Phenotyping Oxford

Information about Phenotyping Oxford

Published on October 17, 2007

Author: Belly

Source: authorstream.com

Content

Eumorphia Phenotype screens for mice Developing an integrated platform :  Eumorphia Phenotype screens for mice Developing an integrated platform Slide2:  EUMORPHIA - the consortium MRC Mammalian Genetics Unit, UK IGBMC, Strasbourg, France MRC Human Genetics Unit, UK MRC Functional Genetics, UK ANIMAGE, Lyon, France CNG/CNRS Paris, France GSF, Munich, Germany GBF, Braunschwieg, Germany NKI, Amsterdam, Netherlands EMBL Monterotondo, Italy CNR-IBC, Monterotondo, Italy Karolinska, Stockholm, Sweden UNIL-IBA, Lausanne, Switzerland UNIGE, Geneva, Switzerland Sanger Institute, Hinxton, UK CNIO, Madrid, Spain Univ. Manchester, UK 18 centres across Europe Importance of standardisation:  Importance of standardisation Better reproducibility of test outcome Better comparability of test outcome Sharing of phenome results Reduction in the number of mice used in research EUMORPHIA:  EUMORPHIA Phenotyping Working groups to develop and standardise primary and secondary phenotyping protocols for all body systems To develop them in collaboration with other centres throughout the world and in consultation with clinicians, human geneticists, physiologists and informaticians Slide5:  Phenotyping - Workpackages Standardisation - animal handling Clinical Chemistry/Haematology Renal systems Central, peripheral nervous system, muscle Behaviour and cognition Imaging Necropsy, pathology, histology First-line phenotyping Cardiovascular Hormonal/metabolic Allergy and infection Sensory systems Pulmonary Cancer Bone, Cartilage Expression analysis European Mouse Phenotyping Resource for Standardised Screens - EMPReSS What is EMPReSS?:  What is EMPReSS? European Mouse Phenotyping Resource for Standardised Screens The EMPReSS provides a platform for the systematic and standardised primary characterisation of mouse mutant models It is a comprehensive database of validated SOPs for systematic screens and tests that allows us to describe the phenotype of a mouse Slide7:  www.eumorphia.org How was EMPReSS constructed?:  How was EMPReSS constructed? The SOPs are categorised according to the experience required and the amount of specialised equipment. The primary tests are divided into: Primary - for those tests that are simple to apply and require little specialist equipment Primary extended - which give further information on the phenotype, but require more specialised skills or equipment. Slide9:  Working groups established SOPs discussed and drafted Validation between centres Discussion of validation results Revision of SOPs Revalidation between centres Additional validation between centres Review of SOPs by EMPReSS resource team Review and sign-off by Eumorphia scientist outside working group Slide10:  BALB/cByJ (+ BALB/cAnN) AnN ENU mutagenesis at Harwell C57BL/6J (+ C57BL/6N) C3H/HeBFeJ (+ C3H/HeN) FeJ ENU mutagenesis at GSF/HeN at Harwell 129/SvPas (+ 129S6/SvEvTac) Inbred strains for validation EMPReSS to date:  EMPReSS to date WP groups established March 2003 All relevant WPs have contributed A total of 161 SOPs, both primary and primary extended, have been submitted and accepted by EMPReSS along with annexes Validation of the SOPs:  Validation of the SOPs The SOPs are subjected to evaluation by one or a number of the partners. The validation levels are given at the top of each SOP Validation by testing on selected inbred mouse strains and/or selected mutants at one EUMORPHIA laboratory Validation by testing on selected inbred mouse strains and/or selected mutants at two EUMORPHIA laboratories Full comparison of results of testing on selected inbred mouse strains and/or selected mutants at more than two EUMORPHIA laboratories 35% 44% 21% Slide13:  0 20 40 60 80 100 CNR GSF 0 20 40 60 80 100 0 20 40 60 80 100 MRC ICS 0 20 40 60 80 100 C57BL/6 C3HeH BALB/c 129/Sv Global % PPI 0 5 10 15 20 25 30 35 0 5 10 15 20 25 30 35 0 5 10 15 20 25 30 35 40 0 3 6 9 12 15 Open field % Centre Time 1st round validation results Audition and Balance:  Audition and Balance Close collaboration between workpackages: 8 Sensory systems 9 Central/peripheral