Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays

Genetic Epidemiology

Volumn 35, Issue 1, 2011, Pages 80-83

  Tandon, Arti ^a,b   Patterson, Nick ^b   Reich, David ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

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

Author keywords

Admixture mapping; African American disease studies; Ancestry informative markers

Indexed keywords

AFRICAN AMERICAN; ANCESTRY INFORMATIVE MARKER; ARTICLE; EUROPEAN AMERICAN; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC MARKER; GENOTYPE; HEREDITY; HUMAN; HUMAN EXPERIMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN AMERICANS; AFRICAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAPPING; COMMERCE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 78650378305     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20550     Document Type: Article

References (21)

1. Bercovici S, Geiger D, Shlush L, Skorecki K, Templeton A. 2008. Panel construction for mapping in admixed populations via expected mutual information. Genome Res 18:661-667.
2. Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM, Oakley-Girvan I, Whittemore AS, Cooney KA, Ingles SA, Altshuler D, Henderson BE, Reich D. 2006. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Natl Acad Sci USA 103:14068-14073.
3. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. 2004. Design and analysis of admixture mapping studies. Am J Hum Genet 74:965-978.
4. Kao WH, Klag MJ, Meoni LA, Reich D, Berthier-Schaad Y, Li M, Coresh J, Patterson N, Tandon A, Powe NR, Fink NE, Sadler JH, Weir MR, Abboud HE, Adler SG, Divers J, Iyengar SK, Freedman BI, Kimmel PL, Knowler WC, Kohn OF, Kramp K, Leehey DJ, Nicholas SB, Pahl MV, Schelling JR, Sedor JR, Thornley-Brown D, Winkler CA, Smith MW, Parekh RS, Family Investigation of Nephropathy and Diabetes Research Group. 2008. MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet 40:1185-1192.
5. Kopp JB, Smith MW, Nelson GW, Johnson RC, Freedman BI, Bowden DW, Oleksyk T, McKenzie LM, Kajiyama H, Ahuja TS, Berns JS, Briggs W, Cho ME, Dart RA, Kimmel PL, Korbet SM, Michel DM, Mokrzycki MH, Schelling JR, Simon E, Trachtman H, Vlahov D, Winkler CA. 2008. MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 40:1175-1184.
6. McKeigue PM. 1998. Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63:241-251.
7. Montana G, Pritchard JK. 2004. Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 75:771-789.
8. 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.
9. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly M, Reich D. 2004. Methods for high-density admixture mapping of disease genes. Am J Hum Genet 74:1001-1013.
10. Price AL, Weale ME, Patterson N, Myers SR, Need AC, Shianna KV, Ge D, Rotter JI, Torres E, Taylor KD, Goldstein DB, Reich D. 2008. Long-Range LD Can Confound Genome Scans in Admixed Populations. Am J Hum Genet 83:132-135.
11. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. 2009. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5:e1000519.
12. Reich D, Patterson N, Jager PL, McDonald GJ, Waliszewska A, Tandon A, Lincoln RR, Deloa C, Fruhan SA, Cabre P, Bera O, Semana G, Kelly MA, Francis DA, Ardlie K, Khan O, Cree BA, Hauser SL, Oksenberg JR, Hafler DA. 2005. A whole-genome admixture scan finds a candidate gene for multiple sclerosis susceptibility. Nat Genet 37:1113-1118.
13. Reich D, Patterson N, Ramesh V, De Jager PL, McDonald GJ, Tandon A, Choy E, Hu D, Tamraz B, Pawlikowska L, Wassel-Fyr C, Huntsman S, Waliszewska A, Rossin E, Li R, Garcia M, Reiner A, Ferrell R, Cummings S, Kwok PY, Harris T, Zmuda JM, Ziv E; Health, Aging and Body Composition (Health ABC) Study. 2007. Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels. Am J Hum Genet 80:716-726.
14. Sankararaman S, Kimmel G, Halperin E, Jordan MI. 2008a. On the inference of ancestries in admixed populations. Genome Res 18:668-675.
15. Sankararaman S, Sridhar S, Kimmel G, Halperin E. 2008b. Estimating local ancestry in admixed populations. Am J Hum Genet 82:290-303.
16. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager P, Yi Z, De Thé G, Essex M, Kanki PJ, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O'Brien SJ, Reich D. 2004. A high density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74:979-1000.
17. Sundquist A, Fratkin E, Do CB, Batzoglou S. 2008. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Res 18:767-782.
18. Tang H, Coram M, Wang P, Zhu X, Risch N. 2006. Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet 79:1-12.
19. The International HapMap Consortium. 2003. The International HapMap Project. Nature 426:789-796.
20. Tian C, Hinds DA, Shigeta R, Kittles R, Ballinger DG, Seldin MF. 2006. A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am J Hum Genet 79:640-649.
21. Zhu X, Cooper RS, Elston RC. 2004. Linkage analysis of a complex disease through use of admixed populations. Am J Hum Genet 74:1136-1153.