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Subject: [DNA] reproducibility of Illumina BeadChip calls
Date: Thu, 24 Jan 2008 20:20:21 EST


23andMe now offers downloads of results as a dataset, so thanks to Megan
Smolenyak's foresight in having her husband tested at both deCODEme and 23andMe, I
was able to compare the raw data.

The two companies overlap on 562532 SNPs. They agreed on 560128 calls, or
99.6%. 23andMe didn't make a call on 1970 SNPs where deCODEme did, and deCODEme
didn't make a call on 399 records where 23andMe did. That leaves a mere 35
records where they actually made different calls. In all of those cases, one
company would make a homozygous call while the other company made a heterozygous
call -- there were no cases where they made a completely discordant call. All in
all, I'd say that is pretty impressive.

Apparently 23andMe is not reporting their custom SNPs that consistently
resulted in no-calls for their initial customers. For instance, the original list
of SNPs for mtDNA has been pruned from 2272 to 1970 in the reports I've seen.
Those 1970 SNPs still result in a couple of hundred no-calls for some people,
however, with the sites varying from person to person. The off-the-shelf
Illumina BeadChip must be using SNPs that have proved to be more robust.

Ann Turner





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