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The Status of the Mouse Genome

The Status of the Mouse Genome. 19. 18. 17. 16. 15. 13. 11. 12. 9. 14. 10. 8. Y. 6. 5. 7. 4. 3. 2. 1. WGS. Finished. Draft. Gap. X. Build 37. 17. More details – Build 37. Spanned: 709. Gaps. Unspanned : 105. WGS Shotgun Sequence. (<1%). Draft Sequence.

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The Status of the Mouse Genome

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  1. The Status of the Mouse Genome

  2. 19 18 17 16 15 13 11 12 9 14 10 8 Y 6 5 7 4 3 2 1 WGS Finished Draft Gap X Build 37

  3. 17 More details – Build 37 Spanned: 709 Gaps Unspanned: 105 WGS Shotgun Sequence (<1%) Draft Sequence Genome length (bases + gaps): 2.72 Mb Genome length – unplaced: 2.65 Mb Scaffold N50: 39.3 Mb

  4. Why include non-finished sequence?

  5. Mouse Genome- Segmental Duplication University of Washington Evan Eichler ErayTuzanGinger Chang Jeff BaileyXinwei She NCBI Deanna Church Build 36 >95%ID, 10 Kb MGSCv3 >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

  6. Duplications in human and mouse Inter-chromosomal Intra-chromosomal Both Mouse Human Mouse has an increased amount of intra-chromosomal duplication when compared to human

  7. Potentially collapsed repeats Known issues in the mouse genome

  8. Strain Differences Known issues in the mouse genome

  9. Strain Differences Known issues in the mouse genome

  10. Large-scale structural variation Strain Differences Two different 129 contigs (129/SvEvTac and 129/SvJ) map to same location inC57BL/6J (Interferon cluster)

  11. What happens now? Genome Reference Consortium Washington University Genome Sciences Center (WUGSC) Wellcome Trust Sanger Institute (WTSI) European Bioinformatics Institute (EBI) National Center for Biotechnology Information (NCBI)

  12. Genome Reference Consortium Fix errors Curation Represent additional alleles Community outreach

  13. Acknowledgments Mouse Genome Sequencing Consortium Wellcome Trust Sanger Institute Washington University Genome Sequencing Center Broad Institute Genome Center Baylor College of Medicine Cold Spring Harbor Laboratory Genome Therapeutics Corporation Harvard Partners Genome Center Joint Genome Institute NIH Intramural Sequencing Center UK-MRC Sequencing Consortium The University of Oklahoma Advanced Center for Genome Technology The University of Texas Southwest

  14. Acknowledgments NCBI Assembly & Annotation RichaAgarwala Hsiu-Chuan Chen Josh Cherry Deanna Church Mike DiCuccio WratkoHlavina Melissa Landrum Donna Maglott Yuri Kapustin Paul Kitts Kim Pruitt Victor Sapojnikov Sasha Souvorov Baylor College of Medicine Donna Muzny Shannon Dugan Richard Gibbs Duplication Analysis Evan Eichler Jeff Bailey Ginger Cheng Xinwei She Mario Ventura Mariano Rocchi Broad Institute April Cook Mike Fitzgerald Kerstin Linblad-Toh Eric Lander Sanger Institute Christine Nicholson Sean Humphrey Darren Grafham Jane Rogers Washington University GenomeSequencing Center Susie Rock Tina Graves Bob Fulton Rick Wilson

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