November 29, 2012
Past 5,000 years prolific for changes to human genome
The human genome has been busy over the past 5,000 years. Human populations have grown exponentially, and new genetic mutations arise with each generation. Humans now have a vast abundance of rare genetic variants in the protein-encoding sections of the genome1, 2. A study published today in Nature3 now helps to clarify when many of those rare variants arose. Researchers used deep sequencing to locate and date more than one million single-nucleotide variants — locations where a single letter of the DNA sequence is different from other individuals — in the genomes of 6,500 African and European Americans. Their findings confirm early work by Akey1 suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years. Researchers also saw the genetic stamp of the diverging migratory history of the two groups.
The large sample size — 4,298 North Americans of European descent and 2,217 African Americans — has enabled the researchers to mine down into the human genome, says study co-author Josh Akey, a genomics expert at the University of Washington in Seattle. He adds that the researchers now have “a way to look at recent human history in a way that we couldn’t before.” Akey and his colleagues were able to dig out genetic variants occurring in less than 0.1% of the sample population — a resolution that is a full order of magnitude finer than that achieved in previous studies, says Alon Keinan, a statistical geneticist at Cornell University in Ithaca, New York, who was not involved with the study. Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. On average, 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. “There’s so many of [variants] that exist that some of them have to contribute to disease,” says Akey
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