What is IMPC?
IMPC MembersThe IMPC is currently composed of 17 research institutions and 5 national funders.
- Global infrastructure recognised by the G7
- Creating 20,000 knockout mouse strains on a single background strain
- Characterizing each through a standardized phenotyping protocol
- Integrating the data to existing mouse and human disease resources
- Providing Strains and phenotype data for use by the research community
What does IMPC do?
- Standardized allele production and phenotyping pipelines
- Quality control
- Statistical analysis
- Disease association
- Free data access and visualizationl
- Embryonic and adult data
- Human disease association
- ES cells and mouse ordering
How does IMPC work?
These two strategies have been shown to yield different targeting efficiencies (Skarnes et al., 2011).
- tm1a: KO first allele (reporter-tagged insertion allele): 0
- tm1b: Reporter-tagged deletion allele (post-Cre): 0
- tm1c: Conditional allele (post-Flp): 0
- tm1d: Deletion allele (post-Flp and Cre with no reporter): 0
- tm1e: targeted, non-conditional allele: 0
- tm1: Reporter-tagged deletion allele (with selection cassette): 0
- tm1.1: Reporter-tagged deletion allele (post Cre, with no selection cassette): 0
- tm1.2: Reporter-tagged deletion allele (post Flp, with no reporter and selection cassette): 0
IMPC alleles viable for high throughput pipieline
- (i) Small Deletions (single cut strategy)
- (ii) Exon Deletion / large Deletions (2 cut strategy)
Alleles on request
- (i) Loxp-flanked critical regions
- (ii) Point Mutations
- (iii) Conditional & lacZ reporter Allele - Insertion of dsVector
- NHEJ Alleles (small deletions):
- Large Deletion/ Exon deletion:
The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a mammalian genome.
The IMPC Steering Committee provides the governance for the overall consortium. Participants are tasked with making key strategic decisions including selection of participating organizations, approving and coordinating key operational decisions such as phenotyping platforms and pipeline used, quality assurance and operating standards, and IT organization. Membership provides stakeholders with an opportunity to influence key activities as they develop.
The Adult and Embryonic Phenotype Pipeline
The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. The pipeline is currently in development. The protocols in the core IMPC Pipeline are currently being developed by the IMPC phenotyping working groups and the current versions on this site are still under final review. The phenotyping working groups are working closely with the data wranglers to complete an agreed first version. Updates on the progress of this will be available through IMPReSS.You can click on the protocols below for more information.
Statistics to PhenotypeThe selection of the statistical method is an important step in the process of phenotype data analysis and is dependent on the experimental implementation, and the variable characteristics (e.g. continuous or categorical).
The statistical analysis was done using an R package developed for IMPC called PhenStat.
PhenStat is a statistical analysis tool suite developed based on known variation in experimental workflow and design of phenotyping pipelines (Kurbatova N et al, 2015).
More information about the way IMPC uses disease data.
Explore Disease Data
The ultimate goal of studying model organisms is to translate what is learned into useful knowledge about normal human biology and disease.
The IMPC disease details page contains known gene associations (via orthology to human disease genes) and known mouse models from the literature (from MGI) for the disease as well as predicted gene candidates and mouse models based on the phenotypic similarity of the disease clinical symptoms and the mouse phenotype annotations. The phenotypic similarity is calculated using the PhenoDigm algorithm (Phenotype comparisons for DIsease Genes and Models) developed by the Monarch Initiative which will allow integration of data from model organisms to identify data-supported gene candidates for human genetic diseases (Link to Methods). Mouse Genotype-Phenotype and Human disease resources are described below.
Disease details pages
Results are broken down in 2 parts, depending on the association methodology (by gene orthology or by phenotypic similarity).
Clicking the row for a disease/gene will expand the row to show the details of the phenotype terms involved in the association between the disease and the mouse model. The orange number next to the genotype is the PhenoDigm score (see below) which is a percentage-based score . These are ranked from highest to lowest in two groups. The first group will show the manually curated mouse models from MGI. The second group will list the purely phenodigm predicted associations.
Human disease resources
|OMIM (Online Mendelian Inheritance in Man)||An Online Catalog of Human Genes and Genetic Disorders|
|Orphanet||The portal for rare diseases and orphan drugs|
|DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resource)||Interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants|
Mouse Genotype-Phenotype resources
|IMPC (International Mouse Phenotyping Consortium)||Functional catalogue of mouse mammalian genome|
|MGI (Mouse Genome Informatics)||International database resource for the laboratory mouse|