International Mouse Phenotyping Consortium & MRC MOUSE NETWORK Tom Weaver Director, MRC Harwell Mary Lyon Centre

Outline Update on the IMPC Progress  Alleles & Gene Selection  Production  Phenotyping MRC Mouse Network  Objectives  Expectations  Some Ideas For Going Forward

Vision For Next 10 Years... An Encyclopaedia of Mammalian Gene Function  Create KO mice for ALL GENES  Database with associated primary phenotype info;  Discover unforeseen gene function;  Free and unfettered access to MICE  Free thousands of researchers from tool generation;  A rich seam for future hypothesis driven research, with the potential for breakthrough discoveries; A transformative project that will underpin the future of biomedical science and the biology of disease systems.

22 Partners, 13 Production Centres, 9 Countries

IMPC Activities Undertake broad based primary phenotyping of 20,000 mutants from the IKMC resource  A coordinated effort of mouse clinics worldwide Phase I ( ): phenotype up to 5,000 lines  Pipeline development, logistics  Phenotyping technology developments e.g. imaging  Ramp up Phase II ( ): Phenotype 15,000 mutants Data freely available through a Data Coordination Centre, supported by R&D groups at clinics

Value of Program Scientific (Hypothesis Generating) Innovation Bottleneck (SGX) Welfare (NC3R) Financial (Funders) Paradigm Shift in Scientific Culture (MRC MOUSE NETWORK)

Traditional “One Gene at a Time” Approach Clone the Gene Knock It Out in Cells Create A Mouse Study Effect Publish Your Work Share with Other Labs  1 Gene, 1 Mutation, 1 Mouse  3-5 Year Investment in Time and Resources  Expensive & Inefficient  Individual Scientist Driven

Alternative “Whole Genome” Approach Sequence the Genome Mutate EVERY gene Create a Repository of Mice Study Effect “Phenotype” Data Release  All Genes, 20K Mutations and Mouse Strains  Highly Parallel (HTP “Factories”)  Immediate Access & Sharing  Cost Effective  Global Networks Required Share Mice with Other Scientists Study Effect “Phenotype” Publish Work

Status: Raised $200M for Phase 1 Launch – Sept 28th 2011 CentreTotal for Phase 1 MRC Harwell330 Sanger Institute1000 NIH - BaSHBaylor, Sanger, MRC Harwell830 NIH - DTCC UC Davis, TCP, Children’s Oakland, CR 830 NIH - JAX830 TCP, Toronto150 Helmholtz, Munich250 ICS, Strasbourg250 Riken BRC250 MARC, Nanjing250 CNR, Monterotondo250 TOTAL5220

New Homepage for IMPC Portal (Andy Blake)

IMPC Operational Plan

Key Team Harwell They Will Deliver This Project ProductionLacZ Profiling Allele QCArchiving DistributionGenotyping Cohort Breeding Phenotyping Histology Necropsy Finance, HR, Engagement LIMS, Data Portal & Bioinformatics Pathology Training Quality Assurance Martin F.Lydia T.Deen Q.Sara W.Tertius H.Michael C.Mark G. Alison W. Annie M. Liz M.Hilary G.Nanda R. Andy B. Hugh M.

MOUSE PRODUCTION STATUS

IKMC Alleles (will be used in IMPC) Knockout-first, conditional ready allele: Promoter-driven selection cassette Francis Stewart (Dresden) Allan Bradley and Bill Skarnes (WTSI) Wolfgang Wurst (Helmholtz) See Skarnes et al. Nature 474, (2011)

STATUS: From Mouse Production to Cryopreservation Gene selection  Gene selection, and tracking from ES QC to MI, iMits successfully launched  MRC STRATEGY: MMN SELECTION Delivery of ES Cells  KOMP Repository and EUMMCR tm1a=> tm1b allele conversion  Different approaches will be applied across IMPC centres (Harwell Actin- CRE working well) Cryopreservation strategy  tm1a (and tm1b) – sperm freezing

