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I am free of rare homozygous recessives! (well, perhaps)

Gene ExpressionBy Razib KhanOctober 1, 2012 1:11 AM


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I got a notification today from Ian Logan that he set up a page on my genotype using a method which detects rare homozygous SNPs in the ~1 million markers I put up from my 23andMe results. My raw data is online, so anyone can analyze it. Here is the summary of my results:

The program finds about 50 'rare/uncommon' SNPs from the 900,000+ tested by 23andMe. The are no 'homozygous-recessive' results (surprisingly, as 1-2 might be expected).

There are a list other individuals, and sure enough most of them do have a rare recessive homozygous locus or two. I assume that ascertainment bias (the technology finding variation in Europeans better than non-Europeans in most cases) wouldn't result in my case, because I should have less variation, not more (less variation would presumably result in more homozygous recessives). So I am thinking it may simply be that because I'm from a population with greater genetic variation (South Asians) I am less likely to yield a homozygous recessive. In most cases population substructure doesn't yield benefits for South Asians in terms of their genetic variation, because of intra-caste marriage (so the useful scope of 'population' is much smaller than the geographic one), or cousin-marriage among some South Indian Hindus and Muslims generally. But my family background is highly mixed, so I am an appropriately reshuffled Bengali (I have analyzed runs of homozygosity and genome-wide heteozygosity, and I have less than the typical Eurasian of the former and more than the typical Eurasian of the latter). I only point this out to encourage more people to release their genotypes. This is arguably altruistic, as the more genotypes there are, the fewer will be interested in my own results. Though over the long term more data in the public domain, analyzable by interested researchers and motivated enthusiasts, will mean greater gains of understanding.

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