1. Use of mice in biomedical research2. KOMP: Activity and progress to date3. Rationale and planning for phenotyping4. Request for continued support

Presentation Overview

Mice in Biomedical Research• The laboratory mouse has been considered the premiere experimental model of human biology and

disease since 1902 when it was first used to demonstrate how genetic traits could be transferred from parents to offspring via classical or “Mendelian” inheritance in mammals.

• In just over a century, an impressive array of genetic tools, reagents and processes has been developed in the mouse, including:

– Homozygous inbred strains– Recombinant inbred and consomic strains– Transgenic and knockout methods– Monoclonal antibodies– iPS cells

• Evidence that mice have played a key role in biomedical research is provided by the fact that at least 18 Nobel prizes have been awarded for work done using the mouse. Most recently, the 2007 Nobel Prize was awarded to Mario Capecchi, Martin Evans, and Oliver Smithies for their discovery of the "principles for introducing specific gene modifications in mice by the use of embryonic stem (ES) cells.”

The Premiere Model Organism

Janan Eppig, Jax

KOMP Vision

KOMP (2006-11)

ARRA (2010-11)

KOMP2 (2011-21)

R01s

Austin et al., Nature Genetics, 2004

Funded KOMP ProjectsThe Completion of a Comprehensive Mouse Knockout Resource

($47 M - 5 years - funded 9/06)

CHORI-Sanger-UC DavisRegeneron Pharmaceuticals, Inc.

Development and Improvement of Inbred ES Cell Lines for Use in Generation of Mouse Mutants($1.9 M - 2 years - funded 9/06)

U PennsylvaniaSamuel Lunenfeld Research Institute

A Data Coordination Center for the Knockout Mouse Project (KOMP)($2.5M - 5 years - funded 9/06)

The Jackson Lab

The KOMP Repository($4.8M - 4 years - funded 8/07)

UC Davis – CHORI

Goals and Progress

CSD Regeneron EuCOMM NorCOMM TIGM Total

Goal (ES) 5,000 3,500 8,000 500 17,000

Vectors 4991 3116 4271 596

Targeted ES 3064 2038 2883 236 8,221

Mice 189 160 351 12 700

The KOMP Website

www.knockoutmouse.org

Target List

The KOMP Website

www.knockoutmouse.org

Details

Complete information on allele design, vector, genotyping and sequencing primers are provided to the end-user.

The KOMP Repository

www.komp.org

The repository offers vectors, KO ES cells, parental ES lines, and support services. Orders are processed using a standard “shopping cart.”

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WT-orderedmice-orderedcryo-recovery-orderedgermplasm-orderedGLT-orderedmicroinj-orderedpremium-ESC-pckg-orderedESC-ordered

KOMP Repository Activities

Orders have recently increased to about 100/month.

Over 3,000 users have created accounts and registered interest in ~2,500 genes.

Kent Lloyd, UCDavis

Rationale for KOMP2

• Supporting a broad phenotyping effort would provide the following advantages: – A single cohort of mice would go through multiple phenotyping assays, so the

cost of producing multiple cohorts in different laboratories for phenotyping would be eliminated.

– Each mutant mouse strain would be characterized for a broad set of phenotypes in a way that will allow direct comparisons and result in a more thorough description of gene function.

– Quality standards will be established and maintained, so the data will be of the highest reliability.

– The risk of not finding a phenotype will be greatly reduced.– Important, but unpublishable, negative results will be captured.

• 3 workshops: Rome in 2007, Bar Harbor and Toronto in 2008 to establish vision for an IMPC & discuss international, coordinated phenotyping efforts – agreed that the way forward is to develop a business plan

• Medical Research Council/Wellcome Trust workshops in Nov 2008 and Oct 2009 to engage UK scientific community

• NIH Phenotyping meeting, Bethesda October 2009 (survey)

• EC–funded EUMODIC (Helmholtz, Munich; ICS, Strasbourg, MRC Harwell, WTSI) project is now doing broad-based phenotyping of 500 mutant lines – completion 2011

Planning for next phase: Phenotyping

The International Mouse Phenotyping ConsortiumMembers:The Wellcome TrustThe Medical Research CouncilThe Wellcome Trust Sanger CenterMRC HarwellEuropean CommissionThe National Institutes of HealthGerman Mouse ClinicToronto Center for Phenogenomics

Pending members:Australia Phenomics NetworkCzech RepublicInstitut Clinique de la SourisNanjing UniversityUniversitat Autonoma de Barcelona

Current funding:EuMODIC - $7M/yr + matching funds, 150 strainsSanger Mouse Genetics Program - $9M/yr, 200 strainsAustralia Phenomics Network - $10.5M/yr

EMPReSSslim Primary Phenotyping Pipelines

Steve Brown, Harwell, MRC

Phenotyping of KOMP CSD mice at Sanger

http://www.sanger.ac.uk/mouseportal/

Reproduction• Fertility

Developmental Biology• Viability

• Embryonic lacZ pattern• Viability at E14.5

• MRI at E14.5

Neurology• SHIRPA assessment

• Hot plate (pain)• Open field (anxiety)

• Stress-induced hyperthermia

• Brain anatomy

Musculo-skeletal• Grip strength

• X-rays (skeleton)• Bone mineral density• Bone mineral content

Infectious disease susceptibility• Salmonella (bacterial)• Citrobacter (bacterial)• Plasmodium (malaria)

• Flu (viral)

Metabolism• Weight gain curve

• Food intake and energy expenditure)

• Fat/lean tissue assessment by DEXA• Glucose tolerance test

• Serum Insulin• Blood Clinical Chemistry

Senses• Slit lamp (front of the eye)

• Eye fundus (retina)• Auditory brain response (hearing

circuits)

Immune system• Complete blood count• White blood cell profile

• Immunoglobulin subclass profile

Cardiovascular• Blood clinical Chemistry

• Heart weight (hypertrophy)• Heart histology

• Eye fundus (retinal vessels)

Cancer• Micronuclei analysis

Hair and skin• Hair growth rate• Hair follicle stem

cell

General • Visible malformations

• Adult organ lacZ expression• Necropsy

• Tissue banking for histology

Ramiro Ramirez-Solis, WTSI

Genentech/Lexicon Mouse Phenotype Project472 Mouse knockouts were broadly phenotyped

130 (27%) strains had 1 phenotype245 (52%) strains had 2-5 phenotypes

Andy Peterson, Genentech

Cohort breedingPhenotypingData UploadCohort breeding

PhenotypingData Upload

KOMP Repository

Mouse Production

ES cells

Mice/Embryos

DatabaseWeb server

Data

Data

Mouse Phenotyping Center(s)

Mice/Embryos

KOMP ES cells

EuCOMM ES cells

Mice/Embryos

MicroinjectionGermline TransmissionLacZ stainingLethality/FertilityCryopreservation

TrackingAnalysisDisplay

Cohort breedingPhenotypingData Upload

KOMP Phenotyping Scheme