An International Centre for Mouse Genetics MINING PHENOTYPE DATABASES TO IDENTIFY MOUSE MODELS OF...
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An International Centre for Mouse Genetics MINING PHENOTYPE DATABASES TO IDENTIFY MOUSE MODELS OF CLINICAL RELEVANCE Michelle Simon and Ann-Marie Mallon
An International Centre for Mouse Genetics MINING PHENOTYPE
DATABASES TO IDENTIFY MOUSE MODELS OF CLINICAL RELEVANCE Michelle
Simon and Ann-Marie Mallon
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An International Centre for Mouse Genetics Introduction
Introduction EUMODIC EuroPhenome
(www.europhenome.org)www.europhenome.org EMPRESS (European Mouse
Phenotyping Resource of Standardised Screens) ) Data capture
procedure. Data display / Website. Other phenotyping portals Sanger
mouse portal, K312 Portal IMPC Overview of IMPC MPI2 Consortium
Informatics Plans Worked Example. Tasks.
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An International Centre for Mouse Genetics INTRODUCTION -
EUMODIC EUMODIC Pilot project to phenotype 500 mouse mutants using
standardised pipelines called EMPReSSlim (battery of simple tests
to detect defects in as many body systems as possible) e.g. SHIRPA,
Clinical Chemistry etc Actual phenotype measurements are
captured
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An International Centre for Mouse Genetics INTRODUCTION EUMODIC
(II) Partners MRC Harwell UK Institut Clinique de la Souris France
Helmholtz Zentrum Mnchen Germany The Wellcome Trust Sanger
Institute UK CMHD, Canada Each clinic has its own version of the
phenotyping pipelines EuroPhenome (www.europhenome.org) Raw and
automatically annotated phenotype data from high throughput
projects such as EUMODIC
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An International Centre for Mouse Genetics EuroPhenome Data
Capture SOPs DefinitionDefining data StandardsData Capture in
LIMSData Export to Centralised DBValidation and QC
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An International Centre for Mouse Genetics EMPRESS (EUROPEAN
MOUSE PHENOTYPING RESOURCE OF STANDARDISED SCREENS)
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An International Centre for Mouse Genetics EMPRESS Experimental
Procedures designed by Scientists Standard operating procedures
(SOPs). SOPs stored in EMPReSS RDBMS Standardised Mouse Phenotyping
(across centres and consortiums) Defined measured parameters with
bounds Defined derived parameters Environmental and other Metadata
recorded Ontology Annotation (Mammalian Phenotype and Entity
Quality PATO approaches)
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An International Centre for Mouse Genetics EMPRESS
http://empress.har.mrc.ac.uk/ Comprehensive database of
standardised phenotyping protocols. Search procedures
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An International Centre for Mouse Genetics EMPRESS Four
different phenotyping pipelines Procedures
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An International Centre for Mouse Genetics EMPReSS Unique
Empress Identifier Different Parameters Measurement types and
increments Ontology Annotation - Mammalian Phenotype
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An International Centre for Mouse Genetics EMPReSS SLIM,
Primary Phenotyping Screen 21 different procedures
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An International Centre for Mouse Genetics Phenotype Data
Capture Automatic data annotation of significant phenodeviants with
MP ontology terms
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An International Centre for Mouse Genetics EuroPhenome Data
Annotation Model Mutant Cohort Data for 1 parameter or derived
parameter Compared to the control cohort or running baseline
control Statistical Analysis (Mann U Whitney/T-test or Fishers
Exact) Mean, SD, SE and P value calculated If P value is
significant annotate with MP term from EMPReSS which is assigned to
that parameter Stored in Annotation Database
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An International Centre for Mouse Genetics EUROPHENOME
STATISTICS Number of Lines
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An International Centre for Mouse Genetics Data in Europhenome
502Lines 2,505 30,276 Mice
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An International Centre for Mouse Genetics Number of Lines with
significant annotations by Procedure
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An International Centre for Mouse Genetics EUROPHENOME (Gene
