International Mouse Phenotyping Consortium Mark Moore, Ph.D.

A meeting at the Banbury Centre, Cold Spring Harbor in 2003 published a proposal for high throughput Gene Knockouts and Phenotyping for every gene in the mouse genome.

Nat Genet Sep;36(9): The European dimension for the mouse genome mutagenesis program. Auwerx JAuwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmeliet P, Chambon P, Cox R, Davidson D, Davies K, Duboule D, Forejt J,Granucci F, Hastie N, de Angelis MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Müller W, Partanen J, Ricciardi-Castagnoli P,Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocchini-Valentini G, Wagner E, Wahli W, Wurst W.Avner PBaldock RBallabio ABalling RBarbacid MBerns ABradley ABrown SCarmeliet PChambon PCox RDavidson DDavies KDuboule DForejt JGranucci FHastie Nde Angelis MHJackson IKioussis DKollias GLathrop MLendahl UMalumbres Mvon Melchner HMüller WPartanen JRicciardi-Castagnoli PRigby PRosen BRosenthal NSkarnes BStewart AFThornton JTocchini-Valentini GWagner EWahli WWurst W

Numbers of KOs reported per gene Number of targeted genes Number of times each gene KO’d

Money lost due to repetitive work 3308 unique genes have been KO’d 6310 total number of mice (all alleles) Approximately 3,000 re-hits Assume a cost of $50,000/KO repeats of no additional value 10% represents 300 = $15,000,000 25% represents 750 = $37,500,000 50% represents 1,500 = $75,000,000 80% represents 2,400 = $120,000,000

KOMP Goals: Phase 1 “…a high-throughput international effort to produce…knockouts for all mouse genes, and place these resources into the public domain.” KO alleles –null, ideally “conditional-ready” (loxP or flp) –contain reporter (LacZ or EGFP) Methods –combination of targeting and trapping Deliverables –mutant ES cell lines, sperm, frozen embryos –Public domain resource Beyond Phase 1 –histochemical analysis of transgene expression –phenotypic data –searchable database

KOMP-IMPC Alleles WTSI (Allan Bradley and Bill Skarnes) Helmholtz (Wolfgang Wurst)

KOMP-IMPC Alleles Regeneron Approach

IKMC Alleles

The KOMP Repository

KOMP Repository Activities

KOMP Customer orders by month Late 2008 – early 2010 Each order saves $20,000-50,000 KOMP is already saving more money than it spends

KOMP + Other Goals and Progress

The IKMC have produced over 10,000 KO ES cell lines

IKMC

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 Phenotyping Background

Why the IMPC Build a resource of KO mice and associated encyclopedia of gene functions Free thousands of researchers from tool generation This resource will be revolutionize research for the next years Novel genes will be brought to light that would otherwise be ignored Potential for breakthrough discoveries

MRC Harwell (Steve Brown, current Chair, Tom Weaver) MRC (Nathan Richardson, Paula Clements) NIH (Jane Peterson, Eric Green, Jim Battey, Colin Fletcher, Martin Guyer) Sanger Institute (Alan Bradley, Karen Kennedy) Wellcome Trust (Michael Dunn, Clare McVicker) Infrafrontier (Martin Hrabe de Angelis) Helmholtz Zentrum Munich (GMC) (Martin Hrabe de Angelis) Toronto Centre for Phenogenomics (TCP) (Colin McKerlie) Institut Clinique de la Souris (ICS) (Yann Herault) Australian Phenomics Network (Adrienne McKenzie) European Commission (Jacques Remacle, observer) The International Mouse Phenotyping Consortium (IMPC) Steering Committee Secretariat (Mark Moore, Jörg Roßbacher)

IMPC Vision IKMC ( ) ARRA ( ) EUMODIC ( ) IMPC ( ) PI Driven

IMPC Progress Addition of new members bringing total to 10 4 Funding Organizations 6 Mouse phenotyping Centers Response to community-wide surveys Development of workshops Embryology Imaging Technologies Working to actively manage the coordination and development of the multiple centres Launch Phase II 2011?

IMPC Activities Six mouse clinics so far; anticipate worldwide. Phase I ( ) of the preparatory/development period ~4,000 Work to actively manage the coordination and development of the multiple centres Evaluate a final scientific, management and governance plan for the full scale programme to commence in 2016 Launch Phase II Completion of the Genome

Rationale 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.

