Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Leite, Tailce K M ^a   Fonseca, Rômulo M C ^a   de França, Nanci M ^a   Parra, Esteban J ^b   Pereira, Rinaldo W ^a  

^a UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; MELANIN;

ADOLESCENT; AFRICAN AMERICAN; AMERICAN INDIAN; ANCESTRY INFORMATIVE MARKER; ARTICLE; BRAZIL; CONTROLLED STUDY; EUROPEAN AMERICAN; FEMALE; GENE; GENETIC ASSOCIATION; GENETIC MARKER; GENOME ANALYSIS; GENOMIC ANCESTRY; HUMAN; HUMAN CELL; LEUKOCYTE; POPULATION GENETIC STRUCTURE; QUANTITATIVE ANALYSIS; REFLECTOMETRY; SELF REPORT; SIBLING; SKIN COLOR; SKIN PIGMENTATION; SLC24A5 GENE; SOCIAL STATUS; CAUCASIAN; GENETICS; HUMAN GENOME; METABOLISM; NEGRO; SOCIAL CLASS;

ADOLESCENT; AFRICAN CONTINENTAL ANCESTRY GROUP; BRAZIL; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENOME, HUMAN; HUMANS; MELANINS; SIBLINGS; SKIN PIGMENTATION; SOCIAL CLASS;

EID: 80355143424     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027162     Document Type: Article

References (41)

1. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, et al. (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72: 1492-1504.
2. Alves-Silva J, da Silva Santos M, Guimaraes PE, Ferreira AC, Bandelt HJ, et al. (2000) The ancestry of Brazilian mtDNA lineages. Am J Hum Genet 67: 444-461.
3. Carvalho-Silva DR, Santos FR, Rocha J, Pena SD, (2001) The phylogeography of Brazilian Y-chromosome lineages. Am J Hum Genet 68: 281-286.
4. Lins TC, Vieira RG, Abreu BS, Grattapaglia D, Pereira RW, (2010) Genetic composition of Brazilian population samples based on a set of twenty-eight ancestry informative SNPs. Am J Hum Biol 22: 187-192.
5. Callegari-Jacques SM, Grattapaglia D, Salzano FM, Salamoni SP, Crossetti SG, et al. (2003) Historical genetics: spatiotemporal analysis of the formation of the Brazilian population. Am J Hum Biol 15: 824-834.
6. Parra FC, Amado RC, Lambertucci JR, Rocha J, Antunes CM, et al. (2003) Color and genomic ancestry in Brazilians. Proc Natl Acad Sci U S A 100: 177-182.
7. Lins TC, Vieira RG, Abreu BS, Gentil P, Moreno-Lima R, et al. (2011) Genetic Heterogeneity of Self-Reported Ancestry Groups in an Admixed Brazilian Population. J Epidemiol doi:102188/jeaJE20100164.
8. Pena SD, Di Pietro G, Fuchshuber-Moraes M, Genro JP, Hutz MH, et al. (2011) The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected. PLoS One 6: e17063.
9. Santos RV, Fry PH, Monteiro S, Maio MC, Rodrigues JC, et al. (2009) Color, race, and genomic ancestry in Brazil: dialogues between anthropology and genetics. Curr Anthropol 50: 787-819.
10. Pimenta JR, Zuccherato LW, Debes AA, Maselli L, Soares RP, et al. (2006) Color and genomic ancestry in Brazilians: a study with forensic microsatellites. Hum Hered 62: 190-195.
11. 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.
12. Shriver MD, Kittles RA, (2004) Genetic ancestry and the search for personalized genetic histories. Nat Rev Genet 5: 611-618.
13. Parra EJ, Kittles RA, Shriver MD, (2004) Implications of correlations between skin color and genetic ancestry for biomedical research. Nat Genet 36: S54-60.
14. Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, et al. (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112: 387-399.
15. Fonseca RMC, França NM, Pereira RW, (2011) Suggestive linkage to chromosome 1q for bone mineral apparent density in Brazilian sister adolescents. Joint Bone Spine (In Press) Doi:101016/jjbspin201105007.
16. IBGE, (2000) Censo Demográfico 2000, Características gerais da população. Rio de Janeiro Instituto Brasileiro de Geografia e Estatística.
17. ABEP, (2003) Critério de Classificação Econômica Brasil. Associação Brasileira de Empresas de Estatística.
18. Shriver MD, Parra EJ, (2000) Comparison of narrow-band reflectance spectroscopy and tristimulus colorimetry for measurements of skin and hair color in persons of different biological ancestry. Am J Phys Anthropol 112: 17-27.
19. Miller SA, Dykes DD, Polesky HF, (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16: 1215.
20. McKeigue PM, (1998) Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63: 241-251.
21. Rosenberg NA, Li LM, Ward R, Pritchard JK, (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
22. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
23. Bland JM, Altman DG, (1986) Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1: 307-310.
24. Cohen J, (1960) A coefficient of agreement for nominal scales. Educational and Psychological Measurement 20: 37-46.
25. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310: 1782-1786.
26. Norton HL, Kittles RA, Parra E, McKeigue P, Mao X, et al. (2007) Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. Mol Biol Evol 24: 710-722.
27. Valenzuela RK, Henderson MS, Walsh MH, Garrison NA, Kelch JT, et al. (2010) Predicting phenotype from genotype: normal pigmentation. J Forensic Sci 55: 315-322.
28. Izagirre N, Garcia I, Junquera C, de la Rua C, Alonso S, (2006) A scan for signatures of positive selection in candidate loci for skin pigmentation in humans. Mol Biol Evol 23: 1697-1706.
29. Ginger RS, Askew SE, Ogborne RM, Wilson S, Ferdinando D, et al. (2008) SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis. J Biol Chem 283: 5486-5495.
30. Dimisianos G, Stefanaki I, Nicolaou V, Sypsa V, Antoniou C, et al. (2009) A study of a single variant allele (rs1426654) of the pigmentation-related gene SLC24A5 in Greek subjects. Exp Dermatol 18: 175-177.
31. Stokowski RP, Pant PV, Dadd T, Fereday A, Hinds DA, et al. (2007) A genomewide association study of skin pigmentation in a South Asian population. Am J Hum Genet 81: 1119-1132.
32. Helgason A, Hrafnkelsson B, Gulcher JR, Ward R, Stefansson K, (2003) A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes. Am J Hum Genet 72: 1370-1388.
33. Viera AJ, Garrett JM, (2005) Understanding interobserver agreement: the kappa statistic. Fam Med 37: 360-363.
34. Gravlee CC, Dressler WW, Bernard HR, (2005) Skin color, social classification, and blood pressure in southeastern Puerto Rico. Am J Public Health 95: 2191-2197.
35. Klimentidis YC, Miller GF, Shriver MD, (2009) Genetic admixture, self-reported ethnicity, self-estimated admixture, and skin pigmentation among Hispanics and Native Americans. Am J Phys Anthropol 138: 375-383.
36. Florez JC, Price AL, Campbell D, Riba L, Parra MV, et al. (2009) Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia 52: 1528-1536.
37. Parra EJ, Cameron E, Simmonds L, Valladares A, McKeigue P, et al. (2007) Association of TCF7L2 polymorphisms with type 2 diabetes in Mexico City. Clin Genet 71: 359-366.
38. Parra EJ, Below JE, Krithika S, Valladares A, Barta JL, et al. (2011) Genome-wide association study of type 2 diabetes in a sample from Mexico City and a meta-analysis of a Mexican-American sample from Starr County, Texas. Diabetologia 54: 2038-2046.
39. Soejima M, Koda Y, (2007) Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. Int J Legal Med 121: 36-39.
40. Tsai HJ, Choudhry S, Naqvi M, Rodriguez-Cintron W, Burchard EG, et al. (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.
41. Ruiz-Narvaez EA, Rosenberg L, Rotimi CN, Cupples LA, Boggs DA, et al. (2010) Genetic variants on chromosome 5p12 are associated with risk of breast cancer in African American women: the Black Women's Health Study. Breast Cancer Res Treat 123: 525-530.