Admixture and population stratification in African Caribbean populations

Annals of Human Genetics

Volumn 72, Issue 1, 2008, Pages 90-98

  Benn Torres, J ^a   Bonilla, C ^b   Robbins, C M ^d   Waterman, L ^c   Moses, T Y ^d   Hernandez, W ^a   Santos, E R ^a   Bennett, F ^e   Aiken, W ^e   Tullock, T ^e   Coard, K ^e   Hennis, A ^e,f   Wu, S ^f   Nemesure, B ^f   Leske, M C ^f   Freeman, V ^g,h   Carpten, J ^d   Kittles, R A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF THE WEST INDIES   (Jamaica)

^d TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF THE WEST INDIES   (Jamaica)

^f STONY BROOK UNIVERSITY   (United States)

^g UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^h LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

Ancestry informative markers; Barbados; Caribbean; Genetic admixture; Jamaica; St.Thomas USVI

Indexed keywords

AFRICAN AMERICAN; AFRICAN CARIBBEAN; AMERICAN INDIAN; ARTICLE; BARBADOS; CAUCASIAN; CENTRAL AMERICA; ETHNIC DIFFERENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HEREDITY; HUMAN; JAMAICA; MALE; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; PRIORITY JOURNAL;

AFRICAN CONTINENTAL ANCESTRY GROUP; CARIBBEAN REGION; CULTURE; ECONOMICS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; GEOGRAPHY; HISTORY; HUMANS; INDIANS, NORTH AMERICAN;

EID: 37849026056     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2007.00398.x     Document Type: Article

References (62)

