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Eumorphia Phenotype screens for mice Developing an integrated platform

Eumorphia Phenotype screens for mice Developing an integrated platform. 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

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Eumorphia Phenotype screens for mice Developing an integrated platform

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  1. EumorphiaPhenotype screens for miceDeveloping an integrated platform

  2. 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

  3. 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

  4. EUMORPHIA Phenotyping European Union Mouse Genetics Research for Public Health And Industrial Applications • 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

  5. 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

  6. 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

  7. www.eumorphia.org

  8. 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.

  9. Working groups established SOPs discussed and drafted Validation between centres Discussion of validation results Revision of SOPs Revalidation between centres Review of SOPs by EMPReSS resource team Additional validation between centres Review and sign-off by Eumorphia scientist outside working group

  10. Inbred strains for validation • 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)

  11. 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

  12. 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%

  13. Global % PPI Open field % Centre Time 35 100 30 80 25 60 20 CNR 40 15 10 20 5 0 0 C57BL/6 100 35 80 30 25 60 GSF 20 40 C3HeH 15 10 20 5 0 0 BALB/c 100 40 35 80 30 129/Sv 60 25 MRC 20 40 15 20 10 5 0 0 15 100 80 12 60 9 ICS 40 6 20 3 0 0 1st round validation results

  14. (week 8) (week 8) (week 8) (week 8) (week 9) (week 9) (week 10) 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 Rotarod Y maze ASR & PPI Swim ability

  15. Integrating and ordering tests in different systems - neurobehaviour and sensory Open field (week 8) I Modified SHIRPA (week 8) I Grip strength (week 8) | Rotarod (week 8) I Y maze (week 9) I PPI and ASR (week 9) I Tail Flick (week 9) | Tail Suspension (week 10) | Swim Test (week 10)

  16. EUMORPHIA Phenotyping European Union Mouse Genetics Research for Public Health And Industrial Applications Mutagenesis Informatics Networking and Training

  17. www.eumorphia.org

  18. 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

  19. EUMORPHIAPhenotype 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 An ontology is an explicit formal specification of the terms in a domain (concepts) and the relationships (attributes) amongst them

  20. 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

  21. 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

  22. Beyond Eumorphia EUCOMM Primary Phenotyping EMPReSSslim Mouse lines Mouse clinics GSF, Munich ICS, Strasbourg MRC, Harwell Sanger, Hinxton Refinement of SOPs Additional validation Development of new technologies Secondary Phenotyping Specialist Centres Bioinformatics Statistical analysis Community Databases

  23. M 14 weeks 8 weeks 9 weeks 10 weeks 12 weeks Clinical Chemistry Dysmorphology Simplified IPGTT Calorimetry Dysmorphology / Blood / Metabolism 10 10 10 10 10 10 Haematology Repeat Chemistry 10 10 10 10 Pipeline 1 X ray Bone DEXA 10 10 3 3 FACS analysis of peripheral blood cells Allergy / Immune 10 10 EMPReSSslim Immunoglobin concentration 10 10 13 weeks 14 weeks Echo Cardiography ANP Non-invasive Blood Pressure Cardio 10 10 10 10 10 10 8 weeks Open field Pipeline 2 10 10 9 weeks Acoustic Startle Modified SHIRPA 10 10 Sensory /Behaviour 10 weeks 10 10 Grip Strength Tail suspension Tail flick 10 Number of males 10 10 10 10 10 10 12 weeks Y-maze Number of females 10 Opthalmoscope & Slit Lamp Swim Ability 10 10 Elevated Platform 10 10 5 5 10 10

  24. Beyond Eumorphia EUCOMM Primary Phenotyping EMPReSSslim 500? mouse lines Mouse clinics GSF, Munich ICS, Strasbourg MRC, Harwell Sanger, Hinxton Refinement of SOPs Additional validation Development of new technologies Secondary Phenotyping Specialist Centres Bioinformatics Statistical analysis Community Databases

  25. 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

  26. 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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