nervous and skeletal muscle systems 10 Behaviour and cognition for cross lab validation, integration and ordering of the tests that cover hearing and balance. These include the modified SHIRPA, acoustic startle response, Pre-pulse Inhibition tests and the swim ability test. Open-field Modified SHIRPA Grip strength Y maze ASR & PPI Swim ability Rotarod Integrating and ordering tests in different systems - neurobehaviour and sensory:  Integrating and ordering tests in different systems - neurobehaviour and sensory EUMORPHIA:  EUMORPHIA Mutagenesis Phenotyping Informatics Networking and Training Slide17:  www.eumorphia.org EMPReSS Database:  EMPReSS Database SOPs engineered for XML format Links between SOPs and baseline phenome data - EuroPhenome database assisting validation, EMPReSS evaluation and SOP development EMPReSS will allow systematic integration of the ASSAY with phenotype ontologies EUMORPHIA Phenotype Ontologies:  EUMORPHIA Phenotype Ontologies Informatics We need to develop systematic and comprehensive systems to describing phenotypes - phenotype ontologies Phenotype ontologies will be central to the development and mining of comprehensive animal phenotype databases Integration with SOPs - the assay is central to the development of ontologies Developing ontologies - the centrality of the assay:  Developing ontologies - the centrality of the assay CONCEPT {has_attribute} ATTRIBUTE {characterised_by} ASSAY {has_value} VALUE e.g. Eye {has_attribute} Colour {characterised_by} Visual Inspection {has_value} Brown or Mouse {has_attribute} Body Position {characterised_by} SHIRPA {has_value} Flat All phenotypes are the result of an assay Building international standards:  Building international standards Examine with our partners EMPReSS as a model to develop an international repository for SOPs and baseline data Discussions with developers, managers and users of other related resources worldwide October 2005 Beyond Eumorphia:  Beyond Eumorphia Primary Phenotyping EMPReSSslim Secondary Phenotyping Mouse lines EUCOMM Community Databases Mouse clinics GSF, Munich ICS, Strasbourg MRC, Harwell Sanger, Hinxton Specialist Centres Development of new technologies Bioinformatics Statistical analysis Refinement of SOPs Additional validation Slide28:  M Dysmorphology / Blood / Metabolism Bone Allergy / Immune Cardio Sensory / Behaviour 10 weeks 14 weeks FACS analysis of peripheral blood cells Immunoglobin concentration Dysmorphology 8 weeks Clinical Chemistry X ray DEXA 12 weeks 8 weeks Opthalmoscope & Slit Lamp Acoustic Startle Tail flick Open field Modified SHIRPA Elevated Platform Grip Strength Y-maze 9 weeks 10 weeks Tail suspension Swim Ability Simplified IPGTT 13 weeks 14 weeks Non-invasive Blood Pressure Echo Cardiography ANP 9 weeks Calorimetry 10 12 weeks 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 5 5 10 10 10 10 3 3 Haematology Repeat Chemistry 10 10 Number of males Number of females EMPReSSslim Beyond Eumorphia :  Beyond Eumorphia Primary Phenotyping EMPReSSslim Secondary Phenotyping 500? mouse lines EUCOMM Community Databases Specialist Centres Development of new technologies Bioinformatics Statistical analysis Refinement of SOPs Additional validation Mouse clinics GSF, Munich ICS, Strasbourg MRC, Harwell Sanger, Hinxton Summary:  Summary EMPReSS allows standardisation of primary mouse screening platforms across Europe ensuring reproducibility and comparability of functional genomics research Baseline phenome data provided through validation and SOP development will underpin mouse genetics studies Enhances efforts towards the refinement and reduction of animal use Slide31:  EUMORPHIA - the consortium MRC Mammalian Genetics Unit, UK IGBMC, Strasbourg, France MRC Human Genetics Unit, UK MRC Functional Genetics, UK ANIMAGE, Lyon, France CNG/CNRS Paris, France GSF, Munich, Germany GBF, Braunschwieg, Germany NKI, Amsterdam, Netherlands EMBL Monterotondo, Italy CNR-IBC, Monterotondo, Italy Karolinska, Stockholm, Sweden UNIL-IBA, Lausanne, Switzerland UNIGE, Geneva, Switzerland Sanger Institute, Hinxton, UK CNIO, Madrid, Spain Univ. Manchester, UK 18 centres across Europe

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