Biases and reconciliation in estimates of linkage disequilibrium in the human genome

American Journal of Human Genetics

Volumn 78, Issue 4, 2006, Pages 588-603

  Pe'er, Itsik ^a,c   Chretien, Yves R ^a,d   De Bakker, Paul I W ^a,b,c   Barrett, Jeffrey C ^e   Daly, Mark J ^a,b,c   Altshuler, David M ^a,b,c  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DISEASE ASSOCIATION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENOTYPE; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 33645474288     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/502803     Document Type: Article

References (43)

1. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P (2005) A haplotype map of the human genome. Nature 437:1299-1320
2. Ardlie KG, Kruglyak L, Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299-309
3. Barrett JC, Fry B, Mailer J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265
4. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22:231-238
5. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA (2004) Mapping complex disease loci in whole-genome association studies. Nature 429:446-452
6. Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E (2003) Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet 73:285-300
7. Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Kruglyak L, Nicketson DA (2004) Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 74:610-622
8. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229-232
9. de Bakker P, Yelensky R, Pe'er I, Gabriel SB, Daly M, Altshuler D (2005) Tagging efficiency and study-wide power in genetic association studies. Nat Genet 37:1217-1223
10. Devlin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311-322
11. Evans DM, Cardon LR (2005) A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations. Am J Hum Genet 76:681-687
12. 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
13. Hedrick PW (1987) Gametic disequilibrium measures: proceed with caution. Genetics 117:331-341
14. Hill WG, Weir BS (1994) Maximum-likelihood estimation of gene location by linkage disequilibrium. Am J Hum Genet 54:705-714
15. 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
16. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108
17. International HapMap Consortium (2003) The International HapMap Project. Nature 426:789-796
18. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233-237
19. Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10:1435-1444
20. Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet 13:577-588
21. Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725-738
22. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-144
23. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
24. Lewontin RC (1964) The interaction of selection and linkage. II. Optimum models. Genetics 50:757-782
25. McKeigue PM, Carpenter JR, Parra EJ, Shriver MD (2000) Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet 64:171-186
26. Morton NE, Zhang W, Taillon-Miller P, Ennis S, Kwok PY, Collins A (2001) The optimal measure of allelic association. Proc Natl Acad Sci USA 98:5217-5221
27. Nielsen R, Signorovitch J (2003) Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theot Popul Biol 63:245-255
28. Nothnagel M, Ott J (2002) Statistical gene mapping of traits in humans-hypertension as a complex trait: is it amenable to genetic analysis? Semin Nephrol 22:105-114
29. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719-1723
30. Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, et al (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 33:382-387
31. Pritchard JK, Cox NJ (2002) The allelic architecture of human disease genes: common disease-common variant...or not? Hum Mol Genet 11:2417-2423
32. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1-14
33. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) Linkage disequilibrium in the human genome. Nature 411:199-204
34. Reich DE, Gabriel SB, Altshuler D (2003) Quality and completeness of SNP databases. Nat Genet 33:457-458
35. Reich DE, Lander ES (2001) On the allelic spectrum of human disease. Trends Genet 17:502-510
36. Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 32:135-142
37. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
38. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381-2385
39. Sabatti C, Risch N (2002) Homozygosity and linkage disequilibrium. Genetics 160:1707-1719
40. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, et al (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933
41. Teare MD, Dunning AM, Durocher F, Rennart G, Easton DF (2002) Sampling distribution of summary linkage disequilibrium measures. Ann Hum Genet 66:223-233
42. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, et al (2001) The sequence of the human genome. Science 291:1304-1351
43. Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6:109-118