Development of two multiplex mini-sequencing panels of ancestry informative snps for studies in latin americans: An application to populations of the state of minas gerais (brazil)

Genetics and Molecular Research

Volumn 9, Issue 4, 2010, Pages 2069-2085

  Silva, M C F ^a,b   Zuccherato, L W ^b   Soares Souza, G B ^a,b   Vieira, Z M ^a   Cabrera, L ^c   Herrera, P ^c   Balqui, J ^c,d   Romero, C ^c,d   Jahuira, H ^c,d   Gilman, R H ^c,e   Martins, M L ^a   Tarazona Santos, E ^b  

^a FUNDAÇÃO HEMOMINAS   (Brazil)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c ASOCIACIÓN BENÉFICA PRISMA   (Peru)

^d UNIVERSIDAD PERUANA CAYETANO HEREDIA   (Peru)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Admixture; Latin american; Mini sequencing

Indexed keywords

DNA;

AFRICAN AMERICAN; AMERICAN INDIAN; ANCESTRY INFORMATIVE MARKER; ARTICLE; BRAZIL; CAUCASIAN; GENE FREQUENCY; GENE SEQUENCE; GENETIC MARKER; GENOTYPE; HISPANIC; HUMAN; MULTIPLEX MINI SEQUENCING; POPULATION ADMIXTURE; POPULATION GENETIC PARAMETERS; POPULATION GENETIC STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; URBAN POPULATION;

BRAZIL; ELECTROPHORESIS, CAPILLARY; HUMANS; LATIN AMERICA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 78149421814     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: 10.4238/vol9-4gmr911     Document Type: Article

References (37)

