Friday, October 19, 2007

HapMap part deux

There's a lot of stuff going on right now, but I thought this was the most important. The HapMap project came out with their genotypes for another 2 million SNPs (so now they're up to 3 million SNPs) in their four populations (really three, it could be argued). In the latest Nature they lay out all their findings, including the ones about tests of positive selection.
In a report called "So similar, yet so different" by Erika Check Hayden, she discusses how we're finding a lot more genetic diversity between humans than previously thought:
  • Venter diploid genome
  • CNVs
  • SNPs in this HapMap go-round
here's a snippet about those SNPs:
... in the updated HapMap, 1% of the more than 3 million SNPs that have now been analysed cannot be grouped with their neighbours to mark identical chunks of DNA. These 'untaggable SNPs' reveal parts of the genome that vary greatly between people. “These untaggable SNPs are completely doing their own thing,” McVean says. “It's not a high percentage of SNPs, but it's still a lot of them.”
...then, this great snippet. The second paragraph is pretty interesting, and very related to the research that I've been doing.
Scientists are now obtaining DNA from seven more populations with African, Asian and European ancestry that could help explain the origin of the mystery SNPs. They are also discussing a massive new bout of sequencing in an international project involving Chinese, British and US funders that would use new technologies to sequence the genomes of 1,000 individuals. Along with the two individual genome sequences already released4, these data will fuel a field that is set to explode over the next year: the hunt for genetic signatures that discriminate between smaller and smaller groups.

“The HapMap data can clearly tell you whether you are African or Chinese, but the question becomes, how far can you take that?” asks population geneticist Carlos Bustamante from Cornell University in Ithaca, New York. “Can you predict whether somebody comes from one village or another? We are going to see all kinds of stuff we would never have imagined was possible.”

I'll say what I can about the positive selection paper part of all this in a future post.

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