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Characterizing the admixed African ancestry of African Americans

Fouad Zakharia1, Analabha Basu2, Devin Absher3, Themistocles L Assimes4, Alan S Go5, Mark A Hlatky6, Carlos Iribarren5, Joshua W Knowles4, Jun Li7, Balasubramanian Narasimhan6, Steven Sidney5, Audrey Southwick8, Richard M Myers3, Thomas Quertermous4, Neil Risch259* and Hua Tang1

Author Affiliations

1 Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA

2 Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave., San Francisco, CA 94143, USA

3 HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA

4 Division of Cardiovascular Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA

5 Division of Research, Kaiser Permanente, 2000 Broadway, Oakland, CA 94612, USA

6 Department of Health, Research and Policy, Stanford University School of Medicine, 150 Governors Lane, Stanford, CA 94305, USA

7 Department of Human Genetics, University of Michigan, 1241 E. Catherine St., Ann Arbor, MI 48109, USA

8 Department of Infectious Diseases, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA

9 Department of Epidemiology and Biostatistics, University of California, San Francisco, 185 Berry Street, San Francisco, CA 94107, USA

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Genome Biology 2009, 10:R141  doi:10.1186/gb-2009-10-12-r141

Published: 22 December 2009



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.


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 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.