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Characterizing the admixed African ancestry of African Americans

Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B, Sidney S, Southwick A, Myers RM, Quertermous T, Risch N, Tang H - Genome Biol. (2009)

Bottom Line: 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.

Affiliation: Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA. zakharia@stanford.edu

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.

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.
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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.

Mentions: Figure 3 displays the PCA results of the African Americans and the three closely related African populations (Yoruba, Mandenka, and Bantu). Several features are worth comment. First, despite their genetic similarity, PCA shows clear separation among the Yoruba, Mandenka, and Bantu populations, based on the first two PCs. Second, Figure 3 reveals that the African Americans are placed as a single cluster in the convex hull defined by the three African groups.

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Characterizing the admixed African ancestry of African Americans

Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B, Sidney S, Southwick A, Myers RM, Quertermous T, Risch N, Tang H - Genome Biol. (2009)

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.
© Copyright Policy
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.
Mentions: Figure 3 displays the PCA results of the African Americans and the three closely related African populations (Yoruba, Mandenka, and Bantu). Several features are worth comment. First, despite their genetic similarity, PCA shows clear separation among the Yoruba, Mandenka, and Bantu populations, based on the first two PCs. Second, Figure 3 reveals that the African Americans are placed as a single cluster in the convex hull defined by the three African groups.

Bottom Line: 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.

Affiliation: Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA. zakharia@stanford.edu

ABSTRACT

Background:

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.

View Similar Images In: Results  - Collection
View Article: Pubmed Central - HTML -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=2812948&rFormat=json&query=null&req=5