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The Genographic Project: on to the autosome!

Gene Expression
By Razib Khan
Jul 25, 2012 8:20 PMNov 20, 2019 3:44 AM


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The Genographic Project is now moving beyond uniparental lineages with Geno 2.0. Spencer Wells kindly invited me to a conference call last month where he outlined a lot of the details, so I'll hit the salient points for readers of this weblog: * They're unveiling a new SNP-chip and a new project which moves beyond the Y and mtDNA to the autosome. But they're also expanding their coverage of uniparental markers. * Though there are "only" autosomal 130,000 markers, Wells and his collaborators have selected a subset of markers which are highly informative of population structure (e.g., high Fst). Their SNPs are biased toward those with moderate levels of polymorphism across many populations to maximize the power of diagnosis of differentiation. * They tried really hard to get rid of ascertainment bias. This means that in many previous chips there is a tendency to work off the polymorphism in Europeans, and then examine worldwide variation using this ruler. The problems with this method are obvious. One of the scientists on this project outlined how they worked to look for SNPs which are very informative for populations where ascertainment bias is a particular problem, Oceanians and Amerindians. I was impressed by their punctilious attitude on this question. * The major downside is that they don't have many trait informative SNPs on the marker. This means that they're only interested in phylogenetics and phylogeography, rather than the evolution of specific suites of traits. I'm sure that Wells will say a lot more. But there are a few extra aspects of the current trajectory which are exciting to me. First, they're going to push their genotype results public at some point. Second, they'll be encouraging utilization of the Geno 2.0 chip by giving them to specific researchers and groups. Third,

their population coverage is very thorough.

They have some publications in the pipeline, and it's the last point that has me excited. I saw some slides of the coverage in India, and I'm 99% sure that this data set is the source of the claim from this group that India's caste system predates the Indo-Aryans. Addendum: Also, in some ways they are now moving into 23andMe's space in scientific genealogy. If you are curious, please see Your Genetic Genealogist, as she has a much more thorough post.

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