National Geographic’s DNA database raises doubts

The National Geographic Society is touting its new project to trace humans’ migratory history as an “unprecedented resource for geneticists, historians and anthropologists.” But some research experts in the field

argue that the project is poorly designed and its methods prevent widespread sharing of DNA samples among scientists.

National Geographic and IBM Corp. last week announced a five-year, US$40 million project called the Genographic project to analyze over 100,000 DNA samples from indigenous populations worldwide, including Algonquin, Iroquois and Inuit peoples in Canada. The goal of the project is to trace modern humans’ genetic roots back to an African ancestor that lived some 60,000 years ago, according to new DNA studies.

“There’s a lot of in-between that we don’t know,” said Alexander Moen, Genographic project operational director for National Geographic, adding that while evidence suggests modern human species originated in Africa, scientists don’t know how humans populated the planet. “It’s basically using genetics to fill in the archeological and other historical records to corroborate or look at other theories and hypotheses.”

National Geographic is also inviting members of the general public to take part in the project by going to its Web site and purchasing a cheek swab kit for US$100. Results will be included in the database, which National Geographic also claims will be “one of the largest collections of human population genetic information every assembled.”

But Andrew Paterson, a scientist at the genetics and genomic biology group at the Sick Kids Research Institute in Toronto, said allowing anyone to participate in the study outside of the controlled group is not normally practiced in these types of studies. “Usually there are very clear inclusion criteria for a study,” said Paterson. “The fact that anybody can send a DNA sample in may not be that useful.”

He added that by opening the study to the public, National Geographic may not be prepared to deal with the volume of participants, as analyzing DNA samples is a costly process. “(It’s)  is not a lot for doing very detailed studies,” he said. “I could think of other ways to spend US40 million.”

IBM is providing information technology systems — including its blade server products — at 10 regional sites around the globe and its DB2 database software at National Geographic’s headquarters in Washington, D.C. to collect, store and manage all of the data results sent via a WebSphere portal from abroad. To date, IBM has donated tens of millions of dollars towards the project, according to Genographic project manager Kris Lichter of IBM. The closest regional site to Canada is located at the University of Pennsylvania.

“National Geographic felt that IBM was the only company that could really be able to bring the different pieces of the genographic project together,” said Lichter. “We bring advanced algorithms from our computational biology centre along with those researchers who have deep life sciences domain expertise.”

The project has also received over US$5 million in funding from the Waitt Family Foundation.

At the field sites, IBM will also provide ThinkPads with biometric fingerprint security technology that researchers will use when they gather the data and transmit it across the Internet to the central repository in Washington. “Security is a critical part of this making sure that that data is protected every step of the way,” said Lichter. “We’ve applied the latest security and we will continue to do so very rigorously.”

On site, physical samples will be taken to a secure lab where they will be sequenced and then made electronic. Scientists will then be able to get values around non-medical markers about people’s deep ancestry and how they’ve migrated, explained Lichter.

But Steven Scherer, senior scientist at the genetics and genomic biology group at the Sick Kids Research Institute, which studies common diseases in the population, said in an e-mail that the project could be “riddled” with sample collection and database problems.

“The problem is that there is no control over collecting the samples,” said Scherer, who was in Halifax last week attending the Genome Canada Scientific Advisory Board meeting where he said many geneticists were surprised by the announcement. “Self-reporting is often very inaccurate. There are potential problems with contamination.”

Another problem with the samples is that there are a finite number of them, noted Kenneth K. Kidd, professor of genetics and psychiatry at Yale University’s School of Medicine. Kidd has conducted research on 2,000 DNA samples from 42 different populations around the world (except Australia) to understand how variations arose between different peoples on different continents. “To do those kinds of studies you need a fair amount of DNA and the National Geographic project will not establish permanent cell lines that will allow us to keep generating DNA of that individual.”

This means you can’t share it freely with many other laboratories, he added. “The information will be interesting and useful but so much effort is required to collect the samples that it’s a shame not to go to the additional effort for at least some of them to make it a greater resource.” The Human Genome Diversity Project, in contrast, immortalized each sample before storage, essentially making an inexhaustible supply of cells.

However, Paterson said that may not be necessary. “There’s not a necessity that they make these cell lines do that, especially if they’re using a technology that can work with very small amounts of DNA,” he said.

But a product that an Ottawa-based company has developed for collecting DNA samples could potentially solve this problem. After hearing about the Genographic project DNA Genotek contacted National Geographic about using its flagship product, the Oragene Self-Collection Kit. National Geographic is currently taking a look at it but no decisions have been made yet.

Oragene can collect 50 to 100 times more DNA than with a Buccal Swab, an oral method of collecting saliva from inside the cheek, according to the company. “As long as somebody can spit any amount in the vial, we’ll get some DNA,” said company CEO Ian Curry. “Once it’s in the vial, it’s good for years whereas in Bucccal Swabs depending on which one you use, it may be good for a few weeks.” Curry added Oragene works about 100 per cent of the time while Buccal Swabs fail 30 to 50 per cent of the time, which can cost researchers a lot of money.

The Buccal Swab will be the method used in the public kits while scientists will be collecting blood samples from indigenous peoples. The problem with blood, aside from possible transmission of deadly diseases like the HIV virus, is that it’s more challenging to get DNA out of blood than saliva. “In your blood there’s a thousand red blood cells for every white blood cell,” explained company founder Chaim Birnboim, who created Oragene. “Your red blood cells don’t have any DNA. Your one white blood cell does. In saliva there are no red blood cells.”

Benefits of using Oragene over blood also include reduced cost as no training is required to take samples and blood degrades fairly quickly.

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