Linkage disequilibrium patterns vary substantially among populations

European Journal of Human Genetics

Volumn 13, Issue 5, 2005, Pages 677-686

  Sawyer, Sarah L ^a,c   Mukherjee, Namita ^b,d   Pakstis, Andrew J ^b   Feuk, Lars ^a   Kidd, Judith R ^b   Brookes, Anthony J ^a,e   Kidd, Kenneth K ^b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALGARY   (Canada)

^d INDIAN STATISTICAL INSTITUTE   (India)

^e UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

Genetic diversity; Haplotype map; Linkage disequilibrium; Population genetics; SNPs

Indexed keywords

AFRICA; ALLELE; ARTICLE; EUROPE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; HAPLOTYPE; HUMAN; NEGRO; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAPPING; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENOME, HUMAN; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 18844416564     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201368     Document Type: Article

References (51)

1. Johnson GC, Esposito L, Barratt BJ et al: Haplotype tagging for the identification of common disease genes. Nat Genet 2001; 29: 233-237.
2. Kruglyak L: Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22: 139-144.
3. Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Trends Genet 2002; 18: 19-24.
4. Kidd KK, Morar B, Castiglione CM et al: A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Hum Genet 1998; 103: 211-227.
5. Tishkoff SA, Dietzsch E, Speed W et al: Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 1996; 271: 1380-1387.
6. Tishkoff SA, Goldman A, Calafell F et al: 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 1998; 62: 1389-1402.
7. Tishkoff SA, Pakstis AJ, Stoneking M et al: Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins. Am J Hum Genet 2000; 67: 901-925.
8. Kidd JR, Pakstis AJ, Zhao H et al: Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations. Am J Hum Genet 2000; 66: 1882-1899.
9. Oota H, Pakstis AJ, Bonne-Tamir B et al: The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination. Ann Hum Genet 2004; 68: 93-109.
10. Collins FS, Brooks LD, Chakravarti A: A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 1998; 8: 1229-1231.
11. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 1996; 273: 1516-1517.
12. Reich DE, Cargill M, Bolk S et al: Linkage disequilibrium in the human genome. Nature 2001; 411: 199-204.
13. Cardon LR, Abecasis GR: Using haplotype blocks to map human complex trait loci. Trends Genet 2003; 19: 135-140.
14. Goldstein DB: Islands of linkage disequilibrium. Nat Genet 2001; 29: 109-111.
15. Kauppi L, Sajantila A, Jeffreys AJ: Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum Mol Genet 2003; 12: 33-40.
16. Jeffreys AJ, Kauppi L, Neumann R: Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 2001; 29: 217-222.
17. Jeffreys AJ, Holloway JK, Kauppi L et al: Meiotic recombination hot spots and human DNA diversity. Philos Trans R Soc London Ser B 2004; 359: 141-152.
18. Gibbs RA, Belmont JW, Hardenbol P et al: The International HapMap Project. Nature 2003; 426: 789-796.
19. Couzin J: Genomics. New mapping project splits the community. Science 2002; 296: 1391-1393.
20. Phillips MS, Lawrence R, Sachidanandam R et al: Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 2003; 33: 382-387.
21. Zhang K, Akey JM, Wang N, Xiong M, Chakraborty R, Jin L: Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift. Hum Genet 2003; 113: 51-59.
22. Patil N, Berno AJ, Hinds DA et al: Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001; 294: 1719-1723.
23. Gabriel SB, Schaffner SF, Nguyen H et al: The structure of haplotype blocks in the human genome. Science 2002; 296: 2225-2229.
24. Taillon-Miller P, Bauer-Sardina I, Saccone NL et al: Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat Genet 2000; 25: 324-328.
25. Dawson E, Abecasis GR, Bumpstead S et al: A first-generation linkage disequilibrium map of human chromosome 22. Nature 2002; 418: 544-548.
26. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES: High-resolution haplotype structure in the human genome. Nat Genet 2001; 29: 229-232.
27. Abecasis GR, Noguchi E, Heinzmann A et al: Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 2001; 68: 191-197.
28. Tsunoda T, Lathrop GM, Sekine A et al: Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Hum Mol Genet 2004; 13: 1623-1632.
29. Goddard KA, Hopkins PJ, Hall JM, Witte JS: Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations. Am J Hum Genet 2000; 66: 216-234.
30. Kidd KK, Pakstis AJ, Speed WC, Kidd JR: Understanding human DNA sequence variation. J Hered 2004; 95: 406-420.
31. Jorde LB, Watkins WS, Kere J, Nyman D, Eriksson AW: Gene mapping in isolated populations: new roles for old friends? Hum Hered 2000; 50: 57-65.
32. DeMille MM, Kidd JR, Ruggeri V et al: Population variation in linkage disequilibrium across the COMT gene considering promoter region and coding region variation. Hum Genet 2002; 111: 521-537.
33. Kamatani N, Sekine A, Kigamoto T et al: Large scale single nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP Maps, of 199 drug-related genes in 752 subjects: the analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs. Am J Hum Genet 2004; 75: 190-203.
34. Zhao H, Pakstis AJ, Kidd JR, Kidd KK: Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association. Ann Hum Genet 1999; 63: 167-179.
35. Nothnagel M, Furst R, Rohde K: Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks. Hum Hered 2002; 54: 186-198.
36. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: an allele frequency database for anthropology. Am J Phys Anthropol 2002; 119: 77-83.
37. Chen TJ, Boles RG, Wong LJ: Detection of mitochondrial DNA mutations by temporal temperature gradient gel electrophoresis. Clin Chem 1999; 45: 1162-1167.
38. Howell WM, Jobs M, Gyllensten U, Brookes AJ: Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat Biotechnol 1999; 17: 87-88.
39. Livak KJ: Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 1999; 14: 143-149.
40. Fredman D, Siegfried M, Yuan YP, Bork P, Lehvaslaiho H, Brookes AJ: HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res 2002; 30: 387-391.
41. Wright S: Evolution and the genetics of populations; in The Theory of Gene Frequencies. Chicago, IL: University of Chicago Press, Vol. 2,: 1969, p 511.
42. Hawley ME, Kidd KK: HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 1995; 86: 409-411.
43. Lewontin RC: The interaction of selection and linkage. I. General considerations: heterotic models. Genetics 1964; 49: 49-67.
44. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29: 311-322.
45. Maniatis N, Collins A, Xu CF et al: The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci USA 2002; 99: 2228-2233.
46. Workman PL, Niswander JD: Population studies on southwestern Indian tribes. II. Local genetic differentiation in the Papago. Am J Hum Gen 1970; 22: 24-49.
47. Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK: The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. Am J Hum Genet 2000; 67: 518-522.
48. Zhang S, Pakstis AJ, Kidd KK, Zhao H: Comparisons of two methods for haplotype reconstruction and haplotype frequency estimation from population data. Am J Hum Genet 2001; 69: 906-914.
49. Fallin D, Schork NJ: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 2000; 67: 947-959.
50. Greenwood TA, Rana BK, Schork NJ: Human haplotype block sizes are negatively correlated with recombination rates. Genome Res 2004; 14: 1358-1361.
51. Liu N, Sawyer SL, Mukherjee N et al: Measures of similarity for haplotype block structures show variation among populations. Genet Epidemiol 2004; 27: 385-400.