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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

Additional files

Additional data file 1:

Figure S1 shows PC1 from PCA of African Americans based on all genotype data versus African IA from frappe analysis. The figure shows near-perfect correlation between PC1 and African IA. Figure S2 shows a Frappe analysis of 57 Yoruba, Mandenka, and Bantu speakers, based on estimating admixed ancestry one individual at a time, fixing all others in their defined population. Results show majority assignment to an individual's own population group. Figure S3a shows a PCA of indigenous Africans (n = 94) based on all genotype data. Figure S3b shows a PCA of indigenous Africans (n = 94) based on variable removal of genotype data. Note that the figure shows nearly identical genetic structure to that in Figure 3a, including the separation of Yoruba, Mandenka, and Bantu.

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