Genetic composition of Brazilian population samples based on a set of twenty eight ancestry informative SNPs

American Journal of Human Biology

Volumn 22, Issue 2, 2010, Pages 187-192

  Lins, Tulio C ^a   Vieira, Rodrigo G ^a   Abreu, Breno S ^a   Grattapaglia, Dario ^a,b   Pereira, Rinaldo W ^a  

^a UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^b Ministerio do Meio Ambiente Brazil   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; AMERICAN INDIAN; ARTICLE; BRAZIL; CAUCASIAN; ETHNOLOGY; FEMALE; GENETICS; HUMAN; MALE; NEGRO; POPULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN CONTINENTAL ANCESTRY GROUP; ALLELES; BRAZIL; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; HUMANS; INDIANS, SOUTH AMERICAN; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION;

EID: 77249160660     PISSN: 10420533     EISSN: 15206300     Source Type: Journal    
DOI: 10.1002/ajhb.20976     Document Type: Article

References (47)

1. Abe-Sandes K, Silva WA Jr, Zago MA. 2004. Heterogeneity of the Y chromosome in Afro-Brazilian populations. Hum Biol 76:77-86.
2. Alves-Silva J, da Silva Santos M, Guimaraes PE, Ferreira AC, Bandelt HJ, Pena SD, Prado VF. 2000. The ancestry of Brazilian mtDNA lineages. Am J Hum Genet 67:444-461.
3. Barnholtz-Sloan JS, Pfaff CL, Chakraborty R, Long JC. 2005. Informativeness of the CODIS STR loci for admixture analysis. J Forensic Sci 50: 1322-1326.
4. Benn-Torres J, Bonilla C, Robbins CM, Waterman L, Moses TY, Hernandez W, Santos ER, Bennett F, Aiken W, Tullock T, Coard K, Hennis A, Wu S, Nemesure B, Leske MC, Freeman V, Carpten J, Kittles RA. 2008. Admixture and population stratification in African Caribbean populations. Ann Hum Genet 72 (Part 1):90-98.
5. Blanton RE, Silva LK, Morato VG, Parrado AR, Dias JP, Melo PR, Reis EA, Goddard KA, Nunes MR, Rodrigues SG, Vasconcelos PF, Castro JM, Reis MG, Barreto ML, Teixeira MG. 2008. Genetic ancestry and income are associated with dengue hemorrhagic fever in a highly admixed population. Eur J Hum Genet 16:762-765.
6. Bonilla C, Parra EJ, Pfaff CL, Dios S, Marshall JA, Hamman RF, Ferrell RE, Hoggart CL, McKeigue PM, Shriver MD. 2004a. Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping. Ann Hum Genet 68:139-153.
7. Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. 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.
8. Bortolini MC, Da Silva WAJW, De Guerra DC, Remonatto G, Mirandola R, Hutz MH, Weimer TA, Silva MC, Zago MA, Salzano FM. 1999. Africanderived South American populations: a history of symmetrical and asymmetrical matings according to sex revealed by bi- and uni-parental genetic markers. Am J Hum Biol 11:551-563.
9. Callegari-Jacques SM, Grattapaglia D, Salzano FM, Salamoni SP, Crossetti SG, Ferreira ME, Hutz MH. 2003. Historical genetics: spatiotemporal analysis of the formation of the Brazilian population. Am J Hum Biol 15:824-834.
10. Carvalho-Silva DR, Santos FR, Rocha J, Pena SD. 2001. The phylogeography of Brazilian Y-chromosome lineages. Am J Hum Genet 68:281-286.
11. Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS. 1991. "Touchdown" PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008.
12. Estrela RC, Ribeiro FS, Carvalho RS, Gregorio SP, Dias-Neto E, Struchiner CJ, Suarez-Kurtz G. 2008. Distribution of ABCB1 polymorphisms among Brazilians: impact of population admixture. Pharmacogenomics 9:267-276.
13. Excoffier L, Laval G, Schneider S. 2005. Arlequin version 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50.
14. 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.
15. Ferreira LB, Mendes-Junior CT, Wiezel CE, Luizon MR, Simoes AL. 2006. Genomic ancestry of a sample population from the state of Sao Paulo, Brazil. Am J Hum Biol 18:702-705.
16. Gentil P, Lima RM, Lins TC, Abreu BS, Pereira RW, Oliveira RJ. 2007. Physical activity, Cdx-2 genotype, and BMD. Int J Sports Med 28:1065-1069.
17. Gentil P, Lins TC, Moreno Lima R, Abreu BS, Grattapaglia D, Bottaro M, Oliveira RJ, Pereira RW. 2009. Vitamin-D-receptor genotypes and bonemineral density in postmenopausal women: interaction with physical activity. J Aging Phys Activity 17:31-45.
18. 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.
19. Hunemeier T, Carvalho C, Marrero AR, Salzano FM, Junho Pena SD, Bortolini MC. 2007. Niger-Congo speaking populations and the formation of the Brazilian gene pool: mtDNA and Y-chromosome data. Am J Phys Anthropol 133:854-867.
20. IBGE. 2006. Síntese de indicadores sociais. Rio de Janeiro: IBGE.
21. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, et al. 2008. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 30:69-78.
