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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.
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
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.
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 Program Has Evolved….
Much DiscussionBuild on EUMODIC, MGP, NIH K312Focus GroupsSurveysOperational Workshops (London,
Toronto, Barca)Munich, Nov 2011
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)
Complex Phenotype Search Result“Increased Circulating Cholesterol” AND “Increased Circulating LDL Cholesterol”
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:
Harwell Contacts Who Can HelpTom Weaver: [email protected] Blake: [email protected] Gates: [email protected]