The rise of the rare variant

By Razib Khan | July 9, 2012 1:50 am

A few people have mentioned to me a couple of new papers in Science are out on rare variants. They’re summed up in a short review article. I suspect this is going to be a big deal for some time. For humans we are coming to toward the end of the SNP-age and entering into the whole-genome-age. That means that the emphasis on common variation at the genomic level is going to give way somewhat to rarer, more particular, variation. One of the major takeaways is that a lot of this variation is going to be population specific. What I am curious about is the pattern of population specificity. For example, we could query the history of consanguinity in the Middle East, or endogamy in India, by the patterns of rare variants, which should crisply demarcate populations as a function of divergence. If I read this right we may be entering into a golden age of demographic history reconstruction, as rare variants and whole-genome catalogs of a huge number of humans are going to allow us to generate a very fine-grained map of human population diversity. Populations are only the start. Ultimately it might be highly informative to compare siblings, who may carry different mutational loads, but share much of the same genetic background.

I found the figure below particularly interesting. Apparently it confirms the recent bottleneck of the Finns:

MORE ABOUT: Genomics, Rare Variants
  • Dm

    Drats, none of the genes I want in the Nelson’s target set! The Thomassen (NHLBI GO) exome dataset is pretty amazing, alas their funding has run out and they just finished uploading last bits and pieces in June … nothing more to expect. The GO data are especially helpful with the (huge variety of) African American variants of sub-1% frequency, the AF range where 1000 Genomes couldn’t venture.

    Alas, AFAICT there is nothing even remotely approaching it for S and SE Asians. The 1000 Genomes sequencing data aren’t there yet, but when they trickle in (when?), they still won’t have much impact even on your 1%-ers, let alone the rest of the tail of the frequency distribution :(


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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