International & National contexts

PHENOMIN, as a large scale national infrastructure for Biotechnology and Health, provides services for all French laboratories and is also a major player in the international strategic phenogenomics effort. It aims at:

Implementing mouse genetic engineering,
Securing zootechny, ensuring animal welfare and ethics,
Filling the gap in high-throughput phenotyping by developing new relevant functional assays,
Building a unique resource of models for fundamental research, biotechnological and biopharmaceutical innovation.

PHENOMIN is part of the national research Infrastructure CELPHEDIA

CELPHEDIA aims to develop innovative, standardized and massively parallel technological approaches, in order to accelerate the understanding of the genome and the generation of human or animal disease models and to guarantee efficiency and reliability, thus facilitating national or international access to the models of interest. CELPHEDIA is composed of 15 centers, covering different animal models: rodents, non mammals and non-human primates.

CELPHEDIA has several scientific objectives:

Providing and developing innovative, standardized and massively parallel technological approaches for the scientific community,
Favoring cross-functionality of the results from a model organism to another,
Performing a high throughput analysis of targets effects, either in normal or in pathological situations,
Improving and standardizing processes and protocols and thus facilitates national and international exchanges and access to the models of interest,
Contributing to the international effort in the functional annotation of the genome and the understanding of human diseases.

PHENOMIN teams are leading several CELPHEDIA working groups, thus disseminating their knowledge and expertise over the French territory and for the benefit of different animal models. Please have a look to the last interesting production from the workgroups' network in 2020.

PHENOMIN is part of the European INFRAFRONTIER Infrastructure

PHENOMIN is contributing to INFRAFRONTIER and to the ESFRI-identified pan-European Infrastructure for functional genomics.

INFRAFRONTIER is the European Research Infrastructure for phenotyping and archiving of model mammalian genomes. It provides access to first-class tools and data for biomedical research, and thereby contributes to improving the understanding of gene function in human health and disease using the mouse model.

INFRAFRONTIER aims at

Shaping the European research area in the field of mouse functional genomics and thereby making an important contribution to the study of human disease,
Setting standards for systemic phenotyping of mouse models and for archiving and distribution of mouse mutants un Europe,
Offering highest-quality services and cutting-edge technologies provided by the leading labs in Europe,
Disseminating knowledge by state-of-the-art training courses

The INFRAFRONTIER project has been identified as one of the six research Infrastructure projects for biomedical research that was included in the first ESFRI Roadmap in 2006, which lists pan-European initiatives recommended for implementation. To prepare the implementation phase and to coordinate the transnational activities of the national partners, the INFRAFRONTIER GmbH was established in Germany in 2013.

Raess Michael, Ana Ambrosio de Castro, Valérie Gailus-Durner, Sabine Fessele, Martin Hrabě de Angelis, and the INFRAFRONTIER Consortium. 2016. INFRAFRONTIER: A European Resource for Studying the Functional Basis of Human Disease. Mammalian Genome 27 (7): 445–50. doi:10.1007/s00335-016-9642-y.

INFRAFRONTIER Consortium. 2015. INFRAFRONTIER–Providing Mutant Mouse Resources as Research Tools for the International Scientific Community. Nucleic Acids Research 43: D1171–D1175. doi:10.1093/nar/gku1193.

Soft windowing application to improve analysis of high-throughput phenotyping data

Hamed Haselimashhadi , Jeremy C Mason , Violeta Munoz-Fuentes , Federico López-Gómez, Kolawole Babalola , Elif F Acar , Vivek Kumar , Jacqui White , Ann M Flenniken , Ruairidh King , Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza , Audrey E Christianson , Chih-Wei Hsu, Corey L Reynolds, Denise G Lanza, Isabel Lorenzo, Jennie R Green, Juan J Gallegos , Ritu Bohat , Rodney C Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller , Helmult Fuchs , Lillian Garrett , Lore Becker, Yeon Kyung Kang , David Clary , Soo Young Cho , Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo , Alexandr Bezginov , Ghina Bou About , Marie-France Champy , Laurent Vasseur, Sophie Leblanc, Hamid Meziane , Mohammed Selloum , Patrick T Reilly , Nadine Spielmann , Holger Maier, Valerie Gailus-Durner, Tania Sorg , Masuya Hiroshi , Obata Yuichi , Jason D Heaney , Mary E Dickinson , Wurst Wolfgang , Glauco P Tocchini-Valentini , Kevin C Kent Lloyd , Colin McKerlie , Je Kyung Seong , Herault Yann , Martin Hrabé de Angelis, Steve D M Brown , Damian Smedley , Paul Flicek , Ann-Marie Mallon, Helen Parkinson , Terrence F Meehan

Bioinformatics 2020 Mar 1;36(5):1492-1500.

