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Study Finds European SNP Data Precisely Reflects Geography

NEW YORK (GenomeWeb News) – New research is revealing just how well genetics and geography mesh in European populations.
In a paper appearing online yesterday in Nature, a team of American and Swiss researchers assessed SNPs in the genes of individuals from across Europe and used the data to construct two-dimensional genetic maps. They found that genes were closely tied to geography. In fact, genetics pinpointed most individuals’ geographic origin within a few hundred miles. The results highlight the importance of accounting for geography in genetic studies and suggest precise genetic ancestry tests may not be far off.
“The surprise was just how well and clearly it relates to geography,” University of California at Los Angeles evolutionary biologist John Novembre, who recently completed his post-doctoral research in the University of Chicago’s department of human genetics and was lead author on the paper, told GenomeWeb Daily News. “At the broadest level, it means that geography matters.”
The samples tested were collected as part of a larger study of about 6,000 individuals called the Population Reference Sample, or POPRES, project, Novembre explained. That study, led by GlaxoSmithKline and collaborators, was aimed at developing a reference sample for genetic and pharmacogenetic studies.
Novembre and his colleagues took advantage of this rich data set to ask questions about genetic history, genetic variation, and human population structures.
They initially genotyped 3,192 Europeans at 500,568 loci using Affymetrix 500K SNP chips. After filtering out specific SNPs to minimize linkage disequilibrium patterns and limiting their analysis to individuals with well-defined ancestry, they were left with data on 197,146 loci in 1,387 individuals.
They then created two-dimensional maps revealing genetic patterns in the samples. Although the overall genetic variation across Europe was miniscule, Novembre explained, there were still enough differences to distinguish between geographic populations. Indeed, the two-dimensional genetic map closely resembled a map of Europe.
For half of the individuals tested, the researchers could place them within about 193 miles of their reported geographic origin. When they stretched that to about 435 miles, they could place 90 percent of the individuals.
Moreover, the team was able to distinguish incredibly subtle population effects, including genetic differences between French-, German-, and Italian-speaking individuals in Switzerland. As such, the results are providing new insights into the genetics associated with population structure.
That, in turn, brings a new level of information to genome-wide association studies, suggesting that there may be certain population-related traits that could create false-positive associations in these studies. Being aware of such population stratification effects should help researchers avoid such problems, Novembre said.
In the future, he predicted, whole-genome re-sequencing projects will likely add even greater resolution to this sort of gene-geography study. For the time being, though, Novembre and his colleagues are continuing to tap the POPRES data for more information about populations in other parts of the world, including South Asia, East Asia, and Latin America.
Although the current approach very closely linked most people’s genetics with their origin, Novembre noted, it is much less accurate for individuals who have ancestors from more than one part of the world. That means precise genetic ancestry tests are likely still a ways off. “But the promise is there,” Novembre said, “and it’s very exciting.”

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