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Broad and UCLA Teams Create Recombination Maps for African Americans


As an admixed population, African Americans have both African and European ancestry, and the genomes of African-American people are mosaics that reflect that dual ancestry. There are spots, or switch points, where a stretch of African ancestry genes changes to a segment of European ancestry genes, and vice versa. Those switch points represent historical recombination events that occurred between people of African ancestry and European ancestry, and those points have allowed two groups of researchers to independently build genetic maps of African Americans and compare those maps to ones based on Europeans to study recombination.

"I realized that having such a large sample of admixed individuals with genome-wide SNP data, one could take a completely new approach to inferring recombination and that, in doing so, we could help provide the first high-resolution map for African Americans," says John Novembre at the University of California, Los Angeles. "I also hoped, by comparing it to other maps, that it would help us learn more about why and how recombination rates vary in humans."

Based on those realizations, Novembre and his colleagues developed a genetic map using a cohort of more than 2,500 African Americans and nearly 300 African Caribbeans. As they reported in a July Nature Genetics article, the researchers compared their maps to the one developed by researchers at Decode Genetics based on an Icelandic population as well as to the HapMaps for Europeans and West Africans. From this, Novembre and his team found that recombination rates of the African-American population seemed to be an 80:20 average of the rates of the West African and European HapMaps — reflecting the ancestry ratio of African Americans. "This suggests that the recombination rate modifiers from one ancestry interact with the rate modifiers from the second ancestry in a simple, additive way," Novembre says. He notes, however, that the modifiers could be dominant or recessive on average, and affect the map accordingly. In addition, he and his team found that people with a greater percentage of African ancestry had recombination at more hotspots found in the West African HapMap.

That finding feeds into what the Broad Institute's David Reich and his colleagues determined from their own recombination map, for which they pulled together data for five groups of samples from African Americans, totaling about 30,000 people. "We found regions in the genome where recombinations occur much more often than not," Reich says.

His team also compared its map to existing ones and found that hotspots of recombination are largely the same for people of African descent and of European descent, though there are some spots that are more active in people of West African ancestry. Those spots, Reich adds, are due to a variant of the PRDM9 gene, which encodes a protein that binds a 13-base-pair DNA motif to determine where recombination will occur. About a third of West Africans have a variant of PRDM9 that instead binds a 17-base-pair stretch of DNA, changing where recombination takes place. These results appeared online in Nature in July.

Both groups are now looking to apply this switch point-based approach to study other admixed populations, including Latinos, who often have Amerindian ancestry, European ancestry, and African ancestry.

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