Recent admixture in an Indian population of african ancestry

American Journal of Human Genetics

Volumn 89, Issue 1, 2011, Pages 111-120

  Narang, Ankita ^a   Jha, Pankaj ^a   Rawat, Vimal ^a   Mukhopadhayay, Arijit ^a   Dash, Debasis ^a   Basu, Analabha ^b   Mukerji, Mitali ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CADHERIN; ION CHANNEL;

AFRICA; AFRICAN AMERICAN; AFRICAN INDIAN; ARTICLE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC VARIABILITY; HAPLOTYPE MAP; HUMAN; HUMAN EXPERIMENT; INDIAN; PRIORITY JOURNAL;

IPS;

EID: 80051550770     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2011.06.004     Document Type: Article

References (46)

1. Basu, A., Mukherjee, N., Roy, S., Sengupta, S., Banerjee, S., Chakraborty, M., Dey, B., Roy, M., Roy, B., Bhattacharyya, N.P., et al. (2003). Ethnic India: A genomic view, with special reference to peopling and structure. Genome Res. 13, 2277-2290. (Pubitemid 37265994)
2. Sengupta, S., Zhivotovsky, L.A., King, R., Mehdi, S.Q., Edmonds, C.A., Chow, C.E., Lin, A.A., Mitra, M., Sil, S.K., Ramesh, A., et al. (2006). Polarity and temporality of highresolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am. J. Hum. Genet. 78, 202-221. (Pubitemid 43157561)
3. Indian Genome Variation Consortium. (2008). Genetic landscape of the people of India: a canvas for disease gene exploration. J. Genet. 87, 3-20.
4. Abdulla, M.A., Ahmed, I., Assawamakin, A., Bhak, J., Brahmachari, S.K., Calacal, G.C., Chaurasia, A., Chen, C.H., Chen, J., Chen, Y.T., et al; HUGO Pan-Asian SNP Consortium; Indian Genome Variation Consortium. (2009). Mapping human genetic diversity in Asia. Science 326, 1541-1545.
5. Reich, D., Thangaraj, K., Patterson, N., Price, A.L., and Singh, L. (2009). Reconstructing Indian population history. Nature 461, 489-494.
6. Zhu, X., Luke, A., Cooper, R.S., Quertermous, T., Hanis, C., Mosley, T., Gu, C.C., Tang, H., Rao, D.C., Risch, N., et al. (2005). Admixture mapping for hypertension loci with genome-scan markers. Nat. Genet. 37, 177-181.
7. Basu, A., Tang, H., Arnett, D., Gu, C.C., Mosley, T., Kardia, S., Luke, A., Tayo, B., Cooper, R., Zhu, X., et al. (2009). Admixture mapping of quantitative trait loci for BMI in African Americans: Evidence for loci on chromosomes 3q, 5q, and 15q. Obesity (Silver Spring) 17, 1226-1231.
8. Basu, A., Tang, H., Lewis, C.E., North, K., Curb, J.D., Quertermous, T., Mosley, T.H., Boerwinkle, E., Zhu, X., and Risch, N.J. (2009). Admixture mapping of quantitative trait loci for blood lipids in African-Americans. Hum. Mol. Genet. 18, 2091-2098.
9. Tang, H., Choudhry, S., Mei, R., Morgan, M., Rodriguez- Cintron, W., Burchard, E.G., and Risch, N.J. (2007). Recent genetic selection in the ancestral admixture of Puerto Ricans. Am. J. Hum. Genet. 81, 626-633. (Pubitemid 47330221)
10. Basu, A., Tang, H., Zhu, X., Gu, C.C., Hanis, C., Boerwinkle, E., and Risch, N. (2008). Genome-wide distribution of ancestry in Mexican Americans. Hum. Genet. 124, 207-214.
11. Zakharia, F., Basu, A., Absher, D., Assimes, T.L., Go, A.S., Hlatky, M.A., Iribarren, C., Knowles, J.W., Li, J., Narasimhan, B., et al. (2009). Characterizing the admixed African ancestry of African Americans. Genome Biol. 10, R141.
12. Smith, M.W., and O'Brien, S.J. (2005). Mapping by admixture linkage disequilibrium: Advances, limitations and guidelines. Nat. Rev. Genet. 6, 623-632. (Pubitemid 41044299)
13. Winkler, C.A., Nelson, G.W., and Smith, M.W. (2010). Admixture mapping comes of age. Annu. Rev. Genomics Hum. Genet. 11, 65-89.
14. 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. (Pubitemid 44452981)
15. Xu, S., Huang, W., Qian, J., and Jin, L. (2008). Analysis of genomic admixture in Uyghur and its implication in mapping strategy. Am. J. Hum. Genet. 82, 883-894.
16. Xu, S., and Jin, L. (2008). A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am. J. Hum. Genet. 83, 322-336.
17. Singh, K.S. (2002). People of India, Gujarat: Anthropological survey of India (Mumbai, India: Popular Prakashan Pvt Ltd.), pp. 1295-1297.
18. Gauniyal, M., Chahal, S.M., and Kshatriya, G.K. (2008). Genetic affinities of the Siddis of South India: An emigrant population of East Africa. Hum. Biol. 80, 251-270.
