Transcript TW_NEUROMOUSE_4April2012

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
www.mousephenotype.org
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
Create
It Out
A
in Cells Mouse
Study
Effect
Share
Publish
with
Your
Other
Work
Labs
1 Gene, 1 Mutation, 1 Mouse
3-5 Year Investment in Time and Resources
Expensive & Inefficient
Individual Scientist Driven
Alternative “Whole Genome” Approach
Create a
Sequence
Mutate
Repository
the Genome EVERY gene
of Mice
Study
Effect
“Phenotype”
Data
Release
Share Mice
with Other
Scientists
Study
Effect
“Phenotype”
Publish
Work

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
All Genes, 20K Mutations and Mouse Strains
Highly Parallel (HTP “Factories”)
Immediate Access & Sharing
Cost Effective
Global Networks Required
Status: Raised $200M for Phase 1
Launch – Sept 28th 2011
Centre
Total for Phase 1
MRC Harwell
330
Sanger Institute
NIH - BaSH
NIH - DTCC
1000
Baylor, Sanger, MRC Harwell
830
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
www.mousephenotype.org
(Andy Blake)
IMPC Operational Plan
Key Team Players @ Harwell
They Will Deliver This Project
Martin F.
Production
Lydia T.
Deen Q.
Sara W.
Tertius H.
LacZ Profiling Cohort Breeding
Archiving
Distribution
Allele QC
Michael C.
Necropsy
Phenotyping
Genotyping
Mark G.
Quality Assurance
Pathology
Histology
Training
LIMS, Data Portal & Bioinformatics
Alison W.
Andy B.
Hugh M.
Finance, HR, Engagement
Liz M.
Hilary G.
Nanda R.
Annie 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 ActinCRE working well)
Cryopreservation strategy
 tm1a (and tm1b) – sperm freezing
IKMC Alleles
(will be used in IMPC)
Knockout-first, conditional ready allele:
We Archive &
Promoter-driven selection cassette
Distribute
These Strains
We Phenotype,
Archive &
Distribute
These Strains
Conditional Allele Requires
Breeding
Francis Stewart (Dresden)
Allan Bradley and Bill Skarnes (WTSI)
Wolfgang Wurst (Helmholtz)
See Skarnes et al.
Nature 474, 262-263 (2011)
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
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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
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IMPReSS – International Mouse
Phenotyping Resource 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
Informatics
Infrastructure
“MPI2”
Harwell, Sanger, EBI
(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
Number of Annotations Under top
level term
Pipeline Under Constant Review
(Role for Networks)
700
600
500
Number of Annotations per
top level ontology term
400
300
200
100
0
cardio lung
Distribution of Phenotype Annotations
Viability
 84% of lines have an annotation including
viability and fertility
Viability
%
Lethal
34
Sub-viable
11
Reduced life span
2
Viable
53
Proposed IMPC Embryonic Lethal
Phenotyping Pipeline
viable
>40% expected
homozygous
mutants at weaning
Adult Phenotyping Pipeline
Draft Pipeline
– Under Consultation
E12.5
E14.5
(embryos & placentae)
Histopathology
Embryo μCT
(iodine staining)
viable
(embryos & placentae)
Homozygotes
Homozygotes
Dissection & gross morphology
<40% expected
homozygous
mutants at weaning
(embryos & placentae)
subviable
lacZ staining
Heterozygotes
(embryos & placentae)
Germline transmission
Dissection & gross morphology
≥7 Embryos from Sub-viable Lines
IKMC mES cells (B6N)
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
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
16 Consortia Network; Met January at
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.
case input.
Use
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
MRC
Network
Meetings
Planning &
Reports
2012
Feb Mar Apr May Jun Jul
Sep
Oct Nov Dec
Network
Meeting
(ops)
MMN
Launch
Final
Consortia Project
Action
Meetings
Plan
Jan
Option for operational training (eg
IVF/Cryo, Phenotping).
Portal
Interim MRC Revise Work
Reports Review
Plans
Bioinfo
(MMN
Case
Study)
Portal and iMits on IMPC website
Update MRC MTA
Harwell & Other Production Centres
EUMODIC Now, But InterPhenome with Time.
Infra
Comp
(Emb)
UCL
MPI2
Wash
DC
KOMP2
Wash DC
Apr May
Network
Meeting
(ops)
Consortia Project Meetings
Bioinfo
(MMN
Case
Study)
Training
Project
Tracking
Access To
Mice
Access To
Data
IMPC
Specific
Meeting
Aug
2013
Feb Mar
Infra
Comp
Korea
SUMMARY
KEY INFO PORTALS:
 IMPC: http://www.mousephenotype.org
 MRC MOUSENETWORK PORTAL
 WEB:
http://mrcmousenetwork.har.mrc.ac.uk
 Email Contact:
[email protected]
Harwell Contacts Who Can Help
 Tom Weaver: [email protected]
 Andy Blake: [email protected]
 Hilary Gates: [email protected]
Thank You