Characterizing the admixed African ancestry of African Americans, by Fouad Zakharia, Analabha Basu, Devin Absher, Themistocles L Assimes, Alan S Go, Mark A Hlatky, Carlos Iribarrenl, Joshua W Knowles, Jun Li, Balasubramanian Narasimhan, Steven Sidney, Audrey Southwick, Richard M Myersl, Thomas Quertermous, Neil Risch and Hua Tang
Genome Biology 2009, 10:R141 doi:10.1186/gb-2009-10-12-r141
Accurate, high-throughput genotyping allows for the fine characterization of genetic ancestry. Here we applied recently developed statistical and computational techniques to the question of African ancestry in African Americans using data on more than 500,000 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.
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.
These results are consistent with historical mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and 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 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.
Genome-wide patterns of population structure and admixture in West Africans and African Americans, by Katarzyna Bryc, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean-Marie Bodo, Charles Wambebe, Sarah A. Tishkoff, and Carlos D. Bustamante
PNAS January 12, 2010 vol. 107 no.2, 786-791 doi: 10.1073/pnas.0909559107
Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.