Statistical power of association using the extreme discordant phenotype design

Pharmacogenetics and Genomics

Volumn 16, Issue 6, 2006, Pages 401-413

  Zhang, Ge ^a   Nebert, Daniel W ^a   Chakraborty, Ranajit ^a   Jin, Li ^a,b,c  

^a UNIVERSITY OF CINCINNATI MEDICAL CENTER   (United States)

^b FUDAN UNIVERSITY   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

Association study; Environmental exposure; Extreme discordant phenotype; Selective genotyping; Statistical power

Indexed keywords

DRUG; ENVIRONMENTAL CHEMICAL;

ALLELE; ARTICLE; DRUG TOXICITY; ENVIRONMENTAL EXPOSURE; EXTREME DISCORDANT PHENOTYPE; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC SUSCEPTIBILITY; GENOTYPE; PHARMACOGENOMICS; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RISK FACTOR; SAMPLING; STATISTICAL ANALYSIS; TREND STUDY;

ALLELES; CHI-SQUARE DISTRIBUTION; DATA INTERPRETATION, STATISTICAL; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SAMPLE SIZE;

EID: 33744471383     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/01.fpc.0000204995.99429.0f     Document Type: Article

References (50)

1. Morton NE, Collins A. Tests and estimates of allelic association in complex inheritance. Proc Natl Acad Sci U S A 1998; 95:11389-11393.
2. Vink JM, Boomsma DI. Gene finding strategies. Biol Psychol 2002; 61:53-71.
3. Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989; 121:185-199.
4. Carey G, Williamson J. Linkage analysis of quantitative traits: increased power by using selected samples. Am J Hum Genet 1991; 49:786-796.
5. Cardon LR, Fulker DW. The power of interval mapping of quantitative trait loci, using selected sib pairs. Am J Hum Genet 1994; 55:825-833.
6. Cardon LR, Smith SD, Fulker DW, Kimberling WJ, Pennington BF, DeFries JC. Quantitative trait locus for reading disability on chromosome 6. Science 1994; 266:276-279.
7. Daniels SE, Bhattacharrya S, James A, Leaves NI, Young A, Hill MR, et al. A genome-wide search for quantitative trait loci underlying asthma. Nature 1996; 383:247-250.
8. Hager J, Dina C, Francke S, Dubois S, Houari M, Vatin V, et al. A genome-wide scan for human obesity genes reveals a major susceptibility locus on chromosome 10. Nat Genet 1998; 20:304-308.
9. Haseman JK, Elston RC. The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 1972; 2:3-19.
10. Risch N, Zhang H. Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 1995; 268:1584-1589.
11. Risch NJ, Zhang H. Mapping quantitative trait loci with extreme discordant sib pairs: sampling considerations. Am J Hum Genet 1996; 58:836-843.
12. Gu C, Todorov A, Rao DC. Combining extremely concordant sibpairs with extremely discordant sibpairs provides a cost effective way to linkage analysis of quantitative trait loci. Genet Epidemiol 1996; 13:513-533.
13. Knapp M. Evaluation of a restricted likelihood ratio test for mapping quantitative trait loci with extreme discordant sib pairs. Ann Hum Genet 1998; 62 (Pt 1):75-87.
14. Rogus JJ, Harrington DP, Jorgenson E, Xu X. Effectiveness of extreme discordant sib pairs to detect oligogenic disease loci. Genet Epidemiol 1997; 14:879-884.
15. Xu X, Rogus JJ, Terwedow HA, Yang J, Wang Z, Chen C, et al. An extreme-sib-pair genome scan for genes regulating blood pressure. Am J Hum Genet 1999; 64:1694-1701.
16. Martin N, Goodwin G, Fairburn C, Wilson R, Allison D, Cardon LR, et al. A population-based study of personality in 34000 sib-pairs. Twin Res 2000; 3:310-315.
17. Fullerton J, Cubin M, Tiwari H, Wang C, Bomhra A, Davidson S, et al. Linkage analysis of extremely discordant and concordant sibling pairs identifies quantitative-trait loci that influence variation in the human personality trait neuroticism. Am J Hum Genet 2003; 72:879-890.
18. Abecasis GR, Cookson WO, Cardon LR. The power to detect linkage disequilibrium with quantitative traits in selected samples. Am J Hum Genet 2001; 68:1463-1474.
