Mouse Models and Resources

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Mouse Models and Resources
Richard Woychik, Ph.D. The Jackson
Laboratory Muriel Davisson, Ph.D. Janan Eppig,
Ph.D
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In 1958 all the known genes of the mouse could be
displayed on a single display board by mutant
mice -
Congress of Genetics, Toronto, 1958
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Types of Mouse Strains Available

• Inbred Strains
• Hundreds world-wide
• 40 as part of the Phenome Panel
• Special Inbreds
• Wild-derived Inbreds
• Recombinant Inbreds
• Congenic Inbreds
• Consomic inbred
• Recombinant congenics

• Mutant Strains
• Trangenic/Targeted mutations
• Insertional mutations (e.g. gene traps)
• Agent induced mutations (e.g. ENU, radiation)
• Chromosome aberrations
• Spontaneous mutations

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Mouse Resources Available
Mice/frozen embryos The Jackson Laboratory gt3000
strains MMRRC (USA) 1000 strains EMMA
(Europe) 3700 strains Japan 2200 (Riken.
Kumamoto) Individual investigators
5-6000 GenSat transgenics Deltagen and Lexicon
purchase 251 KO strains Mutant ES cells Bay
Genomics 2000 Lexicon - Omnibank 100,000s Regen
eron 500-1,000 Riken Gen Sci Ctr 50,000
ENU-mutated genomes US Europe 1000s of
ENU-mutated genomes as sperm
Muriel Davisson and colleagues
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Expected New ES cells and mouse strains
NIH KOMP 25,000 knockout ES
cells/mice EUCOMM 12,000 gene
traps 8000 targeted mutations 300
turned into mice NORCOMM 12,000 gene
trap 1000 targeted
mutations Sanger Center 15,000 TIGM
25,000 International Gene Trap
Consortium (IGTC) 100,000 over 5 years
If 10-20 made into mice, gt4000-5000 strains
Muriel Davisson and colleagues
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Other Mouse Resources
NIH Transcriptome Project cDNA libraries BAC,
PAC, YAC libraries JAX Backcross mapping
panels Services Pathology Phenotyping Cryopreser
vation - speed cryo. Rederivation Rapid colony
expansion Custom breeding Colony management
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Realization of the full power of the mouse
depends on facilitating seamless exchange of
resources, and making integrated genetic,
genomic, and phenotypic information available to
promote knowledge discovery.
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Mouse Genome Informatics (MGI) Consortium

• Janan Eppig, Ph.D.
• Carol Bult, Ph.D.
• Judy Blake, Ph.D.
• Martin Ringwald, Ph.D.
• Jim Kadin, Ph.D.
• Joel Richardson, Ph.D.

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For the laboratory mouse, the Mouse Genome
Informatics (MGI) provides

• the recognized international community database
  resource for mouse
• an integrated view of genomic biological data
• the definitive reference data sets for mouse
  genomic and biological information
• a structured, integrated database for gathering,
  managing, analyzing and accessing these data

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Achondroplasia
MGI GOAL to facilitate use of mouse as a model
for human biology and disease.
Homozygous mutant and control

• short domed skull
• short-limbed dwarfism
• malocclusion
• bulging abdomen as adults
• respiratory problems
• shorted lifespan

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Data Integration is a primary MGI activity
Data
Gather data from multiple sources
Sets
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Factor out common objects identify new objects
Integrated
Assemble integrated objects
Database
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Integrated views reveal data relationships not
evident in the original source data.
Knowledge
Discovery
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Mouse Genome Informatics Database

• Sequences Maps
• sequence representation
• C57BL/6J genomic sequence
• SNPs and strain variants
• adding biological context to computational gene
  models

• Genes Gene Products
• nomenclature
• gene characterization
• transcripts, proteins, gene products
• functional annotation
• orthologs paralogs

• Phenotype
• mutant allele definitions
• QTL
• strain characteristics
• phenotype vocabularies
• disease models (human)
• comparative phenotypes

• Gene Expression
• mouse anatomy
• time, tissue, level of expression
• range of assays results
• emphasis on embryonic stages

• Tumor Biology
• tumor classifications descriptions
• strain incidence
• histopathology images
• tumor genetics