1. Amundadottir, L. T., Sulem, P., Gudmundsson, J., Helgason, A., Baker, A., Agnarsson, B. A., Sigurdsson, A., Benediktsdottir, K. R., Cazier, J. B., Sainz, J., Jakobsdottir, M., Kostic, J., Magnusdottir, D. N., Ghosh, S., Agnarsson, K., Birgisdottir, B., Le Roux, L., Olafsdottir, A., Blondal, T., Andresdottir, M., Gretarsdottir, O. S., Bergthorsson, J. T., Gudbjartsson, D., Gylfason, A., Thorleifsson, G., Manolescu, A., Kristjansson, K., Geirsson, G., Isaksson, H., Douglas, J., Johansson, J. E., Balter, K., Wiklund, F., Montie, J. E., Yu, X., Suarez, B. K., Ober, C., Cooney, K. A., Gronberg, H., Catalona, W. J., Einarsson, G. V., Barkardottir, R. B., Gulcher, J. R., Kong, A., Thorsteinsdottir, U. & Stefansson, K. (2006) A common variant associated with prostate cancer in European and African populations. Nat Genet 38, 652-8.
2. Bertoni, B., Budowle, B., Sans, M., Barton, S. A. & Chakraborty, R. (2003) Admixture in Hispanics: Distribution of ancestral population contributions in the Continental United States. Hum Biol 75, 1-11.
3. Bonilla, C., Parra, E. J., Pfaff, C. L., Dios, S., Marshall, J. A., Hamman, R. F., Ferrell, R. E., Hoggart, C. L., Mckeigue, P. M. & Shriver, M. D. (2004a) Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping. Ann Hum Genet 68, 139-53.
4. Bonilla, C., Shriver, M. D., Parra, E. J., Jones, A. & Fernandez, J. R. (2004b) Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city. Hum Genet 115, 57-68.
5. Bortolini, M. C., Da Silva, W. A. J., De Guerra, D. C., Remonatto, G., Mirandola, R., Hutz, M. H., Weimer, T. A., Silva, M. C., Zago, M. A. & Salzano, F. M. (1999) African-derived South American populations: A history of symmetrical and asymmetrical matings according to sex revealed by bi- and uni-parental genetic markers. Am J Human Biol 11, 551-563.
6. Bravi, C., Sans, M., Bailliet, G., Martinez-Marignac, V., Portas M, B. I., Bonilla, C. & Bianchi, N. (1997) Characterization of Mitochondrial DNA and Y- Chromosome Haplotypes in a Uruguayan Population of African Ancestry. Human Biology 69, 641-652.
7. Cardon, L. R. & Palmer, L. J. (2003) Population stratification and spurious allelic association. Lancet 361, 598-604.
8. Chakraborty, R., Ferrell, R., Stern, M., Haffner, S., Hazuda, H. & Rosenthal, M. (1986) Relationship of non-insulin dependent diabetes mellitus to Amerindian admixture in the Mexican Americans of San Antonio, Texas. Genet Epidemiol 3, 435-454.
9. Choudhry, S., Coyle, N. E., Tang, H., Salari, K., Lind, D., Clark, S. L., Tsai, H. J., Naqvi, M., Phong, A., Ung, N., Matallana, H., Avila, P. C., Casal, J., Torres, A., Nazario, S., Castro, R., Battle, N. C., Perez-Stable, E. J., Kwok, P. Y., Sheppard, D., Shriver, M. D., Rodriguez-Cintron, W., Risch, N., Ziv, E. & Burchard, E. G. (2006) Population stratification confounds genetic association studies among Latinos. Hum Genet 118, 652-64.
10. Collins-Schramm, H. E., Chima, B., Operario, D. J., Criswell, L. A. & Seldin, M. F. (2003) Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population. Hum Genet 113, 211-9.
11. Da Silva, W. A., Jr., Bortolini, M. C., Meyer, D., Salzano, F. M., Elion, J., Krishnamoorthy, R., Schneider, M. P., De Guerra, D. C., Layrisse, Z., Castellano, H. M., Weimer, T. D. & Zago, M. A. (1999) Genetic diversity of two African and sixteen South American populations determined on the basis of six hypervariable loci. Am J Phys Anthropol 109, 425-37.
12. Dickerson, P. & Johnson, P. (2006) U.S. Census Bureau, International Data Base. U.S. Census Bureau, Population Division/International Programs Center.
13. Donoghue, E. (2002) Black women/white men: The sexual exploitation of female slaves in the Danish West Indies. Trenton, NJ: Africa World Press.
14. Emmer, P. & Carrera Damas, G. (eds.) (1999) New Societies:THe Caribbean in the long sixteenth century. London: UNESCO Publishing/ Macmilln Education Ltd.
15. Falush, D., Stephens, M. & Pritchard, J. (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164, 1567-1587.
16. 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., Oakley-Girvan, I., Whittemore, A. S., Cooney, K. A., Ingles, S. A., Altshuler, D., Henderson, B. E. & Reich, D. (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Natl Acad Sci U S A 103, 14068-73.
17. Guitar, L. (2002) Documenting the myth of Taino extinction. Journal of Caribbean Amerindian History and Anthropology, on-line journal, 33 paragraphs.
18. Halder, I. & Shriver, M. (2003) Measuring and using admixture to study the genetics of complex diseases. Human Genomics 1, 41-51.
19. Hall, N. A. T. & Higman, B. W. (1992) Slave society in the Danish West Indies: St. Thomas, St. John, and St. Croix. Baltimore: Johns Hopkins University Press.
