIntosh I. A case-control study of nonsyndromic oral clefts in Maryland. Ann Epidemiol. 11:2001;434-442
36. Hamajima N., Yuasa H., Matsuo K., Kurobe Y. Detection of gene-environment interaction by case-only studies. Jpn J Clin Oncol. 29:1999;490-493
37. Garcia-Closas M., Thompson W.D., Robins J.M. Differential misclassification and the assessment of gene-environment interactions in case-control studies. Am J Epidemiol. 147:1998;426-433
38. Garcia-Closas M., Rothman N., Lubin J. Misclassification in case-control studies of gene-environment interactions: assessment of bias and sample size. Cancer Epidemiol Biomarkers Prev. 8:1999;1043-1050