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PRODID:-//Cornell U. Department of Computer Science//Brown Bag Seminar//EN
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SUMMARY:Brown bag: Amy Williams
DESCRIPTION:Title: Efficient and effective haplotype phase inference of
	 large scale genetic datasets\nSpeaker: Amy Williams\nAbstract: The
	 recent and ongoing explosion of genetic data has enabled wide-ranging
	 discoveries but created computational and analytic challenges. One such
	 challenge is the inference of haplotypes—a series of DNA variants that
	 occur on a single chromosome copy in an individual. While haplotypes are
	 essential to many genetic studies\, direct haplotype assays are costly.
	 In this talk\, I describe two methods for inferring haplotypes from
	 genotype datasets\, one that applies to families\, the other to
	 unrelated individuals. Inferring haplotypes in pedigree family data has
	 been shown to be NP-hard\, yet the hardness proof relies on large
	 numbers of recombination events that do not occur in real genetic data.
	 The family-based method HAPI takes advantage of the sparsity of
	 recombination events to infer both minimum recombinant and maximum
	 likelihood haplotypes for nuclear families in polynomial time on real
	 data. When applied to a dataset containing 103 nuclear familes\, HAPI
	 ran over 300 times faster than state of the art methods. The second
	 method\, HAPI-UR\, applies to unrelated and/or trio and duo family data.
	 Using adapted form of a commonly used hidden Markov model (HMM)\,
	 HAPI-UR runs more than 18 times faster than other methods and also
	 achieves comparable or greater accuracy. These improvements are
	 practically important because error rates in inferred haplotypes drop
	 with sample size. We used HAPI-UR to infer haplotypes in a dataset of
	 more than 58\,000 samples and show that its error rate continues to drop
	 with sample size\, even using samples of diverse ancestry. The talk
	 concludes with a discussion of ongoing applications of these methods to
	 genetic studies and future directions.
LOCATION:Gates 122
UID:2014-09-09
STATUS:CONFIRMED
DTSTART:20140909T160000Z
DTEND:20140909T170000Z
ORGANIZER;CN=Jonathan Shi:http://www.cs.cornell.edu/~jshi/brownbag/
DTSTAMP:20260408T121931Z
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