1. Mouse Genome Annotation Summit, 12 Mar 2008 The Status of the Mouse Genome

2. Mouse Genome Annotation Summit, 12 Mar 2008 12 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19 X Y WGS Finished Draft Gap Build 37

3. Mouse Genome Annotation Summit, 12 Mar 2008 17 More details – Build 37 Gaps Spanned: 709 Unspanned: 105 WGS Shotgun Sequence Draft Sequence Genome length (bases + gaps): 2.72 Mb Genome length – unplaced: 2.65 Mb Scaffold N50: 39.3 Mb (<1%)

4. Mouse Genome Annotation Summit, 12 Mar 2008 Why include non-finished sequence?

5. Mouse Genome Annotation Summit, 12 Mar 2008 >95% ID, >10 KB Mouse Genome- Segmental Duplication MGSCv3 Build 36 >95%ID, 10 Kb All duplication >5 Kb: MGSCv3: 1.95% Build 36: ~4.6% MGSCv3- >60% of duplication chrUn Build 36: largely intra-chromosomal duplication University of Washington Evan Eichler Eray Tuzan Ginger Chang Jeff Bailey Xinwei She NCBI Deanna Church

6. Mouse Genome Annotation Summit, 12 Mar 2008 Duplications in human and mouse Inter-chromosomal Intra-chromosomal Both Human Mouse Mouse has an increased amount of intra-chromosomal duplication when compared to human

7. Mouse Genome Annotation Summit, 12 Mar 2008 Known issues in the mouse genome Potentially collapsed repeats

8. Mouse Genome Annotation Summit, 12 Mar 2008 Known issues in the mouse genome Strain Differences

9. Mouse Genome Annotation Summit, 12 Mar 2008 Known issues in the mouse genome Strain Differences

10. Mouse Genome Annotation Summit, 12 Mar 2008 Large-scale structural variation Two different 129 contigs (129/SvEvTac and 129/SvJ) map to same location in C57BL/6J (Interferon cluster) Strain Differences

11. Mouse Genome Annotation Summit, 12 Mar 2008 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. Mouse Genome Annotation Summit, 12 Mar 2008 Genome Reference Consortium Fix errors Curation Represent additional alleles Community outreach

13. Mouse Genome Annotation Summit, 12 Mar 2008 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 Acknowledgments

14. Mouse Genome Annotation Summit, 12 Mar 2008 NCBI Assembly & Annotation Richa Agarwala Hsiu-Chuan Chen Josh Cherry Deanna Church Mike DiCuccio Wratko Hlavina Melissa Landrum Donna Maglott Yuri Kapustin Paul Kitts Kim Pruitt Victor Sapojnikov Sasha Souvorov 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 Baylor College of Medicine Donna Muzny Shannon Dugan Richard Gibbs Sanger Institute Christine Nicholson Sean Humphrey Darren Grafham Jane Rogers Washington University Genome Sequencing Center Susie Rock Tina Graves Bob Fulton Rick Wilson Acknowledgments