Methods for High-Density Admixture Mapping of Disease Genes

American Journal of Human Genetics

Volumn 74, Issue 5, 2004, Pages 979-1000

  Patterson, Nick ^a   Hattangadi, Neil ^a,c,d   Lane, Barton ^a   Lohmueller, Kirk E ^e   Hafler, David A ^a,c   Oksenberg, Jorge R ^f   Hauser, Stephen L ^f   Smith, Michael W ^g   O'Brien, Stephen J ^g   Altshuler, David ^a,c,d   Daly, Mark J ^a,b   Reich, David ^a,c,h  

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

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e GEORGETOWN UNIVERSITY   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g SAIC FREDERICK INC   (United States)

^h HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; CALCULATION; DISEASE ACTIVITY; DISEASE PREDISPOSITION; EMPIRICISM; ETHNOLOGY; GENE FLOW; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC MARKER; GENOME; HISPANIC; HUMAN; POPULATION GENETICS; PRIORITY JOURNAL;

EID: 2342622086     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/420871     Document Type: Article

References (69)

1. Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, Nemesh J, Lane CR, Schaffner SF, Bolk S, Brewer C, Tuomi T, Gaudet D, Hudson TJ, Daly M, Groop L, Lander ES (2000) The common PPARγ Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat Genet 26:76-80
2. Balding DJ, Nichols RA (1995) A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96:3-12
3. Barcellos LF, Oksenberg JR, Begovich AB, Martin ER, Schmidt S, Vittinghoff E, Goodin DS, Pelletier D, Lincoln RR, Bucher P, Swerdlin A, Pericak-Vance MA, Haines JL, Hauser SL, Multiple Sclerosis Genetics Group (2003) HLA-DR2 dose effect on susceptibility to multiple sclerosis and influence on disease course. Am J Hum Genet 72:710-716
4. Baum LE, Petrie T, Soules G, Weiss N (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Stat 41:164-171
5. Bickel PJ, Doksum KA (2001) Mathematical statistics: basic ideas and selected topics. Vol I. Second edition. Prentice Hall, New Jersey
6. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 33:228-237
7. Briscoe D, Stephens JC, O'Brien SJ (1994) Linkage disequilibrium in admixed populations: Applications in gene mapping. J Hered 85:59-63
8. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 33:518-521
9. Chakraborty R, Weiss KM (1988) Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85:9119-9123
10. Chen M-H, Shao Q-M, Ibrahim JG (2000) Monte Carlo methods in Bayesian computation. Springer, New York
11. Collins FS, Guyer MS, Charkravarti A (1997) Variations on a theme: cataloging human DNA sequence variation. Science 278:1580-1581
12. Collins-Schramm HE, Chima B, Operario DJ, Criswell LA, Seldin MF (2003) Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population. Hum Genet 113:211-219
13. Corbo RM, Scacchi R (1999) Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a "thrifty" allele? Ann Hum Genet 63:301-310
14. Crocq MA, Buguet A, Bisser S, Burgert E, Stanghellini A, Uyanik G, Dumas M, Macher JP, Mayerova A (1996) BalI and MspI polymorphisms of the dopamine D3 receptor gene in African Blacks and Caucasians. Hum Hered 46:58-60
15. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229-232
16. Davey Smith G, Neaton JD, Wentworth D, Stamler R, Stamler J (1998) Mortality differences between black and white men in the USA: contribution of income and other risk factors among men screened for the MRFIT. MRFIT Research Group. Multiple Risk Factor Intervention Trial. Lancet 351: 934-939
17. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997-1004
18. Donner H, Rau H, Walfish PG, Braun J, Siegmund T, Finke R, Herwig J, Usadel KH, Badenhoop K (1997) CTLA4 alanine-17 confers genetic susceptibility to Graves' disease and to type 1 diabetes mellitus. J Clin Endocrinol Metab 82: 143-146
19. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis. Cambridge University Press, Cambridge
20. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587
21. Farrer LA, Cupples LA, Haines JL, Hyman B, Kukull WA, Mayeux R, Myers RH, Pericak-Vance MA, Risch N, van Duijn CM (1997) Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease: a meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 278:1349-1356
22. 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
23. Gelman A, Carlin JB, Stern HS, Rubin DB (1995) Bayesian data analysis. Chapman and Hall, London
24. Giallourakis C, Stoll M, Miller K, Hampe J, Lander ES, Daly MJ, Schreiber S, Rioux JD (2003) IBD5 is a general risk factor for inflammatory bowel disease: replication of association with Crohn disease and identification of a novel association with ulcerative colitis. Am J Hum Genet 73:205-211
25. Gilks WR, Best NG, Tan KKC (1995) Adaptive rejection Metropolis sampling within Gibbs sampling. Appl Stat 44:455-472
26. Gilks WR, Richardson S, Spiegelhalter DJ (Eds) (1996) Markov Chain Monte Carlo in practice. Chapman and Hall, London
27. Gilks WR, Wild P (1992) Adaptive rejection sampling for Gibbs sampling. Appl Stat 41:337-348
28. Halder I, Shriver MD (2003) Measuring and using admixture to study the genetics of complex disease. Hum Genom 1: 52-62
29. Hill AV, Allsopp CE, Kwiatkowski D, Anstey NM, Twumasi P, Rowe PA, Bennett S, Brewster D, McMichael AJ, Greenwood BM (1991) Common west African HLA antigens are associated with protection from severe malaria. Nature 352: 595-600
30. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4:45-61
31. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72:1492-1504
32. Kurtzke JF, Beebe GW, Norman JE Jr (1979) Epidemiology of multiple sclerosis in US veterans. 1. Race, sex, and geographic distribution. Neurology 29:1228-1235
33. Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363-2367
34. Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11:241-247
35. Lautenberger JA, Stephens JC, O'Brien SJ, Smith M (2000) Significant admixture linkage disequilibrium across 30 cM around the FY locus in African-Americans. Am J Hum Genet 66:969-978
36. Lockwood JR, Roeder K, Devlin B (2001) A Bayesian hierarchical model for allele frequencies. Genet Epidemiol 20: 17-33
37. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN (2003) Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet 33:177-182
38. McKeigue PM (1997) Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. Am J Hum Genet 60:188-196
39. - (1998) Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in populations, by conditioning on parental admixture. Am J Hum Genet 63:241-251
40. 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
41. Mead S, Mahal SP, Beck J, Campbell T, Farrall M, Fisher E, Collinge (2001) Sporadic-but not variant-Creutzfeldt-Jakob disease is associated with polymorphisms upstream of PRNP exon 1. Am J Hum Genet 69:1225-1235
42. Nakajima T, Jorde LB, Ishigami T, Umemura S, Emi M, Lalouel JM, Inoue I (2002) Nucleotide diversity and haplotype structure of the human angiotensinogen gene in two populations. Am J Hum Genet 70:108-123
43. Nicholson G, Smith A, Jónsson F, Gústafson Ó, K S, Donnelley P (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J Roy Stat Soc Ser B 64:695-715
44. Oksenberg JR, Barcellos LF, Cree BA, Baranzini SE, Bugawan TL, Khan O, Lincoln RR, Swerdlin A, Mignot E, Lin L, Goodin D, Erlich HA, Schmidt S, Thomson G, Reich DE, Pericak-Vance MA, Haines JL, Hauser SL (2004) Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans. Am J Hum Genet 74:160-167
45. Osei-Hyiaman D, Hou L, Zhiyin R, Zhiming Z, Yu H, Amankwah AA, Harada S (2001) Association of a novel point mutation (C159G) of the CTLA4 gene with type 1 diabetes in West Africans but not in Chinese. Diabetes 50:2169-2171
46. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, Allison DB, Deka R, Ferrell RE, Shriver MD (1998) Estimating African-American admixture proportions by use of population-specific alleles. Am J Hum Genet 63: 1839-1851
47. Permutt MA, Elbein SC (1990) Insulin gene in diabetes. Analysis through RFLP. Diabetes Care 13:364-374
48. Pfaff CL, Parra EJ, Bonilla C, Hiester K, McKeigue PM, Kamboh MI, Hutchinson RG, Ferrell RE, Boerwinkle E, Shriver MD (2001) Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet 68:198-207
49. Rabiner LR (1989) A tutorial on hidden Markov models. Proceedings of the IEEE 77:257-286
50. Rees DC, Cox M, Clegg JB (1995) World distribution of factor V Leiden. Lancet 346:1133-1134
51. Ripley BD (1987) Stochastic simulation. Wiley, New York
52. Rioux JD, Daly MJ, Silverberg MS, Lindblad K, Steinhart H, Cohen Z, Delmonte T, et al (2001) Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 29:223-228
53. Risch N (1992) Mapping genes for complex disease using association studies with recently admixed populations. Am J Hum Genet Suppl 51:13
54. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
55. Risch NJ (2000) Searching for genetic determinants in the new millennium. Nature 405:847-856
56. Rosendaal FR, Koster T, Vandenbroucke JP, Reitsma PH (1995) High risk of thrombosis in patients homozygous for factor V Leiden (activated protein C resistance). Blood 85: 1504-1508
57. Rotimi C, Puras A, Cooper R, McFarlane-Anderson N, Forrester T, Ogunbiyi O, Morrison L, Ward R (1996) Polymorphisms of renin-angiotensin genes among Nigerians, Jamaicans, and African Americans. Hypertension 27:558-563
58. Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112:387-399
59. Siddiqui A, Kerb R, Weale ME, Brinkmann U, Smith A, Goldstein DB, Wood NW, Sisodiya SM (2003) Association of multidrug resistance in epilepsy with a polymorphism in the drug-transporter gene ABCB1. N Engl J Med 348:1442-1448
60. Siffert W, Forster P, Jockel KH, Mvere DA, Brinkmann B, Naber C, Crookes R, et al (1999) Worldwide ethnic distribution of the G protein β3 subunit 825T allele and its association with obesity in Caucasian, Chinese, and Black African individuals. J Am Soc Nephrol 10:1921-1930
61. Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O'Brien SJ (2001) Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 69:1080-1094
62. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, et al (2004) A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74:1001-1013 (in this issue)
63. Soldevila M, Calafell F, Andres AM, Yague J, Helgason A, Stefansson K, Bertranpetit J (2003) Prion susceptibility and protective alleles exhibit marked geographic differences. Hum Mutat 22:104-105
64. Stephens JC, Briscoe D, O'Brien SJ (1994) Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. Am J Hum Genet 55:809-824
65. Thompson EA, Guo SW (1991) Evaluation of likelihood ratios for complex genetic models. J Math Appl Med Biol 8:149-169
66. Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, et al (2003) Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 423:506-511
67. Wallin MT, Page WF, Kurtzke JF (2003) Multiple sclerosis in US veterans of the Vietnam era and later military service: race, sex, and geography. Ann Neurol 55:65-71
68. Wilson JF, Goldstein DB (2000) Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population. Am J Hum Genet 67:926-935
69. Zheng C, Elston RC (1999) Multipoint linkage disequilibrium mapping with particular reference to the African-American population. Genet Epidemiol 17:79-101