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SUMMARY:Population-based analysis of genome structural variation using bro
 ad\, highly parallel population sequencing - McCarroll\, S (Harvard Univer
 sity)
DTSTART:20100715T110000Z
DTEND:20100715T113000Z
UID:TALK25519@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Accurate and complete characterization of genome variation in 
 the largest possible number of individuals will be required to understand 
 the role of genome variation in disease.  We present a novel analytical fr
 amework\, informed by population genetics\, for characterizing genome stru
 ctural polymorphism using sequence data distributed across hundreds or tho
 usands of genomes.  Our approach integrates diverse features of next-gener
 ation sequencing (NGS) data  read pairs\, read depth\, and the distributio
 n of evidence across samples and around each genomic locus  to identify ge
 nomic loci where multiple features of NGS data from many genomes coalesce 
 around a population-genetic model of alternate structural alleles segregat
 ing within a population. We instantiated this framework in software (Genom
 e STRucture in Populations).  Genome STRiP identified structural polymorph
 isms across 180 genomes with unprecedented sensitivity and accuracy\, even
  when sequencing was shallow (2 - 4x) in each individual genome.  We devel
 oped a framework for genotyping structural polymorphisms by integrating mu
 ltiple types of NGS information (read depth\, read pairs\, split reads)\, 
 and used this approach to accurately genotype more than nine thousand dele
 tion polymorphisms\, allowing the production of a phased SNP/deletion hapl
 otype map for the 1000 Genomes Project.\n
LOCATION:Seminar Room 1\, Newton Institute
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