IMPC Phenotyping Proposal The proposal will be shaped by: EUMODIC results The Sanger MGP Publicly available data (Lexicon and Deltagen) ENU screens phenotyping results Survey Results from UK, NIH, EU Recommendations from workshops in the UK and US Future workshops in Europe, US, Canada and UK

EMPReSSslim Primary Phenotyping Pipelines 20 phenotyping platforms 406 phenotype parameters 155 metadata parameters

WTSI Mouse Genetics Program

2009 Mouse Pipeline Survey If No, then why?

Please list the top 3 diseases that have been modeled using knockout mice. Disease or condition# of votes Cancer21 immune system diseases7 obesity7 Alzheimers5 atherosclerosis5 diabetes5 ApoE heart disease2 autoimmunity2 cyctic fibrosis2 Huntington Disease2 Stem cells- bone marrow transplants2

Please list the top 3 questions in biology or medicine that you feel remain to be answered...and that you think could best be studied using knockout mice. Topic of question# of votes cancer15 Aging5 epigenetics4 stem cells4 embryogenesis3 brain function2 consciousness2 degenerative nerve disease2 Heart disease2 Memory2 organogenesis2 regeneration2 schizophrenia2

Survey Summary Report Question #2: Thinking beyond your laboratory, what do you see as the 3 essential tests, analyses, and/or examinations that would most likely reveal the utility of a mutant mouse line in your field? Two caveats: the numbers of mice used per test are limited to 5-10 and the tests must be high throughput (100’s/y). behavior metabolism immuno MMRC Survey Conducted by Kent Lloyd

Survey Summary Report MMRC Survey Conducted by Kent Lloyd >2000 s and ~300 respondents

Key Areas of Unmet Need Cancer Need longer time line to study Fits with aging Challenge? Aging Critical need cited in all surveys and workshops Strongly augments: Cancer, Cardiovascular, Metabolic, Neurodegeneration and Bone Research Embryology A rich source of phenotype data ~30% KOs E.L. Very Specialized Skill Sets Req. Need HTP approach Meeting at TCP April 9-10

IMPC Phenotyping Core group of tests at all centres Agreed upon minimum cohort size (7?) Test and recommend additions to or dropping phenotypic tests from the pipeline Groups are encouraged to add tests to the phenotyping platform where possible Each centre is encouraged to incorporate a challenge assay or assays to the platform Each centre should develop networks of collaborators MRI and/or micro CT likely to be added Incorporate study of embryonic lethals

Phenotyping Progression Primary Screen (Thousand(s) per years) Second Level Testing (Hundreds per year ) Tertiary In-Depth (dozens per year)

Mouse Phenotyping and Production/Distribution Centers Mouse Clinics ES to mouse Production (optional) Archiving (optional) Primary Phenotyping Secondary Phenotyping Production Centers Re-animation Mouse production ArchivingDistribution Secondary Phenotyping

IMPC Next Steps Form Steering Committee Develop Requirements Document Informatics Explore new ways to lower mouse costs Continue exploring commercial options Mice Form Tech Development Group First Tasks: Imaging Recommendation (&Pathology) Embryonic Lethal Analysis Tech Dev Develop final plan for IMPC Pipeline Operating plan for review of pipeline Phenotyping Working groups in each area Devise how to test models at centers Challenge Models

IMPC Cost Projections

IMPC Phase II Projections Phenotyping the remaining 15,000 KOs Project Costs

Next 3 years ( ) EUMODIC project will come to completion UC, Davis has funding to support the creation and limited analysis of 312 KO mouse lines The WTSI is funded to analyse 200 KO lines per year MLC Harwell planning to analyse 100 KO lines per year Toronto Centre for Phenotyping (TCP) has capacity to produce and analyse KO mouse lines per year. InfraFrontiers is developing the vital infrastructure for the continuation and expansion of mouse Phenotyping New centres at UAB (Barcelona) and the Czech Republic will be constructed and come online NIH has raised funding to launch Phenotyping

IMPC, a global and still expanding research initiative:  Download link of procedure to join the IMPC