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

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.

www.mousephenotype.org

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 (2011-2016): phenotype up to 5,000 lines Pipeline development, logistics Phenotyping technology developments e.g. imaging Ramp up

Phase II (2016-2021): 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

Centre Total for Phase 1

MRC Harwell 330

Sanger Institute 1000

NIH - BaSH Baylor, Sanger, MRC Harwell 830

NIH - DTCC UC Davis, TCP, Children’s Oakland, CR 830

NIH - JAX 830

TCP, Toronto 150

Helmholtz, Munich 250

ICS, Strasbourg 250

Riken BRC 250

MARC, Nanjing 250

CNR, Monterotondo 250

TOTAL 5220

New Homepage for IMPC Portal (Andy Blake) www.mousephenotype.org

IMPC Operational Plan

Key Team Players @ HarwellThey Will Deliver This Project

Production LacZ Profiling

Allele QCArchiving

Distribution Genotyping

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, 262-263 (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, 262-263 (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 & SynergiesSee 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 DiscussionBuild on EUMODIC, MGP, NIH K312Focus GroupsSurveysOperational Workshops (London,

Toronto, Barca)Munich, Nov 2011

IMPC Adult Phenotyping Pipeline

+ LacZReporter

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 IMPReSS – International Mouse Phenotyping Resource of Standardised ScreensResource of Standardised Screens

IMPReSS (Annie Mallon)Now Live www.mousephenotype.org/impress

Data Wranglers

Protocols and Parameters for 13 Platforms

Uploaded to the IMPReSS database

In process of organizing calls for other SOPs

SEE HANDOUT

Phenotyping Progress @ 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 InformaticsInfrastructure“MPI2”

Harwell, Sanger, EBI

(Pilot: www.europhenome.org)(Pilot: www.europhenome.org)

EuroPhenome (Annie Mallon)(www.europhenome.org)

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 %

Lethal 34

Sub-viable 11

Reduced life span 2

Viable 53

84% of lines have an annotation including viability and fertility

Draft Pipeline – Under Consultation

Dis

sect

ion

& g

ross

mor

phol

ogy

(em

bryo

s &

pla

cent

ae)

lacZ

sta

inin

g(e

mbr

yos

& p

lace

ntae

)

E12.5

≥7 Embryos from Sub-viable Lines

Adult Phenotyping Pipeline

IKMC mES cells (B6N)

Germline transmission

Heterozygotes

Homozygotes

Homozygotes

>40% expected homozygous mutants at weaningvi

able

subviable

<40% expected homozygousmutants at weaning

Dis

sect

ion

& g

ross

mor

phol

ogy

(em

bryo

s &

pla

cent

ae)

His

topa

thol

ogy

(em

bryo

s &

pla

cent

ae)

Em

bryo

μC

T(io

dine

sta

inin

g)

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 CriticalFIRST 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

Consortium Principal Investigator

Bone and Cartilage Raj Thakker, Oxford

Cardiovascular Patricia Munroe, QMU

Development Andrew Copp, UCL

Drug Targets: UK-China (MADD) Dario Alessi, Dundee

Haematopoiesis and Cancer Claus Nerlov, Edinburgh

Host Response to Pneumonia Peter Andrews, Leicester

Immune System Werner Muller, Manchester

Innate Immunity David Hume, Edinburgh

Liver Disease (UK Gold) Raj Thakker, Oxford

Models of Diabetes and Obesity (MODO) Tony Vidal-Puig; Anthony Coll, Camb

Neurodegenerative Disease & Aging (nPad) Jean Manson, Edinburgh

Neuromouse Kay Davies, Oxford; Lizzy Fisher, Prion/UCL

Opthamology Ian Jackson, Edinburgh; Marcela Vertruba, Cardiff

Renal (RUMP) Robert Unwin, KCL; Matthew Bailey, Edinburgh

Respiratory Charlotte Dean, Matthew Hind, Imperial

Tissue Recomdelling and Fibroblast Disease (TiReFiC) Chirs Buckley, Birmingham; Jill Norman, UCL

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, 20-40 People

Please Update Your Action Plan This Month (Hilary will Email 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, [email protected]

+44(0)778-0666-0922

MRC Mouse Network Timeline of Activity

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May

MRC Network Meetings

MMN Launch

Network Meeting

(ops)

Network Meeting

(ops)

Planning & Reports

Final Action

Plan

Interim Reports

MRC Review

TrainingBioinfo (MMN Case

Study)

Bioinfo (MMN Case

Study)

Option for operational training (eg IVF/Cryo, Phenotping).

Consortia Project Meetings

Consortia Project MeetingsRevise Work

Plans

2012 2013

Project Tracking

Access To Mice

Access To Data

Portal Portal and iMits on IMPC website

EUMODIC Now, But InterPhenome with Time.

Update MRC MTA Harwell & Other Production Centres

IMPC Specific Meeting

Infra Comp (Emb) UCL

MPI2 Wash

DC

KOMP2 Wash DC

Infra Comp Korea

SUMMARY

KEY INFO PORTALS: IMPC: http://www.mousephenotype.org MRC MOUSENETWORK PORTAL

WEB: http://mrcmousenetwork.har.mrc.ac.ukEmail Contact:

[email protected]

Harwell Contacts Who Can HelpTom Weaver: [email protected] Blake: [email protected] Gates: [email protected]

Thank You