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Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
Church isca2012
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Church isca2012

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Presentation given at the ISCA consortium meeting May 2012 in Bethesda, MD

Presentation given at the ISCA consortium meeting May 2012 in Bethesda, MD

Published in: Technology
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  • Transcript

    • 1. Genome Representation and Variant Identification Deanna M. Church ISCA Consortium Conference
    • 2. From Green ED et al. Nature 2011
    • 3. CEPH: A=1.000 G=0http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes
    • 4. Multiple Suspectsubmissions 1000G Frequency Data YRI: A=0.5852 G=0.4148 Sudmant et al., 2010
    • 5. Kidd et al, 2007 APOBEC clusterBLACK: DeletionWhite: Insertion
    • 6. http://www.ncbi.nlm.nih.gov/dbvar
    • 7. Variant Call Ambiguity start stop Probes with decreased signal intensity Probes with expected signal intensity breakpoint breakpoint Inner start Inner stop Outer start Outer stop Inner start Inner stop
    • 8. Fosmid clone (40 Kb +/- 1 Kb)Variant Call Ambiguity Outer start Outer stop 20Kb Clone has an insertion relative to the genomeClone has a deletionrelative to the genome 60 Kb
    • 9. Large-Scale Variation Complicates Genome Assembly Sequences from haplotype 1 Sequences from haplotype 2Old Assembly model: compress into a consensusNew Assembly model: represent both haplotypes
    • 10. MHC (chr6)Chr 6 representation (PGF)Alt_Ref_Locus_2 (COX)
    • 11. Church et al., 2011 PLoS Biologyhttp://genomereference.org
    • 12. UGT2B17 MHC MAPT GRCh37 (hg19) 7 alternate haplotypes at the MHC Alternate loci released as: FASTA AGP Alignment to chromosomehttp://genomereference.org
    • 13. Richa AgarwalaEugene Yaschenko
    • 14. 71 Novel PATCHES: Additional sequence added70 Fix PATCHES: Chromosome will update in GRCh38 Summer of 2013 Releasing patches quarterly
    • 15. GRCh37 chr17GRCh37 Myo19 Fix Patch
    • 16. Dennis et al., 2012 1q32 1q21 1p211p21 patch alignment to chromosome 1
    • 17. Thanks! The Genome Reference Consortium The Genome Center at Washington University The Wellcome Trust Sanger Institute The European Bioinformatics Institute The National Center for Biotechnology InformationChurch group at NCBI For Slides: 1000 Genome browser: Valerie Schneider Evan Eichler Doug Slotta Nathan Bouk Eugene Yaschenko Hsiu-Chuan Chen Victor Ananiev Peter Meric Lon Phan Victor Ananiev Steve Sherry Chao Chen Alt-Aware Alignments: Rob Cohen John Lopez Richa Agarwala Deanna Church John Garner Eugene Yaschenko Tim Hefferon Cliff Clausen Chunlin Xiao Steve Sherry NCBI

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