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Data Access

• web browser http//www.informatics.jax.org
• search for and retrieve data
• interactively explore details
• generate map views
• download data sets
• programmers
• instructions for making connections to MGI
• ftp site for daily database public reports
• schema browser to formulate SQL queries

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MGI Homepage
www.informatics.jax.org
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Gene-Central
Nomenclature
Mapping
Orthologs
Sequence
Phenotype
Gene Ontology
Expression
Links
Protein domain
Clones/probes
References
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For mouse, MGI is the authoritative source for
strain, gene, and allele nomenclature
functional annotations (Gene Ontology)
gene-to-sequence associations for nucleotide and
protein sequences Mammalian Phenotype
Ontology genotype-to-phenotype and
genotype-to-human disease associations
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A few MGI stats (Feb. 2006)
30,942 gene records (w/ sequence 27,868) 17,083
annotated to GO 15,679 mouse/human
orthologs 14,828 mouse/rat orthologs 99,810
references gt15,200 established phenotypic
alleles representing gt6,450 unique
genes 5,837 QTL phenotype records
representing 2,821 QTLs gt9,300,000 number of
mouse nucleotide sequences
integrated in MGI
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MGI providesconsensus/meta data views and data
detail.the ability to ask complex questions
that simultaneously address area of sequences,
genes, mutations, phenotypes, expression, and
function.
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Example consensus/meta data
Mouse Tumor Frequency Grid

• Strain x tissue
• Cells color coded according to tumor frequency
• Clicking on a cell queries database for
  underlying data

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Example complex query

• Give me a data set of RefSeq RNA sequences for
  all genes in mouse that have been annotated as
  kinases, are expressed in the heart, and have
  mutant alleles associated with heart or
  cardiovascular system phenotypes. Restrict to
  sequences from the C57BL/6J strain.

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download or BLAST
link to sequence
link to gene
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Asking questions of the MGI integrated resource

• What genes are within 10kb of a mouse STS and
  have known human and rat homologs?
• For all genes involved in cell adhesion on
  Chromosome 2, produce a FASTA sequence file for
  analysis.
• What markers of type Gene on Chromosome 11
  between 41 and 98Mb, have a function of ion
  channel activity and mutant alleles that have
  behavioral or neurological defects?
• What are the mouse models for human osteopetrosis
  that include abnormalities in tooth morphology
  and where the mutation arose spontaneously?
• What genes with transcription factor activity are
  expressed at 15 days of embryonic development in
  the somites?

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Some resources that use MGI curated data

• NCBI EntrezGene
• Ensembl
• UCSC
• GO (Gene Ontology) Consortium
• Gene-Cards
• Other species-specific databases
• (for gene symbols/names, mapping, homologies)
• UniGene
• SwissProt
• Genome Topographer
• The Dysmorphic Human-Mouse Homology Database
• Many others indirectly (via NCBI)
• Several Pharmas (for their internal use)

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Mouse Phenome Project

• International community effort
• Characterize the genetic/phenotypic variability
  inbred laboratory mouse strains
• Phenotype data assembled into a data base (MPD)
• Coordinated by Molly Bogue at JAX oversight by
  Carol Bult

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Inbred Strains in the Mouse Phenome Project
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Serum cholesterol levels after 7 weeks on
high-fat diet
Bev Paigen, TJL
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Diversity among inbred strainsCholesterol
Non- HDL-C
HDL-C
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Diversity among inbred strainsBlood parameters
WBC
Hct ()
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Mouse Phenome Project www.jax.org/phenome

• Large variety of phenotypes
• High density SNP discovery (Wiltshire et al.,
  Novartis Institute, Mural et al., Celera
  Genomics)
• NIEHS sponsored re-sequencing of 15 of the
  phenome strains
• Phenotypic diversity At least as great as that
  which exists in the human population

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International Mouse Strain Resources
Goal find my mouse a global catalog of
mouse resources

• Where are the mouse resources I need?
• In what state are they maintained?
• How can I find more information about a mouse
  strain or
• cell line?
• How can I find more information about the
  mutations and
• alleles carried by a strain and their
  phenotypes?
• How can I contact the holder to obtain this
  mouse resource?

