HapMap "dumpster diving"

Jennifer Couzin of Science has a conference report about the HapMap, and many of its uses.

It's a good summary. I especially liked this:

Another group at the Broad Institute is examining data that were sequenced and publicly released by HapMappers but didn't make it into the final HapMap because they were deemed erroneous. "This project is kind of a dumpster dive," says the Broad Institute's Steven McCarroll. He and his colleagues found that thousands of the flaws are actually inherited DNA deletions. They've identified 10 commonly deleted genes, including two for sex steroid hormone metabolism and three for drug metabolism. They're now studying whether those deletions might contribute to disease.

I think this is an important message that isn't often articulated:

Despite such enthusiasm, some researchers say they're not certain just how the HapMap will aid their own genetic studies. The map's central goal is to help identify genes behind common diseases such as cancer, but it's not always clear how to apply it. When it comes to evolution studies, for example, the map may be biased because it prefers common SNPs to rare ones. "The HapMap project was not about studying population history," says NHGRI's James Mullikin. But it's being used often by researchers in that area.

Of course, there's nothing magical about an association study -- just genotype a lot of people who have a disease. And it's surprisingly easy lately with gene chips to survey all these SNPs at once. But the key is that these SNPs are usually not the mutations we're looking for. The hope is that they are markers for the mutations, and that the key mutations will be on long enough linkage blocks to be found. Sometimes it will work, but the question is, how often?

But in terms of population history -- now there we might see some interesting results....

References:

Couzin J. 2006. The HapMap gold rush: researchers mine a rich deposit. Science 312:1131. DOI link