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, 10 (12), R141

Characterizing the Admixed African Ancestry of African Americans

Affiliations

Characterizing the Admixed African Ancestry of African Americans

Fouad Zakharia et al. Genome Biol.

Abstract

Background: Accurate, high-throughput genotyping allows the fine characterization of genetic ancestry. Here we applied recently developed statistical and computational techniques to the question of African ancestry in African Americans by using data on more than 450,000 single-nucleotide polymorphisms (SNPs) genotyped in 94 Africans of diverse geographic origins included in the HGDP, as well as 136 African Americans and 38 European Americans participating in the Atherosclerotic Disease Vascular Function and Genetic Epidemiology (ADVANCE) study. To focus on African ancestry, we reduced the data to include only those genotypes in each African American determined statistically to be African in origin.

Results: From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority contributions being from West and West-Central Africa, and only modest variation in these African-ancestry proportions among individuals. Furthermore, by principal components analysis, we found little evidence of genetic structure within the African component of ancestry in African Americans.

Conclusions: These results are consistent with historic mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and they cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans. Our results also indicate that the genetic architecture of African Americans is distinct from that of Africans, and that the greatest source of potential genetic stratification bias in case-control studies of African Americans derives from the proportion of European ancestry.

Figures

Figure 1
Figure 1
Principal components analysis of Africans, U.S. Caucasians, and African Americans. Inset bar plot displays individual ancestry estimates for African Americans from a supervised structure analysis by using frappe with K = 7, fixing six African and one U.S. Caucasian populations. The color scheme of the bar plot matches that in the PCA plot.
Figure 2
Figure 2
Principal components analysis of Africans, U.S. Caucasians, and African Americans including (a) all genotypes, and (b) only the genotypes of African origin in the African Americans. Comparison of (a) and (b) demonstrates the effective elimination of the European ancestry component from African Americans by using saber.
Figure 3
Figure 3
Principal components analysis of three West and Central West African populations (Mandenka, Yoruba, and Bantu) and African Americans by using only African-origin genotypes in the African Americans.
Figure 4
Figure 4
Individual ancestry estimates in African Americans by using only their African genotypes, from a supervised structure analysis with frappe, including all six African populations and U.S. Caucasians as fixed (K = 7). Color coding of populations is the same as that in Figure 1.
Figure 5
Figure 5
Principal components analysis of African Americans based on African-derived genotypes only. Little evidence for structure exists in the African component of ancestry.

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