Power-based, phase-informed selection of single nucleotide polymorphisms for disease association screens

Genetic Epidemiology

Volumn 30, Issue 6, 2006, Pages 459-470

  Saccone, Scott F ^a   Rice, John P ^a   Saccone, Nancy L ^a,b  

^a WASHINGTON UNIVERSITY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Gametic phase; Linkage disequilibrium; Sample size; Statistical power; Tag SNP

Indexed keywords

ALGORITHM; ALLELE; ARTICLE; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DISEASE ASSOCIATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN GENOME PROJECT; LEAVE ONE OUT TEST; LINKAGE ANALYSIS; MARKER GENE; MATHEMATICAL COMPUTING; METHODOLOGY; NUCLEOTIDE SEQUENCE; POWER ANALYSIS; R2 BIN TAGGING METHOD; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 7; COMPUTER SIMULATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC LINKAGE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SAMPLE SIZE;

EID: 33747626097     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20159     Document Type: Article

References (29)

1. Abecasis GR, Cookson WOC. 2000. GOLD-graphical overview of linkage disequilibrium. Bioinformatics 16:182.
2. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
3. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120.
4. Cousin E, Genin E, Mace S, Ricard S, Chansac C, del Zompo M, Deleuze JF. 2002. Association studies in candidate genes: strategies to select SNPs to be tested. Hum Hered 56:151-159.
5. Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J et al. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548.
6. Devlin B, Risch N. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311-322.
7. Excoffier L, Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
8. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
9. Genin E. 2002. Selection of single nucleotide polymorphisms for association studies in candidate genes. Genet Epidemiol 21(Suppl. 1):S614-S619.
10. Gordon D, Finch SJ, Nothnagel M, Ott J. 2002. Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 54:22-33.
11. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. 2005. Whole-genome patterns of common DNA variation in three human populations. Science 307:1072-1079.
12. Hu X, Schrodi SJ, Ross DA, Cargill M. 2004. Selecting tagging SNPs for association studies using power calculations from genotype data. Hum Hered 57:156-170.
13. James JW. 1971. Frequency in relatives for an all-or-none trait. Ann Hum Genet 35:47-48.
14. Ke X, Cardon LR. 2003. Efficient selective screening of haplotype tag SNPs. Bioinformatics 19:287-288.
15. Kempthorne O. 1957. An Introduction to Genetic Statistics. New York: Wiley.
16. Olson JM, Wijsman EM. 1994. Design and sample-size considerations in the detection of linkage disequilibrium with a disease locus. Am J Hum Genet 55:574-580.
17. Pfeiffer RM, Gail MH. 2003. Sample size calculations for population and family-based case-control association studies on marker genotypes. Genet Epidemiol 25:136-148.
18. Pritchard JK, Przeworski M. 2001. Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1-14.
19. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517.
20. Sham P. 1998. Statistics in Human Genetics. London: Arnold.
21. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. 2002. The generic genome browser: a building block for a model organism system database. Genome Res 12:1599-1610.
22. Stram DO, Haiman CA, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Pike MC. 2003. Choosing haplotype-tagging snps based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study. Hum Hered 55:27-36.
23. Taillon-Miller P, Bauer-Sardina I, Saccone NL, Putzel J, Laitinen T, Cao A, Kere J, Pilia G, Rice JP, Kwok P-Y. 2000. Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat Genet 25:324-328.
24. Taillon-Miller P, Saccone SF, Saccone NL, Duan S, Kloss EF, Lovins EG, Donaldson R, Phong A, Ha C, Flagstad L, Miller S, Drendel A, Lind D, Miller RD, Rice JP, Kwok P-Y. 2004. Linkage disequilibrium maps constructed with common SNPs are useful for first-pass disease association screens. Genomics 84:899-912.
25. The International HapMap Consortium. 2003. The International HapMap Project. Nature 426:789-796.
26. The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437:1299-1320.
27. Thompson EA, Deeb S, Walker D, Motulsky AG. 1988. The detection of linkage disequilibrium between closely linked markers: RFLPs at the AI-CIII apolipoprotein genes. Am J Hum Genet 42:113-124.
28. Tiret L, Poirier O, Nicaud V, Barbaux S, Herrmann S-M, Perret C, Raoux S, Francomme C, Lebard G, Tregouet D, Cambien F. 2002. Heterogeneity of linkage disequilibrium in human genes has implications for association studies of common diseases. Hum Mol Genet 11:419-429.
29. Zondervan KT, Cardon LR. 2004. The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89-100.