IKMC Alleles (will be used in IMPC) Knockout-first, conditional ready allele: Promoter-driven selection cassette Francis Stewart (Dresden) Allan Bradley and Bill Skarnes (WTSI) Wolfgang Wurst (Helmholtz) See Skarnes et al. Nature 474, (2011) We Archive & Distribute These Strains Conditional Allele Requires Breeding We Phenotype, Archive & Distribute These Strains

Harwell Production Status  444 MMN Genes “Assigned” to MRC and in progress (BaSH & MRC) =>assume 220 GLTS (50% Pass Rate)  53 tm1a alleles (legacy/imported) undergoing cre-deletion  88 Genes Received as ES cells  9 GLTs: first one is “IGF1R”  6 months from MI to access

NEUROMOUSE Gene List & Synergies See Handout Progress  28 genes in progress  5 ES cells in Allele QC, rest awaiting receipt! Genes “Overlapping” interest with other members of network  5 with other consortia  Neuodegenerative disease and aging, cancer, Development, Vision, Respiratory Synergy w/ Other Production Centres  E.g. we nominate, they KO =>50 lines with China (MADD)  8 Genes from NEUROMOUSE (JAX, TCP, ICS,…)

PHENOTYPING STATUS

Phenotyping Program Has Evolved…. Much Discussion  Build on EUMODIC, MGP, NIH K312  Focus Groups  Surveys  Operational Workshops (London, Toronto, Barca)  Munich, Nov 2011

IMPC Adult Phenotyping Pipeline + LacZ Reporter 23 platforms, 100’s of parameters/metadata

Protocol Development Working Groups  LacZ  Fertility & Viability  SHIRPA/Dysmorphology  Open Field  Grip Strength/Startle, PPI  ECG/Echo  Calorimetry/IPGTT  ABR  Body Composition/ X-ray  Slit lamp/ Ophthalmoscope  Hematology/Clin Chem/Insulin  Heart Wt./Gross Pathology/Block Banking  FACS, IGs IMPReSS – International Mouse Phenotyping Resource of Standardised Screens

IMPReSS (Annie Mallon) Now Live  Data Wranglers  Protocols and Parameters for 13 Platforms  Uploaded to the IMPReSS database  In process of organizing calls for other SOPs  SEE HANDOUT

Phenotyping MRC (Sara Wells & Tertius Hough)  Recruiting & Reorg Complete (breeding stations), All Equipment In place  SOPs Complete For Agreed Tests (MASSIVE TASK!)  Pilot data for echo/ultrasound, challenge plethysmography, ABR  31 TM1A alleles cre-deletion underway (Tm1B)  12 TM1B alleles in cohort production, first full cohort started this month.  Data will be in INTERPHENOME

INTERPHENOME Mouse Phenotyping Informatics Infrastructure “MPI2” Harwell, Sanger, EBI (Pilot:

EuroPhenome (Annie Mallon) ( 26,258 mice 8.22M data points 3,416 annotations

Gene and Phenotype Search Tools

Complex Phenotype Search Result “Increased Circulating Cholesterol” AND “Increased Circulating LDL Cholesterol”

EuroPhenome Heatmaps

New phenotypes revealed (Steve Brown) Srsf4 (serine/arginine-rich splicing factor 4)  Not annotated in MGI Pipeline Screening: Annotations in different systems  Reduced RBC count, haemoglobin concentration, haematocrit across sexes and zygosities  Much lower Grip Strength in both sexes  More subtle changes in Calorimetry and Opthalmoscope 74% (131/176) genes with no prior annotations had significant phenotypes

cardio lung Pipeline Under Constant Review (Role for Networks) Number of Annotations per top level ontology term

Distribution of Phenotype Annotations Viability Viability% Lethal34 Sub-viable11 Reduced life span2 Viable53  84% of lines have an annotation including viability and fertility

Draft Pipeline – Under Consultation Dissection & gross morphology (embryos & placentae) lacZ staining (embryos & placentae) E12.5 ≥7 Embryos from Sub-viable Lines Adult Phenotyping Pipeline IKMC mES cells (B6N) Germline transmission Heterozygotes Homozygotes >40% expected homozygous mutants at weaning viable subviable <40% expected homozygous mutants at weaning Dissection & gross morphology (embryos & placentae) Histopathology (embryos & placentae) Embryo μCT (iodine staining) E14.5 viable Proposed IMPC Embryonic Lethal Phenotyping Pipeline