20. Hanis, C., Chakraborty, R., Ferrell, R. & Schull, W. (1986) Individual admixture estimates: Disease associations and individual risk of diabetes and gallbladder disease among Mexican-Americans in Starr County, Texas. Am J Phys Anthropol 70, 433-441.
21. Higman, B. W. (1984) Slave populations of the British Caribbean, 1807-1834. Baltimore: Johns Hopkins University Press.
22. Hirschhorn, J. N., Lohmueller, K., Byrne, E. & Hirschhorn, K. (2002) A comprehensive review of genetic association studies. Genet Med 4, 45-61.
23. Hoggart, C. J., Shriver, M. D., Kittles, R. A., Clayton, D. G. & Mckeigue, P. M. (2004) Design and analysis of admixture mapping studies. Am J Hum Genet 74, 965-78.
24. Homa, D. M., Mannino, D. M. & Lara, M. (2000) Asthma mortality in U.S. Hispanics of Mexican, Puerto Rican, and Cuban heritage, 1990-1995. Am J Respir Crit Care Med 161, 504-9.
25. Kittles, R. A., Baffoe-Bonnie, A. B., Moses, T. Y., Robbins, C. M., Ahaghotu, C., Huusko, P., Pettaway, C., Vijayakumar, S., Bennett, J., Hoke, G., Mason, T., Weinrich, S., Trent, J. M., Collins, F. S., Mousses, S., Bailey-Wilson, J., Furbert-Harris, P., Dunston, G., Powell, I. J. & Carpten, J. D. (2006) A common nonsense mutation in EphB2 is associated with prostate cancer risk in African American men with a positive family history. J Med Genet 43, 507-11.
26. Kittles, R. A., Chen, W., Panguluri, R. K., Ahaghotu, C., Jackson, A., Adebamowo, C. A., Griffin, R., Williams, T., Ukoli, F., Adams-Campbell, L., Kwagyan, J., Isaacs, W., Freeman, V. & Dunston, G. M. (2002) CYP3A4-V and prostate cancer in African Americans: Causal or confounding association because of population stratification? Hum Genet 110, 553-60.
27. Knight, F. (ed.) (1997) The slave societies of the Caribbean. London: UNESCO Publishing/Macmillan Education Ltd.
28. Knight, F. W. (1990) The Caribbean, The Genesis of a Fragmented Nationalism. New York: Oxford University Press.
29. Long, J. (1991) The genetic structure of admixed populations. Genetics 127, 417-428.
30. Martinez-Cruzado, J., Toro-Labrador, G., Ho-Fung, V., Estevez-Montero, M., Lobaina-Manzanet, A., Padovani-Claudio, D., Sanchez-Cruz, H., Ortiz-Bermudez, P. & Sanchez-Crespo, A. (2001) Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico. Hum Biol 73, 491-511.
31. Martinez-Cruzado, J. C., Toro-Labrador, G., Viera-Vera, J., Rivera-Vega, M. Y., Startek, J., Latorre-Esteves, M., Roman-Colon, A., Rivera-Torres, R., Navarro-Millan, I. Y., Gomez-Sanchez, E., Caro-Gonzalez, H. Y. & Valencia-Rivera, P. (2005) Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am J Phys Anthropol.
32. Martinez-Marignac, V. L., Valladares, A., Cameron, E., Chan, A., Perera, A., Globus-Goldberg, R., Wacher, N., Kumate, J., Mckeigue, P., O'donnell, D., Shriver, M. D., Cruz, M. & Parra, E. J. (2006) Admixture in Mexico City: Implications for admixture mapping of Type 2 diabetes genetic risk factors. Hum Genet.
33. Mckeigue, P. M. (2005) Prospects for admixture mapping of complex traits. Am J Hum Genet 76, 1-7.
34. Miljkovic-Gacic, I., Ferrell, R. E., Patrick, A. L., Kammerer, C. M. & Bunker, C. H. (2005) Estimates of African, European and Native American Ancestry in Afro-Caribbean men on the island of Tobago. Hum Hered 60, 129-33.
35. Montana, G. & Pritchard, J. K. (2004) Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 75, 771-89.
36. Parra, E., Marcini, A., Akey, J., Martinson, J., Batzer, M., Cooper, R. S., Forrester, T., Allison, D., Deka, R., Ferrel, R. & Shriver, M. (1998) Estimating African American Admixture Proportions by Use of Population-Specific Alleles. Am J Hum Genet 63, 1839-1851.
37. Parra, E. J., Kittles, R. A., Argyropoulos, G., Pfaff, C. L., Hiester, K., Bonilla, C., Sylvester, N., Parrish-Gause, D., Garvey, W. T., Jin, L., Mckeigue, P. M., Kamboh, M. I., Ferrell, R. E., Pollitzer, W. S. & Shriver, M. D. (2001) Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. Am J Phys Anthropol 114, 18-29.
38. 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., Daly, M. J. & Reich, D. (2004) Methods for high-density admixture mapping of disease genes. Am J Hum Genet 74, 979-1000.
39. Pfaff, C., Parra, E., Bonilla, C., Heister, K., Mckeigue, P., Kamboh, M., Hutchinson, R., Ferrell, R., Boerwinkle, E. & Shriver, M. (2001) Population structure in admixed populations: Effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet 68, 198-207.
40. Pritchard, J., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
41. Reich, D. & Patterson, N. (2005) Will admixture mapping work to find disease genes? Philos Trans R Soc Lond B Biol Sci 360, 1605-7.
