Specialised Phenotyping - metabolic and behavioral phenotyping pipelines

INFRAFRONTIER2020 project - Trans-national Access call

October 2018


Context and aims of the call

Main objective of this INFRAFRONTIER2020 Trans-national Access call is to facilitate access for the wider biomedical research community to the unique infrastructure and scientific expertise of the participating INFRAFRONTIER mouse clinics, where mouse mutant lines can be tested through specialised metabolic- and behavioural phenotyping pipelines. Disturbed energy balance regulation results in obesity and in numerous related metabolic disorders such as type 2 diabetes mellitus. We offer specialised phenotyping pipelines comprising state-of-the-art test assays monitoring disease related parameters. In-depth behavioural phenotyping supports the elucidation of the molecular and genetic basis of behavioural impairments that are relevant for human neuropsychiatric disorders such as anxiety disorders, post-traumatic stress disorder, depression, schizophrenia, autism, attention-deficit hyperactivity disorder, Parkinson’s and Alzheimer’s Disease.

Access will be granted on the basis of scientific excellence and supports the development and in depth characterisation of mouse models for investigating gene function and human pathophysiology.  INFRAFRONTIER will provide open access to all characterised disease models and phenotyping data.


Access modalities
  • The EC Horizon 2020 funded INFRAFRONTIER2020 project (2017 – 2020) supports eligible customers with a free-of-charge mouse model phenotyping service implemented as a Trans-national Access activity supporting a total of 9 projects in this first call.
  • The access unit offered covers the specialised metabolic or behavioural phenotyping of a mouse mutant line, and the preparation of a comprehensive phenotyping report.
  • Participating mouse clinics are the German Mouse Clinic (GMC), the Czech Centre for Phenogenomics (CCP), and PHENOMIN-ICS.
  • Centre specific collaboration agreements will be established between applicants and the mouse clinics.  Selected projects will be allocated to the mouse clinics based on scope of submitted project proposals.
  • Starting material for the phenotyping projects are either experimental cohorts (10-12 mutant and control mice, 10-15 weeks of age, acceptance depending on health certificates, GMC and PHENOMIN-ICS) or a breeding nucleus and then cohorts are bred by mouse clinics (CCP). Mouse mutants from various sources (transgenes, knockout mice, mutants from mutagenesis screens like ENU) and of different genetic backgrounds can be accepted.
  • The phenotyping pipelines to be used will be specialised metabolic- or behavioural phenotyping pipelines based on published IMPReSS SOPs (IMPReSS: http://www.mousephenotype.org/impress), or on local mouse clinic SOPs. Details of the specific mouse clinic specialised phenotyping pipelines are described on page 5 of the application form.
  • Support will be provided by the mouse clinics to analyse and interpret the phenotype data.
  • The analysed mouse models and the generated phenotype data will be made available to the scientific community. An optional grace period of up to 1 year for mouse resources and phenotype data may apply, with immediate release of mouse resources and data after expiry of the grace period. A phenotyping report with all phenotype data will be prepared, and data will also be uploaded onto a public phenotype database of the mouse clinics and / or onto the IMPC portal at http://www.mousephenotype.org. Mouse mutant lines will be deposited into the INFRAFRONTIER/EMMA repository for subsequent use by the scientific community, and will be distributed using the applicant’s institutional MTAs. 
  • Costs: The access to the INFRAFRONTIER2020 phenotyping service is free of charge. However, the shipment cost of mouse mutant lines to the participating mouse clinics must be borne by the applicants.
  • Eligibility: The INFRAFRONTIER2020 Trans-national Access call is open and proposals can be submitted from applicants around the world. Seven projects must be allocated to applicants from EU Member States and Associated Countries, and two projects can be allocated to applicants from third countries.
  • Application: Service requests for the INFRAFRONTIER2020 specialised phenotyping service can be made via an application form. Applications for the Trans-national Access activity must include a short description of the research plans for utilising the phenotyped  mouse model that is being characterised by the INFRAFRONTIER2020 TA service.
  • Selection procedure: Proposals from eligible customers for free of charge access to the INFRAFRONTIER2020 specialised phenotyping service will be subject to a review procedure. The review will be based on short descriptions of the projects involving the mouse mutants that will be phenotyped by the TA service. A mixed panel of members of INFRAFRONTIER and of an external Evaluation Committee will assess service requests supported by the TA activity. In addition to scientific merit of applicants, relevance and quality of preliminary data, soundness of the proposal and research plans, and the project objectives and prospects for exploitation of phenotype data will be assessed. In a further step experts of the mouse clinics will assess the technical feasibility of projects.
  • The technical evaluation of projects may require the provision of additional data such as:

     - Information on the genetic modification of your mutant mouse line if applicable (e.g. affected gene, MGI ID of the gene, type of mutation, ES-cell line used, genetic background (e.g. number of backcross generations)

     - Description of DNA modification (vector, remaining non-recipient DNA, donor organism)

     - Mutant phenotype(s), special housing or care requirements

     - Current sanitary status

     - Intellectual property rights (who generated and who owns the mouse line

  • Applicants will be informed on the outcome of the evaluation within 6 weeks after the end of the call for which the TA application was submitted. All applications will be handled with strict confidentiality.
  • Acknowledgements: Please do acknowledge any support under this scheme in all resulting publications with ‘Part of this work has been funded by the European Union Research and Innovation programme Horizon 2020 (Grant Agreement Number 730879)’. The participating infrastructure, which provided the service, should be specifically mentioned in any publication resulting from the service.


  • Timeline: Closing of call on 15 November 2018 - Evaluation process until 15 December 2018
Specialised phenotyping pipelines

German Mouse Clinic @ Helmholtz Zentrum München:  In-depth metabolic phenotyping

The German Mouse Clinic can support 3 projects in this TA call.

Disturbed energy balance regulation results in obesity and in numerous related metabolic disorders such as type 2 diabetes mellitus. We offer specialized phenotyping pipelines comprising state-of-the-art test assays monitoring disease related parameters such as body mass, body composition (determined by DXA, X-ray µCT, qNMR, and MRI), blood glucose and insulin levels in addition to further clinical chemistry and endocrinology parameters. The pipeline focusses on metabolic functions such as alterations in whole body energy regulation (32-cages indirect calorimetry system: energy expenditure, substrate utilization, physical activity, food and water consumption), energy and macronutrient absorption in the gastrointestinal tract (metabolic cages, bomb calorimetry). Finally, functional tests such as oral and intraperitoneal glucose tolerance tests, insulin tolerance tests, and pyruvate tolerance test provide important information on dysfunctional glucose homeostasis. Glucose clamp studies can be conducted as follow-up. The pipeline can be operated with varying environmental conditions such as energy content and composition of the diet, and ambient temperature.


Czech Centre for Phenogenomics (CCP):  In-depth metabolic phenotyping

The CCP can support 3 projects in this TA call.

The Czech Centre for Phenogenomics (CCP, IMG) can offer a comprehensive primary phenotyping pipeline combined with secondary screens based on metabolic challenges established in our laboratories. The challenges are focused on global metabolomics approaches with deep profiling of small metabolites. The secondary screens will include also mouse cohort preparation, which should contain 10 +10 mutant mice for each gender compared to the same number of wild-type controls.  The experimental cohort will be prepared either by rederivation of animals or from frozen embryos or sperms.

Basic metabolism assessment and metabolomics analysis

We will provide primary metabolism screen combined with one secondary test based on metabolic challenge. The primary metabolism pipeline consists of growth curve analysis, IPGTT, comprehensive 48h indirect calorimetry measurement in Phenomasters system, body composition analysis by in-vivo micro CT, with possibilities to quantify fat tissues deposition (visceral, subcutaneous, brown adipose tissue), clinical biochemistry panel from blood and urine samples and metabolome screen using Q-TOF with following non-targeted metabolomics analysis.

Portfolio of secondary test

From the portfolio of secondary tests we can provide a diet and liver injury based metabolic challenge including diet rich in fat (high fat diet), methionine choline-deficient (MCD) diet, or custom-tailored diet or intoxication model based on tetrachloride injection, or by diet supplemented with 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). With advantage of climate control system during indirect calorimetry measurements, we can involve also temperature or circadian challenge to analysis.

The experimental animal cohorts will be assessed for blood parameters, complete histopathology, and metabolite profiles indicated during by the non-invasive approach. Our center will provide additional analyses including multiplex cytokine assays, analysis of inflammatory cells using flow cytometry, clinical biochemistry, HPLC, and targeted/non-targeted Q-TOF metabolomics assaying small metabolites and their metabolic pathways.


PHENOMIN-ICS:  In-depth behavioral phenotyping of mouse models

The ICS can support 3 projects in this TA call.

Mutant mouse technology represents a powerful means to investigate the genetic basis of behavior and to elucidate the mechanisms underlying neurological and psychiatric disorders.