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IMSR Homepage www.imsr.org
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IMSR Search
Search by strain name, ID, state, and strain type
Search by gene or allele and type of mutation
carried
Search by repository or geographic region
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Result of a search for strains carrying mutant
alleles of the Scna8a gene
Find phenotypic information about mutants/alleles
Find strain information from Holder
Contact a Resource Holder
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Phenotypic allele detail page in MGI for Scn8a6J
Link to IMSR to find strains carrying this allele
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IMSR Currently 20 Repositories
Abbrev. Resource Centers/Consortia
APF Australian Phenomics
Facility CARD Center for Animal Resources
and Development CMMR Canadian Mouse
Mutant Repository EMMA European Mouse
Mutant Archive EMS E.M. Simpson Lab,
University of British Columbia HAR
MRC, Mammalian Genetics Unit, Harwell JAX
The Jackson Laboratory MMHCC Mouse Models of
Human Cancer Consortium MMRRC Mutant Mouse
Regional Resource Center NMICE
Neuromice.org ORNL
Oak Ridge National Laboratory
RBRC RIKEN BioResource Center
TOTAL 17,491 Mice 6,846 ES cell
lines 10,645 (BayGenomics)
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Addressing the Increasing Number of Mouse Lines
Ideal Solution

• A rapid, efficient, proven, reliable and cost
  effective means of removal/ recovery of a line of
  mice from the shelf
• Something modeled on freezing cells for tissue
  culture
• Only lines that are being used for experiments
  are on the shelf
• Eliminates genetic drift
• Long-term storage
• Inexpensive
• Highly reliable as a backup for disasters
• Rapid clean-up to eliminate deleterious agents
  (microbes, viruses, etc.)
• Easy shipment and importation
• Simple importation without
• Crossing international borders

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Embryo Cryopreservation

• Meets many of the requirements
• Reliable long-term storageapproach has been
  around for over 30 years
• Eliminates genetic drift
• Rapid clean-up
• Shipment of embryos can be handled by most
  investigatorsmost institutions have an embryo
  transfer laboratory
• Rapid, efficient and cost-effective.

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Speed Cryo


Single Male
Wild-type female oocytes
Embryos
Hundreds of embryos ready for cryo after
overnight incubation
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Speed Cryo

• Rapid
• Overnight incubation produces hundreds/thousands
  of embryos
• Cost effective
• No expansion of the line eliminates the cage
  costs associated with line expansion
• Efficient
• One protocol fits all samples
• Less technician time to collect embryos
• Amenable to high throughput
• Protocol cleans up the line
• Eliminates most unwanted bacteria, viruses, etc.

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Colony Expansion Through Embryo Transfer
100s Embryos Transferred
100s Age-matched males and females born
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Federation of International Mouse Resources
(FIMRe)
FIMRe homepage
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FIMRe Coordinating Mouse Resources

• Affiliation of 17 major international mouse
  resource centers in North America, Europe, Asia
  and Australia
• To coordinate archiving and distribution of mouse
  strains as cryopreserved embryos and gametes, ES
  cell lines, and live breeding stock

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FIMRe Members
North America (8) The Jackson Laboratory,
Maine Mouse Mutant Regional Resource Centers
(MMRRC) University of California,
Davis University of North Carolina University
of Missouri/Harlan Mouse Models Human Cancer
Consortium (MMHCC) American Type Culture
Collection (ATCC) Canadian Mouse Mutant Resource,
Toronto (CMMR) Canadian Mutagenesis Consortium
Australia (1) Australian Phenomics Facility,
Canberra
Europe (6) European Mouse Mutant Archive - EMMA
GSF Institute of Experimental Genetics,
Germany CNR Istituto di Biologia Cellulare,
Montoretondo, Italy CNRS Institut de
Transgenose, Orleans, France MRC Mammalian
Genetics Unit, Harwell, UK Karolinska
Institutet, Stockholm, Sweden Instituto
Gulbenkian de Ciencia, Oeiras, Portugal Japan
(2) RIKEN BioResource Experimental Animal
Center, Tsukuba Center for Animal Resources and
Development, Kumamoto
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Mission
To cooperate among mouse resource centers
providing mouse resources to scientists world
wide ensuring availability assuring
quality promoting preservation of
genetically defined mice To disseminate
information, affiliated resources, and expertise
in their use to the global biomedical research
community