mouse genome annotation summit, 12 mar 2008 the status of the mouse genome

Mouse Genome Annotation Summit, 12 Mar 2008

The Status of the Mouse Genome


12

1

2

3 4 5 6 7

89

1011 13 14

15 16 17 18

19

X

Y

WGSFinishedDraftGap

Build 37


17

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%)


Why include non-finished sequence?


>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


Duplications in human and mouseInter-chromosomalIntra-chromosomal

Both

Human

Mouse

Mouse has an increased amount of intra-chromosomal duplication when compared to human


Known issues in the mouse genome Potentially collapsed repeats


Known issues in the mouse genome Strain Differences


Large-scale structural variation

Two different 129 contigs (129/SvEvTac and 129/SvJ) map to same location inC57BL/6J (Interferon cluster)

Strain Differences


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)


Genome Reference Consortium

Fix errorsCurationRepresent additional alleles Community outreach


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


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

mouse genome annotation summit, 12 mar 2008 the status of the mouse genome

Documents