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Genotyping Study Uncovers Ancestry, Genetic Patterns in West Africans and African Americans

NEW YORK (GenomeWeb News) – Extensive genetic and ancestral diversity exists within individuals who identify themselves as African American, according to a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, suggesting care should be taken when applying pharmacogenetic research to individuals within this population.

American, African, and French researchers led by University of Pennsylvania geneticist Sarah Tishkoff and Cornell University biological statistics and computational biology researcher Carlos Bustamante used genotyping to explore ancestry and other population patterns in hundreds of African American individuals and about a dozen West African populations. In the process, the team found that genetic patterns in most West African populations largely coincide with language, though geography was also a factor.

"We were able to distinguish among closely related West African populations and showed that genetically inferred ancestry correlates strongly with geography and language, reflecting historic migration events in Africa," Tishkoff said in a statement.

The team's findings also highlighted the genetic diversity existing within individuals who identify themselves as African American, with West African ancestry ranging from around one percent to 99 percent in the individuals involved in the study.

"That some individuals who self-identify as African American show almost no West African ancestry and others show almost complete West African ancestry has implications for pharmacogenomics studies and assessment of disease risk," Tishkoff, Bustamente, and co-workers wrote.

"[I]t appears that the range of genetic ancestry captured under the term African American is extremely diverse, which suggests caution should be used in prescribing treatments based on differential guidelines for African Americans," they added.

Earlier this year, Tishkoff and her team published the largest African genetic study to date. That work started uncovering some of the extensive population structure that exists in sub-Saharan Africa, providing new information about how genetics relate to language, migration, and lifestyle in some African populations.

For the current study, Tishkoff and her team genotyped 146 individuals from 11 West and South African populations using the Affymetrix GeneChip 500K array and incorporated these results with previous genotype data on 365 African Americans, 400 Americans of European ancestry, and 57 Nigerians collected through the HapMap project.

In the West African samples, the researchers found that genetic clusters usually corresponded to language groups, though they also detected patterns related to geography, including genetic gradients from East to West and North to South.

And while they found relatively little differentiation between some populations, others — such as the Fulani, Xhosa, and other populations — had very distinct genetic patterns.

The researchers suspect such patterns, in part, reflect centuries-old migrations by individuals in the Bantu Niger-Kordofanian language group, who moved south from an area around what is now Nigeria and Cameroon into sub-Saharan Africa.

Overall, they noted, "patterns of genomic diversity within Africa are complex and reflect deep historical, cultural, and linguistic impacts on gene flow among populations."

Meanwhile, the team's analyses of African American genotype data detected both African and European ancestry in the individuals tested, though the proportion of each varied greatly from one individual to the next.

In general, the African genetic patterns resembled those found in modern day West African populations classified as "non-Bantu, Niger-Kordofanian-speaking," such as the Igbo and Yoruba from Nigeria and the Brong from Ghana, the researchers explained — a finding that coincides with known historical records and forced migration as a result of the slave trade.

In some individuals this West African ancestry was more than 99 percent, while in others it was less than one percent, the researchers reported.

When they compared autosomal and X chromosome data, the researchers found more African ancestry on the X chromosome, indicating more African ancestry on the maternal side and more paternal European ancestry. And although the median proportion of European ancestry in the African Americans was 18.5 percent, the overall European ancestry varied dramatically between individuals.

"The greatest variation among African-Americans is in their proportion of European ancestry," Tishkoff said in a statement, "which has important implications for the design of personalized medical treatments."

In the future, the researchers noted, more dense genotyping studies and population sequencing studies will be needed to more accurately tease apart African and African American genetic patterns and to find markers for gauging ancestry and improving the application of pharmacogenetics and other personalized treatment approaches.

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