22. Lins TC. 2007. Impact of admixture on the performance of HapMap data in Brazilian population assessed in PTPN22 and VDR genes, Dissertation Thesis. Brasilia: Universidade Catolica de Brasilia. 194 p.
23. Lins TC, Nogueira LR, Lima RM, Gentil P, Oliveira RJ, Pereira RW. 2007. A multiplex single-base extension protocol for genotyping Cdx2, FokI, BsmI, ApaI, and TaqI polymorphisms of the vitamin D receptor gene. Genet Mol Res 6:216-224.
24. Lopez J, Prezioso V. 2001. A better way to optimize: two-step gradient PCR. Eppendorf Bionews 16:3-4.
25. Luizon MR, Mendes-Junior CT, De Oliveira SF, Simoes AL. 2008. Ancestry informative markers in Amerindians from Brazilian Amazon. Am J Hum Biol 20:86-90.
26. Marrero AR, Das Neves Leite FP, De Almeida Carvalho B, Peres LM, Kommers TC, Da Cruz IM, Salzano FM, Ruiz-Linares A, Da Silva Junior WA, Bortolini MC. 2005. Heterogeneity of the genome ancestry of individuals classified as White in the state of Rio Grande do Sul, Brazil. Am J Hum Biol 17:496-506.
27. Martinez-Marignac VL, Valladares A, Cameron E, Chan A, Perera A, Globus-Goldberg R, Wacher N, Kumate J, McKeigue P, ODonnell D, et al. 2007. Admixture in Mexico City: implications for admixture mapping of type 2 diabetes genetic risk factors. Hum Genet 120:807-819.
28. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R. 2004. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 14:414-425.
29. Moreno Lima R, Abreu BS, Gentil P, Lins TC, Grattapaglia D, Pereira RW, Oliveira RJ. 2007. Lack of association between vitamin D receptor genotypes and haplotypes with fat-free mass in postmenopausal Brazilian women. J Gerontol A Biol Sci Med Sci 62:966-972.
30. Parra EJ, Kittles RA, Shriver MD. 2004. Implications of correlations between skin color and genetic ancestry for biomedical research. Nat Genet 36(11 Suppl):S54-S60.
31. Parra FC, Amado RC, Lambertucci JR, Rocha J, Antunes CM, Pena SD. 2003. Color and genomic ancestry in Brazilians. Proc Natl Acad Sci USA 100:177-182.
32. Pena SD. 2005. Reasons for banishing the concept of race from Brazilian medicine. Hist Cienc Saude Manguinhos 12:321-346.
33. 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.
34. Pimenta JR, Zuccherato LW, Debes AA, Maselli L, Soares RP, Moura-Neto RS, Rocha J, Bydlowski SP, Pena SD. 2006. Color and genomic ancestry in Brazilians: a study with forensic microsatellites. Hum Hered 62:190-195.
35. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
36. Rosenberg NA. 2004. Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137-138.
37. Rosenberg NA, Li LM, Ward R, Pritchard JK. 2003. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73:1402-1422.
38. Salzano FM. 2004. Interethnic variability and admixture in Latin America- social implications. Rev Biol Trop 52:405-415.
39. Sans M. 2000. Admixture studies in Latin America: from the 20th to the 21st century. Hum Biol 72:155-177.
40. Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, Silva G, Belmont JW, Klareskog L, Gregersen PK. 2006. European population substructure: clustering of northern and southern populations. PLoS Genet 2:e143.
41. Seldin MF, Tian C, Shigeta R, Scherbarth HR, Silva G, Belmont JW, Kittles R, Gamron S, Allevi A, Palatnik SA, et al. 2007. Argentine population genetic structure: large variance in Amerindian contribution. Am J Phys Anthropol 132:455-462.
42. Shaffer JR, Kammerer CM, Reich D, McDonald G, Patterson N, Goodpaster B, Bauer DC, Li J, Newman AB, Cauley JA, et al. 2007. Genetic markers for ancestry are correlated with body composition traits in older African Americans. Osteoporos Int 18:733-741.
43. Silva WA, Bortolini MC, Schneider MP, Marrero A, Elion J, Krishnamoorthy R, Zago MA. 2006. MtDNA haplogroup analysis of black Brazilian and sub-Saharan populations: implications for the Atlantic slave trade. Hum Biol 78:29-41.
44. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De The G, Essex M, Sankale JL, 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, OBrien SJ, Reich D. 2004. A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet 74:1001-1013.
45. Suarez-Kurtz G, Vargens DD, Struchiner CJ, Bastos-Rodrigues L, Pena SD. 2007. Self-reported skin color, genomic ancestry and the distribution of GST polymorphisms. Pharmacogenet Genomics 17:765-771.
46. Tsai HJ, Choudhry S, Naqvi M, Rodriguez-Cintron W, Burchard EG, Ziv E. 2005. Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations. Hum Genet 118:424-433.
47. Vallone PM, Butler JM. 2004. AutoDimer: a screening tool for primerdimer and hairpin structures. Biotechniques 37:226-231.