19. Van GS, Houwing-Duistermaat JJ, Adolfsson R, van Duijn CM, Van BC. Power of selective genotyping in genetic association analyses of quantitative traits. Behav Genet 2000; 30:141-146.
20. Schork NJ, Nath SK, Fallin D, Chakravarti A. Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects. Am J Hum Genet 2000; 67:1208-1218.
21. Tenesa A, Knott SA, Carothers AD, Visscher PM. Power of linkage disequilibrium mapping to detect a quantitative trait locus (QTL) in selected samples of unrelated individuals. Ann Hum Genet 2003; 67:557-566.
22. Xiong M, Fan R, Jin L. Linkage disequilibrium mapping of quantitative trait loci under truncation selection. Hum Hered 2002; 53:158-172.
23. Nebert DW. Pharmacogenetics and pharmacogenomics: why is this relevant to the clinical geneticist? Clin Genet 1999; 56:247-258.
24. Nebert DW. Extreme discordant phenotype methodology: an intuitive approach to clinical pharmacogenetics. Eur J Pharmacol 2000; 410:107-120.
25. Falconer DS, Mackay TFC. Introduction to quantitative genetics. 4th edition. Harlow: Longman; 1996.
26. Agresti A. Categorical data analysis. New York: Wiley; 1990.
27. Freidlin B, Zheng G, Li Z, Gastwirth JL. Trend tests for case-control studies of genetic markers: power, sample size and robustness. Hum Hered 2002; 53:146-152.
28. Fontana RJ, Lok AS. Noninvasive monitoring of patients with chronic hepatitis C. Hepatology 2002; 36:S57-S64.
29. Sasieni PD. From genotypes to genes: doubling the sample size. Biometrics 1997; 53:1253-1261.
30. Knapp M, Seuchter SA, Baur MP. The haplotype-relative-risk (HRR) method for analysis of association in nuclear families. Am J Hum Genet 1993; 52:1085-1093.
31. Armitage P. Tests for linear trends in proportions and frequencies. Biometrics 1955; 11:375-386.
32. Slager SL, Schaid DJ. Case-control studies of genetic markers: power and sample size approximations for Armitage's test for trend. Hum Hered 2001; 52:149-153.
33. 2-tests in case-control association studies of complex disease genes. Ann Hum Genet 2002; 66:307-321.
34. Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999; 55:997-1004.
35. Bacanu SA, Devlin B, Roeder K. The power of genomic control. Am J Hum Genet 2000; 66:1933-1944.
36. Zheng G. Use of max and min scores for trend tests for association when the genetic model is unknown. Stat Med 2003; 22:2657-2666.
37. Carlborg O, Haley CS. Epistasis: too often neglected in complex trait studies? Nat Rev Genet 2004; 5:618-625.
38. Culverhouse R, Suarez BK, Lin J, Reich T. A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet 2002; 70:461-471.
39. Muller-Myhsok B, Abel L. Genetic analysis of complex diseases. Science 1997; 275:1328-1329.
40. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet 2001; 69:1-14.
41. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 2004; 74:106-120.
42. Akey J, Jin L, Xiong M. Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 2001; 9:291-300.
43. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, et al. Haplotype variation and linkage disequilibrium in 313 human genes. Science 2001; 293:489-493.
44. Schaid DJ. Genetic epidemiology and haplotypes. Genet Epidemiol 2004; 27:317-320.
45. Devlin B, Risch N, Roeder K. Disequilibrium mapping: composite likelihood for pairwise disequilibrium. Genomics 1996; 36:1-16.
46. Clayton D, Chapman J, Cooper J. Use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 2004; 27:415-428.
47. Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet 2003; 361:598-604.
48. Marchini J, Cardon LR, Phillips MS, Donnelly P. The effects of human population structure on large genetic association studies. Nat Genet 2004; 36:512-517.
49. Devlin B, Roeder K, Wasserman L. Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 2001; 60:155-166.
50. Reich DE, Goldstein DB. Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 2001; 20:4-16.