1. Bastos-Rodrigues L, Pimenta JR and Pena SD (2006). The genetic structure of human populations studied through short insertion-deletion polymorphisms. Ann. Hum. Genet. 70: 658-665.
2. Benn-Torres J, Bonilla C, Robbins CM, Waterman L, et al. (2008). Admixture and population stratification in African Caribbean populations. Ann. Hum. Genet. 72: 90-98.
3. Botelho TR (1994). Famílias e Escravarias: Demografia e Família Escrava no Norte de Minas Gerais no Século XIX. Master's thesis, Universidade de São Paulo, São Paulo.
4. Botelho TR, Braga MP and de Andrade CV (2007). Immigration and family in Minas Gerais at the end of the 19th century. Rev. Bras. Hist. 27: 155-176.
5. Cann HM, de Toma C, Cazes L, Legrand MF, et al. (2002). A human genome diversity cell line panel. Science 296: 261-262.
6. Carvalho CM and Pena SD (2005). Optimization of a multiplex minisequencing protocol for population studies and medical genetics. Genet. Mol. Res. 4: 115-125.
7. Chakraborty R (1985). Gene Identity in Racial Hybrids and Estimation of Admixture Rates. In: Genetic Differentiation in Human and Other Animal Populations (Ahuja YR and Neel JV, eds.). Indian Anthropological Association, Delhi, 171-180.
8. Chakraborty R (1986). Gene admixture in human populations: models and predictions. Am. J. Phys. Anthropol. 29: 1-43.
9. Choisy M, Franck P and Cornuet JM (2004). Estimating admixture proportions with microsatellites: comparison of methods based on simulated data. Mol. Ecol. 13: 955-968.
10. Chung CC, Magalhaes WC, Gonzalez-Bosquet J and Chanock SJ (2010). Genome-wide association studies in cancer - current and future directions. Carcinogenesis 31: 111-120.
11. Comas D, Calafell F, Mateu E, Perez-Lezaun A, et al. (1998). Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations. Am. J. Hum. Genet. 63: 1824-1838.
12. Dupanloup I and Bertorelle G (2001). Inferring admixture proportions from molecular data: extension to any number of parental populations. Mol. Biol. Evol. 18: 672-675.
13. Falush D, Stephens M and Pritchard JK (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
14. Glass B and Li CC (1953). The dynamics of racial intermixture; an analysis based on the American Negro. Am. J. Hum. Genet. 5: 1-20.
15. Herrera-Paz EF, Matamoros M and Carracedo A (2010). The Garifuna (Black Carib) people of the Atlantic coasts of Honduras: Population dynamics, structure, and phylogenetic relations inferred from genetic data, migration matrices, and isonymy. Am. J. Hum. Biol. 22: 36-44.
16. Hubisz MJ, Falush D, Stephens M and Pritchard JK (2009). Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Res. 9: 1322-1332.
17. Hughes AL, Welch R, Puri V, Matthews C, et al. (2008). Genome-wide SNP typing reveals signatures of population history. Genomics 92: 1-8.
18. Instituto Brasileiro de Geografia e Estatística (IBGE) (2007). Síntese de Indicadores Sociais: Uma Análise das Condições de Vida da População Brasileira. Available at [http://www.ibge.gov.br/home/estatistica/populacao/condicaodevida/ indicadoresminimos/sinteseindicsociais2007/indic_sociais2007.pdf]. Accessed April 12, 2010.
19. International HapMap Consortium (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
20. Kosoy R, Nassir R, Tian C, White PA, et al. (2009). Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum. Mutat. 30: 69-78.
21. Lai CQ, Tucker KL, Choudhry S, Parnell LD, et al. (2009). Population admixture associated with disease prevalence in the Boston Puerto Rican health study. Hum. Genet. 125: 199-209.
22. Lee SS, Bolnick DA, Duster T, Ossorio P, et al. (2009). Genetics. The illusive gold standard in genetic ancestry testing. Science 325: 38-39.
23. Lins TC, Vieira RG, Abreu BS, Grattapaglia D, et al. (2010). Genetic composition of Brazilian population samples based on a set of twenty-eight ancestry informative SNPs. Am. J. Hum. Biol. 22: 187-192.
24. Luna FV and Klein HS (2004). Economy and slave society: Minas Gerais and São Paulo in 1830. Rev. Bras. Est. Pop. 21: 173-193.
25. Packer BR, Yeager M, Burdett L, Welch R, et al. (2006). SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res. 34: D617-D621.
26. Parra FC, Amado RC, Lambertucci JR, Rocha J, et al. (2003). Color and genomic ancestry in Brazilians. Proc. Natl. Acad. Sci. U. S. A. 100: 177-182.
27. Patterson N, Petersen DC, van der Ross RE, Sudoyo H, et al. (2010). Genetic structure of a unique admixed population: implications for medical research. Hum. Mol. Genet. 19: 411-419.
28. Pfaff CL, Barnholtz-Sloan J, Wagner JK and Long JC (2004). Information on ancestry from genetic markers. Genet. Epidemiol. 26: 305-315.
29. Pritchard JK, Stephens M and Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
30. Rachlin J, Ding C, Cantor C and Kasif S (2005). MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res. 33: W544-W547.
31. Rosenberg NA, Li LM, Ward R and Pritchard JK (2003). Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 73: 1402-1422.
32. Salzano FM and Bortolini MC (2002). The Evolution and Genetics of Latin American Populations. Cambridge University Press, Cambridge.
33. Sans M (2000). Admixture studies in Latin America: from the 20th to the 21st century. Hum. Biol. 72: 155-177.
34. Santos NP, Ribeiro-Rodrigues EM, Ribeiro-Dos-Santos AK, Pereira R, et al. (2010). Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel. Hum. Mutat. 31: 184-190.
35. Tarazona-Santos E, Raimondi S and Fuselli S (2007). Controlling the Effects of Population Stratification by Admixture in Pharmacogenetics. In: Pharmacogenomics in Admixed populations (Guilherme Suarez-Kurtz, ed.). Landes Bioscience, Austin, 1-16.
36. Tian C, Hinds DA, Shigeta R, Kittles R, et al. (2006). A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am. J. Hum. Genet. 79: 640-649.
37. Via M, Ziv E and Burchard EG (2009). Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. Clin. Genet. 76: 225-235.