The Neurobiology and Behavior platform has developed a battery of tests adapted to the mouse. These tests include analyses of sensory responses, motor abilities, cognitive functions as well as behaviors related to neuropsychiatric disorders, such as anxiety, depression or schizophrenia. Tests may be utilized as a package for phenotyping genetically modified mice or to screen for potential therapeutics. The suggested flow scheme is illustrated below, but might be customized upon request, for a similar final budget.

This standard in-depth behavior flow scheme includes analysis of following traits:

1) Measurement of spontaneous activity and food/water intake over a complete day/night cycle (circadian activity);

2) Anxiety-related behavior (elevated plus maze test to evaluate anxiety for height;

3) Learning and memory (object recognition task to evaluate recognition memory to characterize potential memory defects; spontaneous alternation in the Y-maze to evaluate working memory, Pavlonian fear conditioning for measuring emotional learning and memory;

4) General health and Basic sensory-motor functions (clinical observations (modified SHIRPA), grip test to measure the muscular muscle strength, rotarod to measure the ability of an animal to maintain balance on a rotating rod;

5) Social recognition test to evaluate the preference of a mouse for a congener as compared to an object placed in an opposite compartment;

6) Sensory-motor gating / Schizophrenia (acoustic startle reflex and pre-pulse inhibition);

7) Pain sensitivity (hot plate test to evaluate the response to acute thermal pain, shock threshold to assess sensitivity to electrical footshock).

As stated above, for a similar final budget, these tests might be used in a battery for a thorough behavioral screen or together with other specialized tests to address specific scientific questions, such as:

1) The assessment of different aspects of learning and memory processes by using the Morris water maze or the active avoidance;

2) Further evaluation of the motor abilities or neuromotor function (string test for evaluation of the traction force and coordination, crenelated beam and/or automated gait analysis (Digigait) for evaluation of proprioceptive abilities, and/or the Mouse Reaching and Grasping (MoRaG) for fine tune motor gestures);

3) Analysis of the emotional behavior (tail suspension and forced swim tests to evaluate susceptibility to despair, light dark test or marble burying for anxiety). Repeated measurements can also be performed to assess progressive motor alterations observed in degenerative diseases. Further details on the behavioral assays can be found at http://www.phenomin.fr/en-us/tools-technologies/phenotyping-tools/2/.

Participating infrastructures

German Mouse Clinic             www.mouseclinic.de

The German Mouse Clinic (GMC) was founded 2001 at the Helmholtz Zentrum München as the first mouse clinic with open access

Goal:  Characterisation of mouse models for human diseases to understand molecular mechanisms of human disorders and for the development of new therapies.

GMC Strategy: To develop and offer a large scale standardised and comprehensive phenotypic analysis of mouse mutants from various sources (transgenes, knockout mice, mutants from mutagenesis screens like ENU).

Phenotype your mouse mutants: We offer the examination of mouse mutants on the basis of scientific collaboration, using a broad standardised phenotypic check-up with more than 550 parameters. The screens in the German Mouse Clinic are designated to the areas of behaviour, bone and cartilage development, neurology, clinical chemistry, eye development, immunology, allergy, steroid metabolism, energy metabolism, lung function, vision and pain perception, molecular phenotyping, cardiovascular analyses and pathology.


Czech Centre for Phenogenomics (CCP)         www.phenogenomics.cz

The Czech Centre for Phenogenomics provides expertise and services to the biomedical research community, which study the function of genes in biological processes and / or human disorders in vivo using mouse or rat models. CCP covers a full spectrum of genetic engineering services, strain cryopreservation and archiving services, advanced phenotyping and imaging services, as well as specific pathogen free (SPF) animal housing and husbandry.


PHENOMIN-ICS        www.phenomin.fr 

PHENOMIN is founded by three major national nodes:

Institut Clinique de la Souris (ICS), Illkirch near Strasbourg,

Transgenesis and Archiving of Animal Models (TAAM), Orléans, Villejuif) and

Centre for Immunophenomics (CIPHE), Marseille.

They are devoted to serve the scientific community for the usage of mouse models. PHENOMIN constitutes a unique distributed resource for the creation, the care, the phenotyping, the distribution and archiving of animal models for academics and private corporations.

The ICS is a large-scale facility open to the community that ensures the generation of mouse models à la carte, the validation of genetic models, the expansion and preservation and distribution of models with the housing department, and offers in its phenotyping department a series of standardized functional analysis of mouse models that can be performed in a comprehensive pipeline or on demand, as well as for more specialized studies, that cover the major functions and key physiological systems.