1. 1.Use of mice in biomedical research 2.KOMP: Activity and progress to date 3.Rationale and planning for phenotyping 4.Request for continued support Presentation Overview

2. Mice in Biomedical Research The laboratory mouse has been considered the premiere experimental model of human biology and disease since 1902 when it was first used to demonstrate how genetic traits could be transferred from parents to offspring via classical or “Mendelian” inheritance in mammals. In just over a century, an impressive array of genetic tools, reagents and processes has been developed in the mouse, including: – Homozygous inbred strains – Recombinant inbred and consomic strains – Transgenic and knockout methods – Monoclonal antibodies – iPS cells Evidence that mice have played a key role in biomedical research is provided by the fact that at least 18 Nobel prizes have been awarded for work done using the mouse. Most recently, the 2007 Nobel Prize was awarded to Mario Capecchi, Martin Evans, and Oliver Smithies for their discovery of the "principles for introducing specific gene modifications in mice by the use of embryonic stem (ES) cells.”

3. The Premiere Model Organism Janan Eppig, Jax

4. KOMP Vision KOMP (2006-11) ARRA (2010-11) KOMP2 (2011-21) R01s Austin et al., Nature Genetics, 2004

5. Funded KOMP Projects The Completion of a Comprehensive Mouse Knockout Resource ($47 M - 5 years - funded 9/06) CHORI-Sanger-UC Davis Regeneron Pharmaceuticals, Inc. Development and Improvement of Inbred ES Cell Lines for Use in Generation of Mouse Mutants ($1.9 M - 2 years - funded 9/06) U Pennsylvania Samuel Lunenfeld Research Institute A Data Coordination Center for the Knockout Mouse Project (KOMP) ($2.5M - 5 years - funded 9/06) The Jackson Lab The KOMP Repository ($4.8M - 4 years - funded 8/07) UC Davis – CHORI

6. Goals and Progress

7. The KOMP Website www.knockoutmouse.org Target List

8. The KOMP Website www.knockoutmouse.org Details Complete information on allele design, vector, genotyping and sequencing primers are provided to the end-user.

9. The KOMP Repository www.komp.org The repository offers vectors, KO ES cells, parental ES lines, and support services. Orders are processed using a standard “shopping cart.”

10. KOMP Repository Activities Orders have recently increased to about 100/month. Over 3,000 users have created accounts and registered interest in ~2,500 genes. Kent Lloyd, UCDavis

11. Rationale for KOMP 2 Supporting a broad phenotyping effort would provide the following advantages: – A single cohort of mice would go through multiple phenotyping assays, so the cost of producing multiple cohorts in different laboratories for phenotyping would be eliminated. – Each mutant mouse strain would be characterized for a broad set of phenotypes in a way that will allow direct comparisons and result in a more thorough description of gene function. – Quality standards will be established and maintained, so the data will be of the highest reliability. – The risk of not finding a phenotype will be greatly reduced. – Important, but unpublishable, negative results will be captured.

12. 3 workshops: Rome in 2007, Bar Harbor and Toronto in 2008 to establish vision for an IMPC & discuss international, coordinated phenotyping efforts – agreed that the way forward is to develop a business plan Medical Research Council/Wellcome Trust workshops in Nov 2008 and Oct 2009 to engage UK scientific community NIH Phenotyping meeting, Bethesda October 2009 (survey) EC–funded EUMODIC (Helmholtz, Munich; ICS, Strasbourg, MRC Harwell, WTSI) project is now doing broad-based phenotyping of 500 mutant lines – completion 2011 Planning for next phase: Phenotyping

13. The International Mouse Phenotyping Consortium Members: The Wellcome Trust The Medical Research Council The Wellcome Trust Sanger Center MRC Harwell European Commission The National Institutes of Health German Mouse Clinic Toronto Center for Phenogenomics Pending members: Australia Phenomics Network Czech Republic Institut Clinique de la Souris Nanjing University Universitat Autonoma de Barcelona Current funding: EuMODIC - $7M/yr + matching funds, 150 strains Sanger Mouse Genetics Program - $9M/yr, 200 strains Australia Phenomics Network - $10.5M/yr

14. EMPReSSslim Primary Phenotyping Pipelines Steve Brown, Harwell, MRC

15. Phenotyping of KOMP CSD mice at Sanger http://www.sanger.ac.uk/mouseportal/ Reproduction Fertility Reproduction Fertility Developmental Biology Viability Embryonic lacZ pattern Viability at E14.5 MRI at E14.5 Developmental Biology Viability Embryonic lacZ pattern Viability at E14.5 MRI at E14.5 Neurology SHIRPA assessment Hot plate (pain) Open field (anxiety) Stress-induced hyperthermia Brain anatomy Neurology SHIRPA assessment Hot plate (pain) Open field (anxiety) Stress-induced hyperthermia Brain anatomy Musculo-skeletal Grip strength X-rays (skeleton) Bone mineral density Bone mineral content Musculo-skeletal Grip strength X-rays (skeleton) Bone mineral density Bone mineral content Infectious disease susceptibility Salmonella (bacterial) Citrobacter (bacterial) Plasmodium (malaria) Flu (viral) Infectious disease susceptibility Salmonella (bacterial) Citrobacter (bacterial) Plasmodium (malaria) Flu (viral) Metabolism Weight gain curve Food intake and energy expenditure) Fat/lean tissue assessment by DEXA Glucose tolerance test Serum Insulin Blood Clinical Chemistry Metabolism Weight gain curve Food intake and energy expenditure) Fat/lean tissue assessment by DEXA Glucose tolerance test Serum Insulin Blood Clinical Chemistry Senses Slit lamp (front of the eye) Eye fundus (retina) Auditory brain response (hearing circuits) Senses Slit lamp (front of the eye) Eye fundus (retina) Auditory brain response (hearing circuits) Immune system Complete blood count White blood cell profile Immunoglobulin subclass profile Immune system Complete blood count White blood cell profile Immunoglobulin subclass profile Cardiovascular Blood clinical Chemistry Heart weight (hypertrophy) Heart histology Eye fundus (retinal vessels) Cardiovascular Blood clinical Chemistry Heart weight (hypertrophy) Heart histology Eye fundus (retinal vessels) Cancer Micronuclei analysis Cancer Micronuclei analysis Hair and skin Hair growth rate Hair follicle stem cell Hair and skin Hair growth rate Hair follicle stem cell General Visible malformations Adult organ lacZ expression Necropsy Tissue banking for histology General Visible malformations Adult organ lacZ expression Necropsy Tissue banking for histology Ramiro Ramirez-Solis, WTSI

16. Genentech/Lexicon Mouse Phenotype Project 472 Mouse knockouts were broadly phenotyped 130 (27%) strains had 1 phenotype 245 (52%) strains had 2-5 phenotypes Andy Peterson, Genentech

17. Cohort breeding Phenotyping Data Upload Cohort breeding Phenotyping Data Upload KOMP Repository Mouse Production ES cells Mice/Embryos Database Web server Data Mouse Phenotyping Center(s) Mice/Embryos KOMP ES cells EuCOMM ES cells Mice/Embryos Microinjection Germline Transmission LacZ staining Lethality/Fertility Cryopreservation Tracking Analysis Display Cohort breeding Phenotyping Data Upload KOMP Phenotyping Scheme