African and non‐African admixture components in African Americans and an African Caribbean population

Abstract

Admixture is a potential source of confounding in genetic association studies, so it becomes important to detect and estimate admixture in a sample of unrelated individuals. Populations of African descent in the US and the Caribbean share similar historical backgrounds but the distributions of African admixture may differ. We selected 416 ancestry informative markers (AIMs) to estimate and compare admixture proportions using STRUCTURE in 906 unrelated African Americans (AAs) and 294 Barbadians (ACs) from a study of asthma. This analysis showed AAs on average were 72.5% African, 19.6% European and 8% Asian, while ACs were 77.4% African, 15.9% European, and 6.7% Asian which were significantly different. A principal components analysis based on these AIMs yielded one primary eigenvector that explained 54.04% of the variation and captured a gradient from West African to European admixture. This principal component was highly correlated with African vs. European ancestry as estimated by STRUCTURE (r2 = 0.992, r2 = 0.912, respectively). To investigate other African contributions to African American and Barbadian admixture, we performed PCA on ~14,000 (14k) genome-wide SNPs in AAs, ACs, Yorubans, Luhya and Maasai African groups, and estimated genetic distances (FST). We found AAs and ACs were closest genetically (FST = 0.008), and both were closer to the Yorubans than the other East African populations. In our sample of individuals of African descent, ~400 well-defined AIMs were just as good for detecting substructure as ~14,000 random SNPs drawn from a genome-wide panel of markers.

Recombination rates in admixed individuals identified by ancestry-based inference

“…This sample has a mean African-ancestry coefficient of ~0.81 with a 95% quantile range of 0.54-0.96 ( Supplementary Fig. 5), a broad range that is consistent with previous studies of African-American and AfricanCaribbean samples [25][26][27][28] . We used as reference panels for the ancestral populations the HapMap YRI and HapMap CEU panels.…”

An anthropological genetic perspective on creolization in the anglophone caribbean

“…These studies indicate that among African Caribbean populations found in Jamaica, Haiti, the Bahamas, St. Thomas, Barbados, and Trinidad and Tobago, there is about 65-95% African ancestry, 4-27% European ancestry, and 0-6% Native American ancestry (Parra et al, 1998;Molokhia et al, 2003;Miljkovic-Gacic et al, 2005;Benn-Torres et al, 2008;Simms et al, 2008Simms et al, , 2010Simms et al, , 2011Murray, 2010;Wilson et al, 2012). Generally, triparental admixture estimates are quite similar between these Anglophone islands.…”

Prevalence of Glaucoma in an Urban West African Population

“…The higher prevalence of POAG in Afro-Caribbeans than in African Americans might be related to a higher West African genetic admixture. 57,58 Environmental factors, gene-gene and gene-environment interactions, epigenetics, natural selection, and genetic drift also may play a role. 25,59,60 Primary open-angle glaucoma is a complex disease both mechanistically and genetically.…”