Genetic structure of a unique admixed population: Implications for medical research

Human Molecular Genetics

Volumn 19, Issue 3, 2009, Pages 411-419

  Patterson, Nick ^a   Petersen, Desiree C ^b   van der Ross, Richard E ^c   Sudoyo, Herawati ^d   Glashoff, Richard H ^e   Marzuki, Sangkot ^d   Reich, David ^a,f   Hayes, Vanessa M ^b,g  

^a HARVARD UNIVERSITY   (United States)

^b SYDNEY CHILDREN'S HOSPITAL   (Australia)

^c UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^d EIJKMAN INSTITUTE FOR MOLECULAR BIOLOGY   (Indonesia)

^e UNIVERSITY OF STELLENBOSCH   (South Africa)

^f HARVARD MEDICAL SCHOOL   (United States)

^g UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE MAPPING; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HUMAN GENETICS; MEDICAL RESEARCH; MOLECULAR EVOLUTION; POPULATION RESEARCH; POPULATION STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AFRICA; ETHNOLOGY; FEMALE; GENETICS; MALE; POPULATION GENETICS; RACE;

BIOMEDICAL RESEARCH; CONTINENTAL POPULATION GROUPS; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77949897520     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddp505     Document Type: Article

References (34)

1. Destro-Bisol, G., Maviglia, R., Caglià, A., Boschi, I., Spedini, G., Pascali, V., Clark, A. and Tishkoff, S. (1999) Estimating European admixture in African Americans by using microsatellites and a microsatellite haplotype (CD4/Alu). Hum. Genet., 104, 149-157.
2. Parra, E.J., Hoggart, C.J., Bonilla, C., Dios, S., Norris, J.M., Marshall, J.A., Hamman, R.F., Ferrell, R.E., McKeigue, P.M. and Shriver, M.D. (2004) Relation of type 2 diabetes to individual admixture and candidate gene polymorphisms in the Hispanic American population of San Luis Valley, Colorado. J. Med. Genet., 41, e116.
3. Zhu, X., Luke, A., Cooper, R.S., Quertermous, T., Hanis, C., Mosley, T., Gu, C.C., Tang, H., Rao, D.C., Risch, N. and Weder, A. (2005) Admixture mapping for hypertension loci with genome-scan markers. Nat. Genet., 37, 177-181.
4. Freedman, M.L., Haiman, C.A., Patterson, N., McDonald, G.J., Tandon, A., Waliszewska, A., Penney, K., Steen, R.G., Ardlie, K., John, E.M. et al. (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl. Acad. Sci. USA, 103, 14068-14073.
5. Boonzaaier, E., Malherbe, C., Smith, A. and Berens, P. (1996) The Cape Herders: A History of the Khoikhoi of Southern Africa. Ohio University Press, Ohio, USA.
6. Morris, A.G. (1997) The Griqua and the Khoikhoi: biology, ethnicity and the construction of identity. Kronos J. Cape History, 24, 106-118.
7. Balson, S. (2007) Children of the Mist, the lost tribe of South Africa.Interactive Presentations Pty Ltd, Australia.
8. van der Ross, R.E. (2005) Up from Slavery: Slaves at the Cape, their origins, treatment and contribution. Ampersand Press and University of the Western Cape, Cape Town.
9. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1229-1320.
10. The International HapMap Consortium (2003) The International HapMap Project. Nature, 426, 789-796.
11. The International HapMap Constortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-862.
12. Jakobsson, M., Scholz, S.W., Scheet, P., Gibbs, J.R., VanLiere, J.M.,Fung, H.C., Szpiech, Z.A., Degnan, J.H., Wang, K., Guerreiro, R. et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature, 451, 998-1003.
13. Li, J.Z., Absher, D.M., Tang, H., Southwick, A.M., Casto, A.M., Ramachandran, S., Cann, H.M., Barsh, G.S., Feldman, M., Cavalli-Sforza, L.L. and Myers, R.M. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319, 1100-1104.
14. Künsch, H.R. (1989) The jackknife and the bootstrap for general stationary observations. Ann. Statist., 17, 1217-1241.
