Transcript International Mouse Phenotyping Consortium

International Mouse Phenotyping Consortium
Mark Moore, Ph.D.
Why the IMPC
 Build a resource of KO mice and associated
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encyclopedia of gene functions
Free thousands of researchers from tool generation
This resource will be revolutionize research for the
next 20-30 years
Novel genes will be brought to light that would
otherwise be ignored
Potential for breakthrough discoveries
Targeted deletion of the 9p21 non-coding coronary
artery disease risk interval in mice
Axel Visel1,2, Yiwen Zhu1, Dalit May1, Veena Afzal1, Elaine Gong1, Catia Attanasio1,
Matthew J. Blow1,2,
Jonathan C. Cohen3, Edward M. Rubin1,2 & Len A. Pennacchio1,2
Vol 464| 18 March 2010| doi:10.1038/nature08801
Variation in distant-acting regulatory sequences required for cardiovascular
expression of CDKN2A and CDKN2B provides a plausible mechanistic model for
the increased CAD risk associated with the 9p21 region independently
of lipid levels and other known risk factors.
IMPC Vision
PI Driven
IMPC (2011-21)
ARRA (2010-11)
EUMODIC (2008-11)
IKMC (2006-11)
The IKMC (EUCOMM, KOMP, NorCOMM and
TIGM) have produced over 9,000 KO ES cell lines
KOMP Customer orders by month
Late 2008 – early 2010
180
R2 = 0.6
Each order saves $20,000-50,000
KOMP is already saving more
money than it spends
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Curiosities and Biases
 Gateway® Entry Vectors - pENTR
 1 - 17 of 17 products displayed
 Product Name SKU # Product Size List Price (USD)
Qty K2520-02 20 preps $436.00
 AmpliTaq Gold® 360 DNA Polymerase, 250U
 Cat. No. 4398823 $250
 Why do some people think that $1,000 or $2,000
for a proven ES line or mouse is expensive?
The International Mouse Phenotyping Consortium
(IMPC) Steering Committee
The Wellcome Trust (Dr. Michael Dunn)
The Medical Research Council (Dr. Nathan Richardson)
The Wellcome Trust Sanger Center (Dr. Allan Bradley)
MRC Harwell (Dr. Steve Brown)
European Commission (OPEN)
German Mouse Clinic/InfraFrontiers (Dr. Martin Hrabe de
Angelis)
Toronto Centre for Phenogenomics (Dr. Colin McKerlie)
ICS (Strasbourg) (Dr. Yann Herault)
NIH: NHGRI (Dr. Eric Green) NDCD (Dr. James Battey)
Australia Phenomics Network (Adrienne McKenzie)
Other likely members:
The Jackson Labs China Italy (Monterotondo)
Czech Republic Japan
UAB (Barcelona) Korea?Taipai?
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
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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 10-12 worldwide.
 Phase I (2011-2016) 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 2016-2021 Completion of the
Genome
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
1a. Would the current tests reveal phenotypes that would
motivate you to shift your own resources and to take mice
and begin work on them in your lab?
NO
46%
YES
54%
2009 Mouse Pipeline Survey
If No, then why? Limited
Challenge
Models
(e.g.
infectious
agents)
Area not
covered
Funding
Tests
Superficial
and
Insensitive
2009 Mouse Pipeline Survey
2b. Specifics within Larger Fields
Imaging
Histology
Infectious challenge
Ig titers
Blood pressure
Blood chemistry
Flow cytometry
Organ weight
Psychotomimetic challenge
Balance tests
Gene expression
Diet perturbation
Plasma assays
Neonatal lethals
1' & 2' immunization with antigen + adjuvant
Gait analysis
Circadian profile
# of Suggestions
Blood gas analysis
0
2
4
6
8
10
12
14
2009 Mouse Pipeline Survey
Survey Summary Report
What is missing?
Circ/sleep
Diet challenge
Eye/retina
Behavior
CVS
Fertility
Auditory
Immune challenge
M/S soft
Urinalysis
Gene expression
Histopath
Learn/memory
Cancer
Embryogenesis
MMRC Survey Conducted by Kent Lloyd
>2000 e-mails and ~300 respondents
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).
