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SUMMARY:What the 1000 genomes project tells us about systematic bias and b
 atch effects in sec-gen data - Irizarry\, R (Johns Hopkins University)
DTSTART:20100713T153000Z
DTEND:20100713T160000Z
UID:TALK25501@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:First\, we will report findings on systematic biases in this t
 echnology gleaned from analysis of a single chromosome from the 1000 Genom
 es Project Data. While it is known that coverage of whole-genome re-sequen
 cing data is not uniform\, its variation is highly correlated across multi
 ple samples in unrelated populations with a strong platform and date effec
 ts. We will describe how some of these systematic biases affect SNP and CN
 V calls. Second\, we will describe our first steps towards statistical sol
 utions for these problems. Our approach is based on specific genome featur
 es that are highly correlated to differences in coverage in genome regions
 . Note that this work is preliminary and that the technology is moving fas
 t. So by the time I give this talk\, in 3 months\, it might have nothing t
 o do with this abstract.
LOCATION:Seminar Room 1\, Newton Institute
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