19. Ramana, G.V., Su, B., Jin, L., Singh, L.,Wang, N., Underhill, P., and Chakraborty, R. (2001). Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur. J. Hum. Genet. 9, 695-700. (Pubitemid 32923241)
20. International HapMap Consortium. (2003). The International HapMap Project. Nature 426, 789-796.
21. 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., et al. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100-1104. (Pubitemid 351300793)
22. Narang, A., Roy, R.D., Chaurasia, A., Mukhopadhyay, A., and Mukerji, M. (2010). Indian Genome Variation Consortium, and Dash, D. (2010). IGVBrowser-A genomic variation resource from diverse Indian populations. Database (Oxford) 2010, baq022.
23. Patterson, N., Price, A.L., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genet. 2, e190.
24. 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. (Pubitemid 44141658)
25. Pritchard, J.K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959. (Pubitemid 30397141)
26. Falush, D., Stephens, M., and Pritchard, J.K. (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164, 1567-1587. (Pubitemid 37102217)
27. Falush, D., Stephens, M., and Pritchard, J.K. (2007). Inference of population structure using multilocus genotype data: Dominant markers and null alleles. Mol. Ecol. Notes 7, 574-578. (Pubitemid 47035522)
28. Alexander, D.H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664.
29. Excoffier, L., Smouse, P.E., and Quattro, J.M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131, 479-491.
30. Excoffier, L., Laval, G., and Schneider, S. (2005). Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50.
31. Reynolds, J., Weir, B.S., and Cockerham, C.C. (1983). Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105, 767-779. (Pubitemid 14246280)
32. Weir, B.S., and Hill,W.G. (2002). Estimating F-statistics. Annu. Rev. Genet. 36, 721-750. (Pubitemid 36109203)
33. Hill, W.G. (1974). Estimation of linkage disequilibrium in randomly mating populations. Heredity 33, 229-239.
34. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., and Sham, P.C. (2007). PLINK: A tool set for wholegenome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575. (Pubitemid 47330214)
35. Dennis, G., Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao,W., Lane, H.C., and Lempicki, R.A. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3.
36. Mohanty, P.K. (2006). Encyclopaedia of Scheduled Tribes in India (Delhi: Gyan Publication), pp. 81.
37. 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. (Pubitemid 36014209)
38. 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.
39. Jallow, M., Teo, Y.Y., Small, K.S., Rockett, K.A., Deloukas, P., Clark, T.G., Kivinen, K., Bojang, K.A., Conway, D.J., Pinder, M., et al; Wellcome Trust Case Control Consortium; Malaria Genomic Epidemiology Network. (2009). Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat. Genet. 41, 657-665.
40. Vansina, J. (1995). Valleys of the Niger. J. Afr. Hist. 36, 491-495.
41. Chakraborty, R., and Weiss, K.M. (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. (Pubitemid 19001851)
42. Stephens, J.C., Briscoe, D., and O'Brien, S.J. (1994). Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines. Am. J. Hum. Genet. 55, 809-824. (Pubitemid 24298979)
43. Genovese, G., Friedman, D.J., Ross, M.D., Lecordier, L., Uzureau, P., Freedman, B.I., Bowden, D.W., Langefeld, C.D., Oleksyk, T.K., Uscinski Knob, A.L., et al. (2010). Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 329, 841-845.
44. Adeyemo, A., Gerry, N., Chen, G., Herbert, A., Doumatey, A., Huang, H., Zhou, J., Lashley, K., Chen, Y., Christman, M., and Rotimi, C. (2009). A genome-wide association study of hypertension and blood pressure in African Americans. PLoS Genet. 5, e1000564.
45. Risch, N., de Leon, D., Ozelius, L., Kramer, P., Almasy, L., Singer, B., Fahn, S., Breakefield, X., and Bressman, S. (1995). Genetic analysis of idiopathic torsion dystonia in Ashkenazi Jews and their recent descent from a small founder population. Nat. Genet. 9, 152-159.
46. Kalaydjieva, L., Gresham, D., and Calafell, F. (2001). Genetic studies of the Roma (Gypsies): A review. BMC Med. Genet. 2, 5.