IMPC & InfraComp Workshop on Embryonic Lethal Screening Two Day Workshop: April 18th-19th, 2012; Institute of Child Health, UCL  Organizers: Andy Copp (UCL, UK), Janet Rossant (Univ Toronto, Canada), Tom Weaver (Harwell, UK), Tim Mohun (NIMR, UK), Monica Justice (Baylor, USA), Michael Raess (HMGU, Germany) Goal: Agree a consensus strategy for embryonic phenotyping & LacZ analysis Topics:  Scientific Value of Embryology to Research Community  Current Status of Screening – Don’t reinvent the wheel, Funding opportunities  Operational Workflow – Not One Single Pipeline, Best Fits  LacZ Reporter Analysis – Agree Pipeline  Information Technology & Annotation Dev Consortia Input Critical FIRST MAJOR CONTRIBUTION FROM MRC MOUSE NETWORK

Engagement Plan: MRC Mouse Network MRC Mouse Network Will Be a Forum to:  Communicate about IMPC  Encourage Uptake of Resources  Promote Use of Resource Facilitate Collaboration  16 Consortia Formed  7/10 Top Therapeutic Areas  >400 PIs/25% Clinical “MADD” Consortium Example  Novel Drug Target Class  100 Knock Outs  Structures/Assays/Industry Collaboration

Network Consortia 16 Consortia Network; Met January at Harwell

Ambitions For Network Promote IMPC and Mouse Models:  facilitate more road shows, participate in training course(s) Proactive Discussion/Planning:  Assign a “Champion” to be main contact with Harwell. Simplify, streamline the communication (gene lists, issues, ideas). Updated/Revised Plan in April.  Encourage the network to evolve so that individuals can work together rather than simple info flow from Harwell/Pis. Use the portal as a project management/coordination tool. Direct Participation: Actions with Added Value to Program  Pilot Work: Kick-start secondary phenotyping  Active Uptake of Lines/Data Feedback:  We will ask for a report at end of first year (spring 2013), will influence development of the program.  USER CASE SCENARIO => DATA PORTAL

On-line Portal (mrcmousenetwork.har.mrc.ac.uk) Individual members of the MRC Mouse Network will be able to communicate directly to one another in a manner similar to “Facebook”

Key Functionalities Important Functions  Secure Log in (already registered!)  General Information  News  Events  Forum => Incredibly Useful for IMPC Nov 2008, 156 Active Users, 24 Forums, 300 Forum Threads, 8K page views….  My Consortium  All Consortia Demo From Andy Blake Today

Training For Networks The Network will promote training in the form of workshops, training courses, and site visits.  Mouse Genome Browsing, Mutant Mouse Resources  Customize to MMN  Develop Case Studies, eg GWAS => Candidates => Resources Available  2/3 WEEK OF May 2012, Harwell, People

Please Update Your Action Plan This Month (Hilary will Pis) Champion. Need to get your contact actively linked with our scientists. Hilary/Tom can help coordinate. Access to Mice/Samples. Need feedback and start planning now, but be realistic. Your plans for 2’/3’ phenotyping. Primary Phenotyping Data. Help to evaluate. Use case input. Pathology Network. Cross cutting need. Recruiting a senior pathologist to lead. Join our network? Conditional Alleles. Service will be available. Are you interested? Coordinate Funding. Opportunities to look for technical support, pilots, etc… BHF example.

Harwell has an immediate need for an Experienced Pathologist (Permanent B2, sr. lecturer equivalent) Role is to lead the program in animal health and welfare, as well as have overall responsibility for pathology services strategy and management at the Mary Lyon Centre. Opportunity for international collaboration in pathology phenotyping and annotation. Please Contact: Tom Weaver, +44(0)

MRC Mouse Network Timeline of Activity

SUMMARY KEY INFO PORTALS:  IMPC:  MRC MOUSENETWORK PORTAL WEB: Contact: Harwell Contacts Who Can Help Tom Weaver: Andy Blake: Hilary Gates:

Thank You