immunity/infection/inflammation/arthritis/a…
diabetes/metabolism/mitochondrial/endocri…
behavior/neurology/sleep
histology/morphology
hematology/FACS/bleeding
embryonic…
blood chemistry/lipid levels
body composition/diet/growth…
reproduction/litter size/puberty
gene expression
bone density/bone morhology/bone strength
EKG/cardiac defects/cardiovascular…
cancer
proteomics/genotyping/gene…
retina/vision/ophthalmology
imaging/microCT
lacZ
hypertension
hearing
muscle
aging
GI
urinalysis
genotoxic sensitivity/radiation…
biochemistry/cell biology
respiratory
dermatology/hair
karyotype/stem cells
oral/teeth
olfactory
exercise
pharmacodynamics
renal function
vocalization
wound healing
secretory gland
function tests
thrombosis
immuno
behavior
174
205
181
metabolism
MMRC Survey Conducted by
Kent Lloyd
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
Cost Components: MLC, MRC, Harwell
Mouse Production & Archiving:
£21,690
Generation of mice from ES Cells Archiving the mouse line
Viability and Fertility testing Breeding of cohort of 8M & 8F mutants
Housing for phenotyping cohort (8M & 8F mutants & 4 WT controls)
Behaviour: £500
SHIRPA
Gene Expression: £1100
Open Field
Adult WM Embryo WM
Grip Strength
Metabolism: £1300 Rotarod
High Fat Diet
Haematology: £80
Challenge
RBC
IPGTT
WBC
DEXA
Platelet Counts
Weight Curve
etc
Calorimetry
Full Clinical
Immune: £1,060
Chemistry
FACS of PBL
IgG Levels
Total Cost: £27,580
Behavior/Sensory: £400
Hot Plate
PPI
Opthalmoscope
Slit lamp
Cardiovascular: £1100
Non invasive blood
pressure ECG
Echocardiograph
Heart Weights
Bones & Development: £350
Dysmorphology
Weight Curves
Faxitron
New Areas and Cost Challenges
Respiratory: £441
Plethysmograph Challenge
Aging: £18,617 New cohort
production and cage costs for 18 months
Embryology: ?????$$$$$$
Immunology Challenge
Infectious vs defined antigen
?????$$$$$$
IMPC Phenotyping
 Core group of tests at all centres
 Agreed upon minimum cohort size (7?)
 Test and recommend additions to or dropping phenotypic
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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
Production
Centers
ES to mouse
Production
Re-animation
(optional)
Archiving
(optional)
Primary
Phenotyping
Secondary
Phenotyping
Mouse
production
Archiving
Distribution
Secondary
Phenotyping
Informatics
 After meeting with groups from EUMODIC, the EBI,
the JAX and discussions with CASIMIR members,
the emerging picture is to have a stand-alone
database that will collect data from each centre and
provide a user interface to the outside world.
 There have been significant efforts made by
EuroPhenome and the Sanger groups to develop
these tools but there is not sufficient critical mass
in any one program to accomplish the level of
complexity, data volume and number of tasks that
will be required of the IMPC in the future.
Informatics Organization
IMPC Next Steps
Informatics
Mice
Tech Dev
• Form Steering Committee
• Develop Requirements Document
• Explore new ways to lower mouse costs
• Continue exploring commercial options
• Form Tech Development Group
• First Tasks: Imaging Recommendation (&Pathology)
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Embryonic Lethal Analysis
Phenotyping
• Develop final plan for IMPC Pipeline
• Operating plan for review of pipeline
Challenge Models
• Working groups in each area
• Devise how to test models at centers
IMPC Standing Committees
IT
• Chair
• Centre Reps
• Outside experts
QA&QC
• Rotating Chair
• Center Reps
• Outside experts
Finance
• InfraFrontiers
• Funders
• PIs
Animal
Assurance
Technology
Development
• Outside Chair
• Center Reps
• Outside experts
• Center Reps
• Outside experts
IMPC Cost Projections
IMPC Membership
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Funding Organizations
Mouse Clinics and Phenotyping Centres
Mouse Production Groups
Informatics Groups
Secondary Phenotyping Networks (e.g. APN)
Other genetic efforts
 ENU
 Collaborative Cross
 Cre Drivers?
 Open some mouse clinic work as fee for service for
investigator driven?
What Does $900M Buy
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1 new football stadium
2 Airbus 380s
1/3 of the Bay Bridge retrofit
1 new approved pharmaceutical entity (NCE)
Production and phenotyping of 20,000 gene KO lines
 In vivo functional annotation of a mammalian genome
 Transformative event for biologists
 Lower ongoing costs of obtaining mice
 Likely to identify hundreds of new drug targets
 Employ >450 researchers a year for 10 years (avg)
Next 3 years (2010-2013)
 EUMODIC project will come to completion
 UC, Davis has funding to support the creation and
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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 100-200 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
Acknowledgements
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The IMPC Steering Committee
Tom Weaver
Niels Adams
Ramiro Ramirez-Solis
Colin Fletcher
John Hancock
Bill Skarnes
Damian Smedley
Michael Hagn
Paul Schofield
Janan Eppig
Kent Lloyd
The IT group