July 8, 2010 | 4
A team of Boston University scientists reported last week that they had identified a large number of gene variants that were associated with exceptional longevity. Since that story grabbed headlines, however, some skeptics have voiced concerns about the data and the study’s conclusions.
Newsweek reported Wednesday that the concern over the data stems from one of the research tools used by the B.U. scientists—DNA "chips" that identify genetic variants. Essentially, the researchers used two different chips to analyze the genes of people involved in their study. The problem with doing that, according to Duke University geneticist David Goldstein, is that every chip is prone to different types of errors in identifying variants. When several different chips are used within a single study, false positives can result:
The key to keeping false positives at bay is to ensure that cases and control groups are analyzed using exactly the same techniques. If you use one type of chip to analyze your cases and a different type to analyze your control group, "you can see any [variants] that are genotyped differently on the different chips ‘lighting up’ as apparently associated with the trait," says Goldstein, when in fact that pattern is just an experimental artifact.
In the Newsweek article, Kári Stefánsson, founder of decode Genetics, discusses a previously identified problem with one of the chips used in the study, known as the 610-Quad chip:
…it has a strange and relevant quirk regarding two of the strongest variants linked to aging in the B.U. study, called rs1036819 and rs1455311. For any given gene, a person will have two "alleles," or forms of DNA. In the vast majority of people, at the rs1036819 and rs1455311 locations in the genome, these pairs of alleles consist of one "minor" form and one "major" form. But the 610-Quad chip tends to see the wrong thing at those particular locations. It always identifies the "minor" form but not the "major" form, says Stefánsson—even if the latter really is present in the DNA, which it usually is. If you use the error-prone chip in more of your case group than your control group—as the B.U. researchers did—you’re going to see more errors in those cases. And because what you’re searching for is unusual patterns in your cases, you could very well mistake all those errors (that is, false positives) for a genetic link that doesn’t actually exist.
Critics claim that these concerns could easily be dealt with by repeating the analysis using a single, new chip for all of the samples. This is something many feel should have been done before the study was published, and therefore raises questions about how the study was accepted for publication by Science, one of the world’s top research journals, without it.
On Wednesday, the B.U. scientists responded to the criticism in a prepared statement, indicating that they are aware of the technical errors associated with the chip they used and that they are re-examining their data in light of the discovery. They don’t expect that the error will affect the overall accuracy of their model, however.
Regardless of the outcome of this debate, the study’s authors have repeatedly acknowledged that their model is not ready to be used by the public, especially not in the form of genetic tests (products which are likely being created by multiple companies at this moment). So if you’re still hoping to get an idea of how long you might live, your best bet is to pass on any forthcoming genetic tests and simply look at your family tree.
Image of a DNA chip courtesy of iStockPhoto
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