15. Busing, F.M.T.A., Meijer, E. and van der Leeden, R. (1999) Delete-m jackknife for unequal m. Stat. Comput., 9, 3-8.
16. Rudan, I., Carothers, A.D., Polasek, O., Hayward, C., Vitart, V., Biloglav, Z., Kolcic, I., Zgaga, L., Ivankovic, D., Vorko-Jovic, A. et al. (2008) Quantifying the increase in average human heterozygosity due to urbanisation. Eur. J. Hum. Genet., 16, 1097-1102.
17. Copper, R.S., Tay, B. and Zhu, X. (2008) Genome-wide association studies: implications for multiethnic samples. Hum. Mol. Genet., 17, R151-R155.
18. Barreiro, L.B., Neyrolles, O., Babb, C.L., Tailleux, L., Quach, H., McElreavey, K., Helden, P.D., Hoal, E.G., Gicquel, B. and Quintana-Murci, L. (2006) Promoter variation in the DC-SIGN-encoding gene CD209 is associated with tuberculosis. PLoS Med., 3, e20.
19. Richards, M., Rengo, C., Cruciani, F., Gratrix, F., Wilson, J.F., Scozzari, R., Macaulay, V. and Torroni, A. (2003) Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. Am. J. Hum. Genet., 72, 1058-1064.
20. Bedoya, G., Montoya, P., García, J., Soto, I., Bourgeois, S., Carvajal, L., Labuda, D., Alvarez, V., Ospina, J., Hedrick, P.W. and Ruiz-Linares, A. (2006) Admixture dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South American population isolate. Proc. Natl. Acad. Sci. USA, 103, 7234-7239.
21. Helgason, A., Sigurethardottir, S., Gulcher, J.R., Ward, R. and Stefansson, K. (2000) mtDNA and the origin of the Icelanders: deciphering signals of recent population history. Am. J. Hum. Genet., 66, 999-1016.
22. Lind, J.M., Hutcheson-Dilks, H.B., Williams, S.M., Moore, J.H., Essex, M., Ruiz-Pesini, E., Wallace, D.C., Tishkoff, S.A., O'Brien, S.J. and Smith, M.W. (2007) Elevated male European and female African contributions to the genomes of African American individuals. Hum. Genet., 120, 713-722.
23. Tishkoff, S.A., Reed, F.A., Friedlaender, F.R., Ehret, C., Ranciaro, A., Froment, A., Hirbo, J.B., Awomoyi, A.A., Bodo, J.M., Doumbo, O. et al. (2009) The genetic structure and history of Africans and African Americans. Science, 324, 1035-1044.
24. Freedman, M.L., Reich, D., Penney, K.L., McDonald, G.J., Mignault, A.A., Patterson, N., Gabriel, S.B., Topol, E.J., Smoller, J.W., Pato, C.N. et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat. Genet., 36, 388-393.
25. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
26. Hoggart, C., Shriver, M., Kittles, R., Clayton, D. and McKeigue, P. (2004) Design and analysis of admixture mapping studies. Am. J. Hum. Genet., 74, 965-978.
27. Patterson, N., Hattangadi, N., Lane, B., Lohmueller, K.E., Hafler, D.A., Oksenberg, J.R., Hauser, S.L., Smith, M.W., O'Brien, S.J., Altshuler, D. et al. (2004) Methods for high-density admixture mapping of disease genes. Am. J. Hum. Genet., 74, 979-1000.
28. Darvasi, A. and Shifman, S. (2005) The beauty of admixture. Nat. Genet., 37, 118-119.
29. McKeigue, P.M. (2005) Prospects for admixture mapping of complex traits. Am. J. Hum. Genet., 76, 1-7.
30. Templeton, A.R. (2007) Genetics and recent human evolution. Evolution, 61, 1507-1519.
31. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A. and Feldman, M.W. (2002) Genetic structure of human populations. Science, 298, 2381-2385.
32. Patterson, N., Price, A. and Reich, D. (2006) Population Structure and Eigenanalysis. PLoS Genet., 2, e190.
33. Bickel, P.J. and Doksum, K.A. (1977) Mathematical Statistics: Basic Ideas and Selected Topics. Holden-Day, San Francisco, USA.
34. Weir, B.S. and Cockerham, C.C. (1984) Estimating f-statistics for the analysis of population structure. Evolution, 38, 1358-1370.