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With 500,000 Samples Genotyped, AncestryDNA Scientists Begin to Unravel US Population Genetics

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NEW YORK (GenomeWeb) – Ancestry.com's AncestryDNA business has genotyped more than 500,000 individuals since introducing the genetic genealogy service on the Illumina BeadChip platform two years ago.

Now, researchers at the Provo, Utah-based company have begun to combine the genetic data from the service along with the pedigrees of Ancestry.com customers to better understand the genetic diversity of the US population.

Specifically, they conducted a large-scale survey of the ancestry of the US by predicting genetic ethnicity for each individual tested using a curated reference panel of 3,000 single-origin individuals. Those estimates were then combined with birth locations to explore how various ethnicities are distributed across the country.

AncestryDNA scientists unveiled some of those findings at the American Society of Human Genetics Meeting, held this week in San Diego. In a talk entitled, "Genetic Testing of 400,000 Individuals Reveals the Geography of Ancestry in the United States," Yong Wang, a senior data scientist at AncestryDNA, delved into some of the more noteworthy results.

Among them is that self-reported census data on individuals' ethnicity is largely corroborated by the results of the AncestryDNA service. For example, the authors found that individuals from Massachusetts have the highest proportion of Irish genetic ancestry, while individuals from New York have the highest proportion of Southern European genetic ancestry.

These genetic patterns were borne out by US Census data, as Massachusetts has the highest proportion of individuals with self-reported Irish ancestry and New York the highest proportion of individuals with self-reported Italian ancestry in the US.

"The genetic ancestry patterns recapitulate the observations of self-reported ancestry," Wang told BioArray News by phone last week. "You might expect the highest Irish ancestry to be in Massachusetts, but that is anecdotal," Wang said. "The genetics though tell the same story."

While the finding that Massachusetts hosts the greatest number of people with Irish ancestry might not raise too may eyebrows, AncestryDNA's survey provided other insights into US population genetics. For example, about 21 million Americans claimed American ethnicity in the 2000 census, most of whom resided in Arkansas, Kentucky, Tennessee, and West Virginia. According to AncestryDNA's biogeographical analyses though, most people who claim American ethnicity are actually of British ancestry.

AncestryDNA also performed identity-by-descent analysis on the entire sample set and identified over 300 million shared genomic segments among all 400,000 individuals, according to Wang. From that data set, they calculated the average amount of sharing for pairs of individuals born within the same state or from two different states. Among their findings was that individuals from Delaware shared the greatest amount of genomic segments. The scientists were also able to use IBD to track internal migration, revealing the largely westward migration of individuals across the country.

"In general, we found that genetic sharing decreases as the geographic distance between two states increases," said Wong. But that wasn't always the case. Two states that showed a high proportion of IBD were actually Maine and Louisiana. Though it is roughly 1,500 miles from the Pine Tree State to the Bayou State, many individuals in Maine and Louisiana share a common Franco-American ancestry.

Following the British conquest of the province of Acadia, which then included much of the Canadian Maritimes as well as part of Maine, in the mid-18th century, many of the local Acadians were expelled to France, from which they left to settle in Louisiana, developing their own unique Cajun identity. While the expulsion of the Acadians occurred more than 250 years ago, its genetic legacy remains.

"This is really exciting," Jake Byrnes, population genomics senior analyst at AncestryDNA, told BioArray News by phone. "This is modern genetic data but we are finding a lot of signatures of historic events," he said. "We all know that we are in the modern era, but there is really strong evidence that genetic change actually occurs at a very low scale," Byrnes added, meaning that despite internal migration within the US, as well as immigration to the US, the genetic signatures of founding populations tend to stay in place.

"The US is more of a stew than a melting pot," said Byrnes. "Signatures spread, but in general it remains rooted historically."

According to Byrnes, AncestryDNA plans to publish the results of its survey and will continue with its research. The business now has a team of scientists with diverse expertise analyzing the data accumulated through its service. "We are in a unique position to produce innovative results," said Byrnes, noting that the company has access not only to genetic data but online pedigrees. "This gives us a chance to do excellent research, a chance to push the envelope," Byrnes said.

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