Genetic Ancestry Analysis of Epigen-Brazil

The Epigen-Brazil participants were genotyped by the Illumina facility (San Diego, California) using the Omni 2.5M array. We performed the unsupervised tri hybrid (k = 3) ADMIXTURE analyses based on 370,539 SNPs shared by samples from the HapMap Project, the Human Genome Diversity Project (HGDP)23 24 and the Epigen-Brazil study population. As external panels, we used the following HapMap samples: 266 Africans (176 Yoruba in Ibadan, Nigeria [YRI] and 90 Luhya in Webuye, Kenya [LWK]), 262 Europeans (174 Utah residents with Northern and Western European ancestry [CEU] and 88 from Toscans from Italy [TSI]), 170 admixed individuals (77 Mexicans from Los Angeles, California [MEX] and 83 Afro-African from Southwest USA [ASW]), and 93 Native Americans from the HGDP (25 Pima, 22 Karitiana, 25 Maya and 21 Surui). The same set of reference populations was used in analyzing the three cohorts.

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Lima-Costa M.F., Rodrigues L.C., Barreto M.L., Gouveia M., Horta B.L., Mambrini J., Kehdy F.S., Pereira A., Rodrigues-Soares F., Victora C.G, & Tarazona-Santos E. (2015). Genomic ancestry and ethnoracial self-classification based on 5,871 community-dwelling Brazilians (The Epigen Initiative). Scientific Reports, 5, 9812.

Publication 2015

Omni 2.5M array

African Africans Epigen European Hapmap Hybrid Native americans Pima Populations Snps

Corresponding Organization :

Other organizations : Fundação Oswaldo Cruz, London School of Hygiene & Tropical Medicine, Instituto de Saúde, Universidade Federal da Bahia, Universidade Federal de Minas Gerais, Universidade Federal de Pelotas, Hospital do Coração, Universidade de São Paulo

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Protocol cited in 11 other protocols

Variable analysis

independent variables

Unsupervised tri hybrid (k = 3) ADMIXTURE analyses

dependent variables

Genotyping of Epigen-Brazil participants using the Illumina Omni 2.5M array

control variables

370,539 SNPs shared by samples from the HapMap Project, the Human Genome Diversity Project (HGDP), and the Epigen-Brazil study population
HapMap samples: 266 Africans (176 Yoruba in Ibadan, Nigeria [YRI] and 90 Luhya in Webuye, Kenya [LWK]), 262 Europeans (174 Utah residents with Northern and Western European ancestry [CEU] and 88 from Toscans from Italy [TSI]), 170 admixed individuals (77 Mexicans from Los Angeles, California [MEX] and 83 Afro-African from Southwest USA [ASW]), and 93 Native Americans from the HGDP (25 Pima, 22 Karitiana, 25 Maya and 21 Surui)

positive controls

The same set of reference populations was used in analyzing the three cohorts.

negative controls

No negative controls were explicitly mentioned.

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