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Research team develops software to help identify an individual’s geographic origins

By Nikki Somani

July 1, 2012 11:48 p.m.

With only a sample of saliva, a team of four scientists can better pinpoint the geographic origins of an individual’s genes.

The team, composed of researchers at UCLA and Israel’s Tel Aviv University, recently developed spatial ancestry analysis, a software that analyzes information from genes to identify a subject’s ancestry.

The scientists have been working on the technology for about six months, said Wen-Yun Yang, a graduate student on the research team.

This is the first software to correctly identify the ancestry of an individual with mixed parents, said John Novembre, a professor of ecology and evolutionary biology and a researcher involved in the study.

For example, a woman with parents from different countries can now pay a company to find out her ancestors were Thai and German. Previously, the technology available would give her incorrect results somewhere between the two countries, such as Central South Asia, Novembre said.

“One of the really interesting things about collecting this DNA is that it can help us to answer fundamental questions such as human history, where we all came from and where we originated,” said Eleazar Eskin, UCLA professor of computer sciences and human genetics and a co-author of the publication.

Researchers started off with samples of DNA from about 3,000 people with four grandparents from the same geographic region.

The new software analyzed the data, taking into account genetic differences to place people at various locations on a map.

The points formed a map of Europe by the time the analysis was complete.

“It worked really, really well, so we were surprised by the results. Particularly, we were surprised by how simple the method is to give us these results,” Eskin said.

The new software can predict people’s origins fairly accurately ““ within 100 kilometers of the correct location, Eskin said.

The software also takes the curvature of the Earth into account to make it more accurate than older software, Novembre said.

If two people are located close together on the map their DNA will show similar traits, while two people far away will show more differing traits.

“Spatial ancestry analysis is a different way to think of genetic variation,” Eskin said.

Instead of thinking of populations as separate entities, people should consider genetic differences as a continuum, he added.

Some locations close together on a map can show a dramatic change in a portion of DNA, reflecting evolutionary adaptations among individuals from different regions.

The information can tell researchers how the genetic makeup of a group of individuals changes as a result of natural selection, Eskin said.

Using the software, researchers identified about 100 genes associated with natural selection, some of which influenced eye color, skin color and language, Yang said.

The software still has its limitations. It is difficult to analyze the geographic origins of people from more than two different locations, Novembre said.

For example, the Latino population in Los Angeles has much more complicated ancestral origins in several different locations, and therefore the software cannot accurately predict the correct geographic locations, he added.

The software can also be applied to personalized medicine.

Medical researchers are trying to understand how differences in DNA influence disease and responses to drugs, Eskin said. He added that spatial ancestry analysis could provide insight into patient responses to chemotherapy.

Outside of medicine, private genomic companies can use the software to determine an individual’s ancestry for profit, Novembre said.

“It’s a question that fascinates humans,” said Novembre. “Many people are interested in knowing about our origins, and it’s just a part of human identity to think back to our ancestors.”

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Nikki Somani
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