Genographic Project Releases First DNA Data

The Genographic Project is using DNA markers to address anthropological questions of human ancestry and historical migration. 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.

Since its inception, 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 -- learning about the history of our species, learning about the history of how we populated the globe, how we interacted with each other over time, and the family relationship between all humans around the globe.”

After volunteers submit buccal swabs (DNA participation kits cost $99), participants can look up their results, stored a securely in the Genographic Project’s database, via a Web portal. Based on each samples’s genetic profile -- either from mitochondrial DNA or Y chromosome markers -- researchers can place it in a haplogroup, which defines genetic populations. “It tells [participants] about their ancient ancestry,” says Rosset. “Sort of where you fit on the family tree of all humans.”

The database is heavily biased towards 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 also set up 10 laboratories around the world staffed with local scientists to reach people in less developed, more remote regions. “Scientists in research centers around the world are going out and sampling populations, mainly indigenous populations,” 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.”

The Story So Far
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.]”

Rosset points out that even individuals who have gathered genetic information from private companies can use the database. There’s an online tool to import results from other tests and compare their results with participants from the Genographic Project study.

Thanks to IBM’s involvement in building an IT infrastructure to handle the data analysis, including a specialized LIMS, 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 PLoS Genetics paper “offers a brand new analytical approach, which is more accurate than all the previously published approaches,” he says. 

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 longer than 300 base pairs were available in GenBank, which include five mutations believed to distinguish Neanderthal sequences. 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. In fact, none of the Project’s collected samples are as divergent from one another as the Neanderthal samples.

“There is no evidence of this 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.”

This is just the first of many discoveries Rosset expects from the project. “For example, the ancient history of humans in Africa -- our database is already starting to yield interesting answers about how we moved around and interacted with each other. Similar questions exist about North American, and about the effect of ancient empires on the genetic makeup of the world.”

As the database grows, and once the scientist-gathered samples are included, 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.