A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations

American Journal of Human Genetics

Volumn 76, Issue 4, 2005, Pages 681-687

  Evans, David M ^a   Cardon, Lon R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; ASIAN; CHROMOSOME 20; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; HAPLOTYPE; HUMAN; POPULATION; PRIORITY JOURNAL; UNITED KINGDOM; UNITED STATES;

EID: 15944383793     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/429274     Document Type: Article

References (36)

1. Abecasis GR, Noguchi E, Heinzmann A, Traherne JA, Bhattacharyya S, Leaves NI, Anderson GG, Zhang Y, Lench NJ, Carey A, Cardon LR, Moffatt MF, Cookson WOC (2001) Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 68:191-197
2. Cardon LR, Abecasis GR (2003) Using haplotype blocks to map human complex trait loci. Trends Genet 19:135-140
3. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) History and geography of human genes. Princeton University Press, Princeton
4. 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
5. Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet 36:700-706
6. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229-232
7. 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
8. Fearnhead P, Donnelly P (2001) Estimating recombination rates from population genetic data. Genetics 159:1299-1318
9. Freimer N, Sabatti C (2004) The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology. Nat Genet 36:1045-1051
10. Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A (2001) Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet 69:831-843
11. 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
12. The International HapMap Consortium (2003) The International HapMap Project. Nature 426:789-796
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. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159:1805-1817
16. 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
17. 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
18. Kidd JR, Pakstis AJ, Zhao H, Lu R-B, Okonofua FE, Odunsi A, Grigorenko E, Bonne-Tamir B, Friedlaender J, Schulz LO, Parnas J, Kidd KK (2000) Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations. Am J Hum Genet 66:1882-1899
19. Kidd KK, Morar B, Castiglione CM, Zhao H, Pakstis AJ, Speed WC, Bonne-Tamir B, Lu R-B, Goldman D, Lee C, Nam YS, Grandy DK, Jenkins T, Kidd JR (1998) A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Hum Genet 103:211-227
20. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139-144
21. Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213-2233
22. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304:581-584
23. Nielsen R, Signorovitch J (2003) Correcting for ascertainment biases when analyzing SNP data: application to the estimation of linkage disequilibrium. Theor Popul Biol 63:245-255
24. 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
25. 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
26. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1-14
27. 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
28. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
29. Risch NJ (2000) Searching for genetic determinants in the new millennium. Nature 405:847-856
30. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162-1169
31. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989
32. Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Krings M (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271:1380-1387
33. Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK (1998) A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am J Hum Genet 62:1389-1402
34. Tishkoff SA, Pakstis AJ, Stoneking M, Kidd JR, Destro-Bisol G, Sanjantila A, Lu R-b, Deinard AS, Sirugo G, Jenkins T, Kidd KK, Clark AG (2000) Short tandem-repeat polymorphism/Alu haplotype variation at the PLAT locus: implications for modern human origins. Am J Hum Genet 67:901-925
35. Watkins WS, Zenger R, O'Brien E, Nyman D, Eriksson AW, Renlund M, Jorde LB (1994) Linkage disequilibrium patterns vary with chromosomal location: a case study from the von Willebrand factor region. Am J Hum Genet 55:348-355
36. Weiss KM, Clark AG (2002) Linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19-24