Search)
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An International Centre for Mouse Genetics
www.europhenome.org
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An International Centre for Mouse Genetics
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PHENOTYPE SEARCH
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An International Centre for Mouse Genetics
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PHENOMAP
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An International Centre for Mouse Genetics
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XRAYS
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An International Centre for Mouse Genetics
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SANGER MOUSE PORTAL
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An International Centre for Mouse Genetics
http://www.sanger.ac.uk/mouseportal
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An International Centre for Mouse Genetics
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International Mouse Phenotyping Consortium (IMPC)
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An International Centre for Mouse Genetics IMPC 22 Academic,
Government Institutes MRC Harwell (Steve Brown, current Chair
Steering Comm.; Tom Weaver) Sanger Institute (Allan Bradley, Dave
Adams, Karen Kennedy) NIH KOMP2 BASH, Baylor (Monica Justice) DTCC
(UC Davis (Kent Lloyd), TCP, Charles River, Childrens Hospital
Oakland RI) Jackson Lab (Karen Svenson) Toronto Centre for
Phenogenomics (Colin McKerlie) Helmholtz Zentrum Munich (Martin
Hrabe de Angelis) Institut Clinique de la Souris (Yann Herault)
Australian Phenomics Network (Adrienne McKenzie) RIKEN BioResource
Center (Yuichi Obata) MARC (Xiang Gao) CNR (Glauco Toccinni
Valentini) EBI (Paul Flicek) Secretariat (Mark Moore, Executive
Director; Joerg Rossbacher) FUNDERS MRC (Nathan Richardson, Clare
Newland) NIH (Jane Peterson, Eric Green, Jim Battey, Colin
Fletcher, Martin Guyer) Wellcome Trust (Michael Dunn, Clare
McVicker) Infrafrontier (Martin Hrabe de Angelis) Genome Canada
(Cindy Bell) European Commission (Observer status) Canadian
Institutes of Health Research, CIHR (Jane Aubin)
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An International Centre for Mouse Genetics What is IMPReSS?
IMPReSS: International Mouse Phenotyping Resource of Standardised
Screens Launched Tue 13 th March 2012 The successor of EMPReSS -
Inherits historical Pipelines, adds IMPC Pipeline New architecture,
new site, plus some more features
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An International Centre for Mouse Genetics IMPReSS IMPC
Pipeline Adult pipeline agree and embryonic pipeline in
development
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An International Centre for Mouse Genetics Key Concepts: 3Ps
Pipeline Procedure MeasuredParameter MetadataParameter *:* 3Ps have
unique identifiers, Keys, e.g: IMPC_001_001_005_001 contains
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An International Centre for Mouse Genetics Ontology
Associations Structured, controlled vocabulary used worldwide by
scientists to describe phenotypes and beyond Various Collections
but MP is popular Predefined option choices for high throughput
ontology annotation Procedure: Open Field Measured Parameter:
Distance Travelled MP:0001399 - Hyperactivity MP:0001402 -
Hypoactivity MP:0003313 - Abnormal locomotor activation Can compare
baselines against mutants by ontologies associated with the mice to
identify phenotypes and variations and can also QC submitted
data
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An International Centre for Mouse Genetics Homepage
http://www.mousephenotype.org/impress
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An International Centre for Mouse Genetics
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MPI2 ComponentOwnerPartners Project Management, Reporting and
Community Outreach EBIHarwell/Sanger Tracking DatabaseSangerHarwell
SOP and Pheno-DCCHarwellSanger Annotation
PipelinesHarwellSanger/EBI Central Data ArchiveEBISanger/Harwell
Web PortalEBISanger/Harwell
Slide 60
An International Centre for Mouse Genetics New Homepage for
IMPC Portal http://www.mousephenotype.org/
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An International Centre for Mouse Genetics Basic Search
Functionality added Displays subset of iMITS data Many planned
improvements ahead download entire gene list register for gene of
interest will link to IMPC phenotype data as available