Archiver > GENEALOGY-DNA > 2010-11 > 1289051682

From: Steven Bird <>
Subject: Re: [DNA] Illumina (HapMap) versus Affymetrix (Xing, 2010);same samples tested twice
Date: Sat, 6 Nov 2010 08:54:42 -0500
References: <SNT139-w655975E793F584D125B9F6C84C0@phx.gbl>
In-Reply-To: <SNT139-w655975E793F584D125B9F6C84C0@phx.gbl>

Argiedude wrote:
> Both chips had about 30K or 40K SNPs in common, and I used 13597 of them for this comparison. I found that, strangely, the rate of no-calls depended on the population of origin of the sample. A no-call, in this case, is caused if there's a no call in either SNP of the same sample in the Illumina scan or in the Affymetrix scan, it doesn't have to be in both. I don't know if the rate of no-calls was even in both scans or concentrated in one of the two. Kenay and Tuscany had a no-call rate of 1.5%, while CEU, Han, Japan, Yoruba had equally small no-call rates of around 0.3%. Why would the no-call rate depend on the population of origin? Could they have been stored separately from the other 4 populations and suffered a different degree of degradation?

More likely the levels of contamination when the samples were first extracted. If the ddNTP's are not washed out completely, they can cause a "blob" in the laser scan that renders the base unreadable. That would result in a no-call.


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