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Database Releases First Findings

By Allison Proffitt

August 8, 2007 | The Genographic Project — a $40-million collaboration between IBM, the National Geographic Society, and the Waitt Family Foundation — has released the first results from the voluntary genealogical DNA analysis program started in 2005. The findings are published in the open access journal PLoS Genetics.

The Genographic Project is using DNA markers to address anthropological questions of human ancestry and historical migration. (See “Genes, Geography, and History,” Bio•IT World, June 2005) The goal, says IBM Research scientist Saharon Rosset, is to build an ancient and global family tree using mitochondrial DNA markers to trace female migration, and Y chromosome markers for male history.

So far, the project has collected samples from over 78,000 volunteers. More than 21,000 participants agreed to share their data for public research.

Rosset, a mathematician in knowledge discovery & data mining at IBM Research, has been involved in addressing statistical analysis and modeling issues for the project. “The overall objective,” he told Bio•IT World, “is learning about history through genetics, and the family relationship between all humans around the globe.”

The database is heavily biased toward first-world countries in which the Project is well publicized and swab kits are generally affordable. So far, 95 percent of the DNA kits were ordered in the United States and Western Europe. Not surprisingly, the majority of the participants are of West Eurasian, probably European, ancestry.

To balance that trend, the Project has  set up 10 laboratories around the world staffed with local scientists to reach people in less developed, more remote regions.  Says Rosset, “We’re actually going out and focusing on populations that are of great interest in terms of the genetic diversity of the world.”

Rosset says the most exciting thing about the study so far is sharing so much data with scientists around the world. “We’re giving [this database] back out to the public,” says Rosset. “Everyone who opted in filled out an anonymous questionnaire about ethnic origins, so you have some information that goes together with the genetic sample.... This is really an open project, and the openness and the intent to share both the results we collect and the data we collect with the public and scientific communities [is significant.]”

The Story So Far
Thanks to IBM’s involvement in building an IT infrastructure to handle the data analysis, Rosset says that the Project has “normalized the nomenclature and the way in which you do genetic testing on individuals to learn about ancient ancestry.” The paper “offers a brand new analytical approach, which is more accurate than all the previously published approaches.” 

Already scientists are searching and using the new data. One of the first searches looks for traces of Neanderthal DNA in the samples. “The question is, ‘Did modern humans mix or interbreed with Neanderthals as they were populating Europe 30 to 40 thousand years ago?’ “ says Rosset.

Six Neanderthal DNA samples including five distinct mutations are available in GenBank. All five mutations are present within the full Genographic database of 78,590 samples. However, no combination of any two of the five appear together in any given sample.

“There is no evidence of mixing in the mitochondrial DNA,” Rosset says. “It doesn’t mean categorically that there was no intermixing... but even in our huge database, which is very rich in samples of European origin, we find no evidence of Neanderthal sequence in there.”

As the database grows, Rosset believes “it’s going to lead to many exciting finding, and the answers to many fundamental questions about the human population of the world.”

Further Reading:
D.M. Behar et al. “The Genographic Project Public Participation Mitochondrial DNA Database.” PLOS Genetics 3(6): e104 doi:10.1371/journal.pgen.0030104.

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