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Mouse Genome Annotation Summit, 12 Mar 2008
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WGSFinishedDraftGap
Build 37
Mouse Genome Annotation Summit, 12 Mar 2008
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More details – Build 37
GapsSpanned: 709Unspanned: 105
WGS Shotgun Sequence
Draft Sequence
Genome length (bases + gaps): 2.72 MbGenome length – unplaced: 2.65 MbScaffold N50: 39.3 Mb
(<1%)
Mouse Genome Annotation Summit, 12 Mar 2008
>95% ID, >10 KB
Mouse Genome- Segmental DuplicationMGSCv3
Build 36 >95%ID, 10 Kb
All duplication >5 Kb: MGSCv3: 1.95% Build 36: ~4.6%
MGSCv3- >60% of duplication chrUnBuild 36: largely intra-chromosomal duplication
University of WashingtonEvan Eichler
Eray TuzanGinger Chang
Jeff BaileyXinwei SheNCBI
Deanna Church
Mouse Genome Annotation Summit, 12 Mar 2008
Duplications in human and mouseInter-chromosomalIntra-chromosomal
Both
Human
Mouse
Mouse has an increased amount of intra-chromosomal duplication when compared to human
Mouse Genome Annotation Summit, 12 Mar 2008
Known issues in the mouse genome Potentially collapsed repeats
Mouse Genome Annotation Summit, 12 Mar 2008
Large-scale structural variation
Two different 129 contigs (129/SvEvTac and 129/SvJ) map to same location inC57BL/6J (Interferon cluster)
Strain Differences
Mouse Genome Annotation Summit, 12 Mar 2008
What happens now?
Genome Reference ConsortiumWashington University Genome Sciences Center (WUGSC)Wellcome Trust Sanger Institute (WTSI)European Bioinformatics Institute (EBI)National Center for Biotechnology Information (NCBI)
Mouse Genome Annotation Summit, 12 Mar 2008
Genome Reference Consortium
Fix errorsCurationRepresent additional alleles Community outreach
Mouse Genome Annotation Summit, 12 Mar 2008
Mouse Genome Sequencing ConsortiumWellcome Trust Sanger InstituteWashington University Genome Sequencing CenterBroad Institute Genome CenterBaylor College of Medicine
Cold Spring Harbor LaboratoryGenome Therapeutics CorporationHarvard Partners Genome CenterJoint Genome InstituteNIH Intramural Sequencing CenterUK-MRC Sequencing ConsortiumThe University of Oklahoma Advanced Center for Genome TechnologyThe University of Texas Southwest
Acknowledgments
Mouse Genome Annotation Summit, 12 Mar 2008
NCBI Assembly & AnnotationRicha AgarwalaHsiu-Chuan ChenJosh CherryDeanna ChurchMike DiCuccioWratko HlavinaMelissa LandrumDonna MaglottYuri KapustinPaul KittsKim PruittVictor SapojnikovSasha Souvorov
Duplication AnalysisEvan EichlerJeff BaileyGinger ChengXinwei SheMario VenturaMariano Rocchi
Broad Institute April Cook Mike Fitzgerald Kerstin Linblad-Toh Eric Lander
Baylor College of Medicine Donna Muzny Shannon Dugan Richard Gibbs
Sanger Institute Christine Nicholson Sean Humphrey Darren Grafham Jane Rogers
Washington University GenomeSequencing Center Susie Rock Tina Graves Bob Fulton Rick Wilson
Acknowledgments