42. Reich, D., Patterson, N., De Jager, P. L., Mcdonald, G. J., Waliszewska, A., Tandon, A., Lincoln, R. R., Deloa, C., Fruhan, S. A., Cabre, P., Bera, O., Semana, G., Kelly, M. A., Francis, D. A., Ardlie, K., Khan, O., Cree, B. A., Hauser, S. L., Oksenberg, J. R. & Hafler, D. A. (2005) A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility. Nat Genet 37, 1113-8.
43. Reiner, A. P., Ziv, E., Lind, D. L., Nievergelt, C. M., Schork, N. J., Cummings, S. R., Phong, A., Burchard, E. G., Harris, T. B., Psaty, B. M. & Kwok, P. Y. (2005) Population structure, admixture, and aging-related phenotypes in African American adults: The Cardiovascular Health Study. Am J Hum Genet 76, 463-77.
44. Rodas, C. G., Nancy Keyeux, Genoveva. (2003) Mitochondrial DNA Studies Show Asymmetrical Amerindian Admixture in Afro-Colombian and Mestizo Populations. Human Biology 75, 13-30.
45. Rogoziânski, J. (1999) A brief history of the Caribbean: From the Arawak and the Carib to the present. New York: Facts On File.
46. Rouse, I. (1992) The Tainos: Rise & decline of the people who greeted Columbus. New Haven: Yale University Press.
47. Salari, K., Choudhry, S., Tang, H., Naqvi, M., Lind, D., Avila, P. C., Coyle, N. E., Ung, N., Nazario, S., Casal, J., Torres-Palacios, A., Clark, S., Phong, A., Gomez, I., Matallana, H., Perez-Stable, E. J., Shriver, M. D., Kwok, P. Y., Sheppard, D., Rodriguez-Cintron, W., Risch, N. J., Burchard, E. G. & Ziv, E. (2005) Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmatics. Genet Epidemiol 29, 76-86.
48. Sans, M., Weimer, T. A., Franco, M. H., Salzano, F. M., Bentancor, N., Alvarez, I., Bianchi, N. O. & Chakraborty, R. (2002) Unequal contributions of male and female gene pools from parental populations in the African descendants of the city of Melo, Uruguay. Am J Phys Anthropol 118, 33-44.
49. Saul, J., Fondevila, M., Salas, A., Brion, M., Lareu, M. V. & Carracedo, A. (2004) Y-chromosome STR-haplotype typing in El Salvador. Forensic Sci Int 142, 45-9.
50. Saunders, N. J. (2005) Peoples of the Caribbean: An Encyclopedia of Archeology and Traditional Culture. Santa Barbara, Calif.: ABC-CLIO.
51. Seldin, M. F., Morii, T., Collins-Schramm, H. E., Chima, B., Kittles, R., Criswell, L. A. & Li, H. (2004) Putative ancestral origins of chromosomal segments in individual african americans: Implications for admixture mapping. Genome Res 14, 1076-84.
52. Seldin, M. F., Tian, C., Shigeta, R., Scherbarth, H. R., Silva, G., Belmont, J. W., Kittles, R., Gamron, S., Allevi, A., Palatnik, S. A., Alvarellos, A., Paira, S., Caprarulo, C., Guilleron, C., Catoggio, L. J., Prigione, C., Berbotto, G. A., Garcia, M. A., Perandones, C. E., Pons-Estel, B. A. & Alarcon-Riquelme, M. E. (2006) Argentine population genetic structure: Large variance in Amerindian contribution. Am J Phys Anthropol.
53. Shriver, M. D., Parra, E. J., 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, C. J., Mckeigue, P. M. & Kittles, R. A. (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112, 387-99.
54. Sued-Badillo, J. (ed.) (2003) Autochthonous Societies. Paris: UNESCO Publishing/Macmillan Publishers Ltd.
55. Tang, H., Jorgenson, E., Gadde, M., Kardia, S. L., Rao, D. C., Zhu, X., Schork, N. J., Hanis, C. L. & Risch, N. (2006) Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans. Hum Genet.
56. Tian, C., Hinds, D. A., Shigeta, R., Kittles, R., Ballinger, D. G. & Seldin, M. F. (2006) A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am J Hum Genet 79, 640-9.
57. Torroni, A., Rengo, C., Guida, V., Cruciani, F., Sellitto, D., Coppa, A., Calderon, F. L., Simionati, B., Valle, G., Richards, M., Macaulay, V. & Scozzari, R. (2001) Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 69, 1348-56.
58. United States. Dept. Of State. World factbook. Grand Rapids, Minn.: Wayzata Technology.
59. Vallinoto, I. M. V. C., Vallinoto, A. C. R., Valente, C. M. D. & Guerreiro, J. F. (2003) Allele frequency distributions of six hypervariable loci (D1S80, APOB, D4S43,vW1, F13A and DYS19) in two African-Brazilian communities from the Amazon region. Genetics and Molecular Biology 26, 235-240.
60. Yang, N., Li, H., Criswell, L. A., Gregersen, P. K., Alarcon-Riquelme, M. E., Kittles, R., Shigeta, R., Silva, G., Patel, P. I., Belmont, J. W. & Seldin, M. F. (2005) Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: Application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet 118, 382-92.
61. Zhu, X., Luke, A., Cooper, R. S., Quertermous, T., Hanis, C., Mosley, T., Gu, C. C., Tang, H., Rao, D. C., Risch, N. & Weder, A. (2005) Admixture mapping for hypertension loci with genome-scan markers. Nat Genet 37, 177-81.
62. Ziv, E., John, E. M., Choudhry, S., Kho, J., Lorizio, W., Perez-Stable, E. J. & Burchard, E. G. (2006) Genetic ancestry and risk factors for breast cancer among Latinas in the San Francisco Bay Area. Cancer Epidemiol Biomarkers Prev 15, 1878-85.