Eumorphia
Phenotype screens for mice
Developing an integrated
platform
EUMORPHIA - the consortium
 MRC Mammalian Genetics Unit, UK
 IGBMC, Strasbourg, France
 EMBL Monterotondo, Italy
 MRC Human Genetics Unit, UK
 CNR-IBC, Monterotondo, Italy
 MRC Functional Genetics, UK
 Karolinska, Stockholm, Sweden
 ANIMAGE, Lyon, France
 UNIL-IBA, Lausanne, Switzerland
 CNG/CNRS Paris, France
 UNIGE, Geneva, Switzerland
 GSF, Munich, Germany
 Sanger Institute, Hinxton, UK
 GBF, Braunschwieg, Germany
 CNIO, Madrid, Spain
 NKI, Amsterdam, Netherlands
 Univ. Manchester, UK
18 centres across Europe
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
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
Phenotyping - Workpackages
 Standardisation - animal handling
 First-line phenotyping
European
Mouse Phenotyping
Resource for Standardised Screens EMPReSS
 Clinical Chemistry/Haematology
 Cardiovascular
 Renal systems
 Hormonal/metabolic
 Central, peripheral nervous system,
 Allergy and infection
muscle
 Behaviour and cognition
 Imaging
 Necropsy, pathology, histology
 Sensory systems
 Pulmonary
 Cancer
 Bone, Cartilage
 Expression analysis
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
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.
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
Review and sign-off by
Eumorphia scientist outside
working group
Additional validation
between centres
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)
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
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
35%
Validation by testing on selected inbred mouse strains and/or
selected mutants at one EUMORPHIA laboratory
44%
Validation by testing on selected inbred mouse strains and/or
selected mutants at two EUMORPHIA laboratories
21%
Full comparison of results of testing on selected inbred mouse
strains and/or selected mutants at more than two
EUMORPHIA laboratories
Global % PPI
Open field % Centre Time
35
100
80
60
40
20
0
30
25
20
15
10
5
0
35
30
C57BL/6
25
20
15
10
C3HeH
5
0
40
BALB/c
35
30
25
20
129/Sv
15
10
5
0
15
12
9
6
3
0
1st round validation results
100
80
60
40
20
0
100
80
60
40
20
0
100
80
60
40
20
0
CNR
GSF
MRC
ICS
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
(week 8)
Modified
SHIRPA
(week 8)
Grip
strength
(week 8)
Rotarod
(week 8)
Y maze
(week 9)
ASR & PPI
(week 9)
Swim
ability
(week 10)
Integrating and ordering tests in different
systems - neurobehaviour and sensory
Open field (week 8)
Week
8
I
Tests
Modified SHIRPA
Simple openfield
Modified SHIRPA (week 8)
Clickbox
I
Trunk curl
Grip strength (week 8)
Limb grasping
Reaching response
|
Pinnae reflex
Rotarod (week 8)
Corneal reflex
I
Toe pinch
Y maze (week 9)
Air righting
I
Contact righting
PPI and ASR (week 9)
I
Tail Flick (week 9)
|
Tail Suspension (week 10)
|
Swim Test (week 10)
Elevated platform
8
Rotarod
9
ASR/PPI
10
Swim test
EUMORPHIA
Phenotyping
European
Union Mouse
Genetics
Research for
Public Health
And
Industrial
Applications
Mutagenesis
Informatics
Networking and
Training
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
Informatics
An ontology is an explicit formal specification of the terms in
a domain (concepts) and the relationships (attributes)
amongst them
 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
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
• 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
Mouse
lines
Primary
Phenotyping
EMPReSSslim
Refinement of SOPs
Additional validation
Mouse clinics
GSF, Munich
ICS, Strasbourg
MRC, Harwell
Sanger, Hinxton
Secondary
Phenotyping
Bioinformatics
Statistical analysis
Community
Databases
Specialist
Centres
Development of new technologies
EUCOMM
8 weeks
9 weeks
10 weeks
Dysmorphology
Calorimetry
Clinical
Chemistry
10 10
Dysmorphology /
Blood /
Metabolism
10 10
14 weeks
12 weeks
Simplified
IPGTT
10 10
10 10
Haematology
Repeat Chemistry
10 10
Pipeline 1
Bone
X ray
DEXA
10 10
3 3
FACS analysis
of peripheral
blood cells
Allergy / Immune
10 10
Immunoglobin
concentration
EMPReSSslim
10 10
M
ANP
Cardio
13 weeks
Non-invasive
Blood Pressure
10 10
14 weeks
Echo
Cardiography
10 10
10 10
8 weeks
Open field
10 10
Sensory /
Behaviour
Modified
SHIRPA 10 10
Grip
Strength
10 10
Pipeline 2
9 weeks
Acoustic
Startle
10 10
Tail flick
10 10
10 weeks
Tail
suspension
10 10
Y-maze
10 10
Elevated
Platform
10 10
Swim Ability
10 10
10
Number of males
10
Number of females
12 weeks
Opthalmoscope
& Slit Lamp
5 5
Beyond Eumorphia
500?
mouse lines
Primary
Phenotyping
EMPReSSslim
Refinement of SOPs
Additional validation
Mouse clinics
GSF, Munich
ICS, Strasbourg
MRC, Harwell
Sanger, Hinxton
Secondary
Phenotyping
Bioinformatics
Statistical analysis
Community
Databases
Specialist
Centres
Development of new technologies
EUCOMM
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
EUMORPHIA - the consortium
 MRC Mammalian Genetics Unit, UK
 IGBMC, Strasbourg, France
 EMBL Monterotondo, Italy
 MRC Human Genetics Unit, UK
 CNR-IBC, Monterotondo, Italy
 MRC Functional Genetics, UK
 Karolinska, Stockholm, Sweden
 ANIMAGE, Lyon, France
 UNIL-IBA, Lausanne, Switzerland
 CNG/CNRS Paris, France
 UNIGE, Geneva, Switzerland
 GSF, Munich, Germany
 Sanger Institute, Hinxton, UK
 GBF, Braunschwieg, Germany
 CNIO, Madrid, Spain
 NKI, Amsterdam, Netherlands
 Univ. Manchester, UK
18 centres across Europe