INFRAFRONTIER _FactSheet2017 (1.8 MB)

PHENOMIN is a member of the international consortium IMPC

PHENOMIN also participates in the International Mouse Phenotyping Consortium (IMPC) to build the first truly comprehensive, functional catalogue of a mammalian genome. This should fulfill a key item in the National Alliance for life sciences and health (AVIESAN) strategic plan that consists in applying mouse genetics to analyze disease mechanisms and using this knowledge for advanced fundamental research and human health.

The IMPC is currently composed of 19 research institutions and 5 national funders from 11 countries.

Global infrastructure recognised by the G7
Creating 20,000 knockout mouse strains on a single background strain
Characterizing each through a standardized phenotyping protocol
Integrating the data to existing mouse and human disease resources
Providing strains, samples and phenotype data for use by the research community

The IMPC aims to harness the strength of mouse research programs and infrastructures of 18 mouse clinics worldwide in a strategic and coordinated effort to systematically phenotype knockout mice (20,000 genes). We undertake a broad-based, genome-wide study in order to provide the wider research community with a long-lasting resource of annotated mammalian gene function. Resulting high-throughput phenotyping data, as well as created mouse models, are freely available to the international scientific community through a Data Coordination Center.

As a key player in a strategic effort in IMPC consortium, PHENOMIN is committed to produce and phenotype 236 mutant lines by 2018. PHENOMIN is a leading member of IMPC through the coordination of the phenotyping group, which evaluates and implements the phenotyping pipeline with new tests. Furthermore, owing to its unique expertise in mouse immunology, PHENOMIN-CIPHE enables PHENOMIN to perform immunophenotyping of the hundreds of mouse mutants that are in the process of being generated.

A resource of targeted mutant mouse lines for 5,061 genes

Marie-Christine Birling , Atsushi Yoshiki , David J Adams , Shinya Ayabe , Arthur L Beaudet , Joanna Bottomley , Allan Bradley , Steve D M Brown , Antje Bürger, Wendy Bushell , Francesco Chiani, Hsian-Jean Genie Chin , Skevoulla Christou , Gemma F Codner , Francesco J DeMayo , Mary E Dickinson , Brendan Doe , Leah Rae Donahue, Martin D Fray , Alessia Gambadoro , Xiang Gao , Marina Gertsenstein , Alba Gomez-Segura , Leslie O Goodwin , Jason D Heaney , Yann Hérault , Martin Hrabe de Angelis , Si-Tse Jiang , Monica J Justice , Petr Kasparek , Ruairidh E King , Ralf Kühn , Ho Lee , Young Jae Lee, Zhiwei Liu , K C Kent Lloyd , Isabel Lorenzo , Ann-Marie Mallon , Colin McKerlie , Terrence F Meehan , Violeta Munoz Fuentes , Stuart Newman , Lauryl M J Nutter , Goo Taeg Oh, Guillaume Pavlovic , Ramiro Ramirez-Solis, Barry Rosen , Edward J Ryder , Luis A Santos , Joel Schick , John R Seavitt , Radislav Sedlacek , Claudia Seisenberger , Je Kyung Seong , William C Skarnes , Tania Sorg , Karen P Steel , Masaru Tamura , Glauco P Tocchini-Valentini, Chi-Kuang Leo Wang , Hannah Wardle-Jones , Marie Wattenhofer-Donzé, Sara Wells, Michael V Wiles , Brandon J Willis, Joshua A Wood , Wolfgang Wurst , Ying Xu , International Mouse Phenotyping Consortium (IMPC); Lydia Teboul , Stephen A Murray.

Nat Genet 2021 2021 Apr;53(4):416-419.

Human and mouse essentiality screens as a resource for disease gene discovery

Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D,

Nat Commun 2020 Jan 31;11(1):655. doi: 10.1038/s41467-020-14284-2.

Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data.

Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu CW, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy MF, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SDM, Smedley D, Flicek P, Mallon AM, Parkinson H, Meehan TF.

Bioinformatics 2020 Mar 1;36(5):1492-1500.

At the G7 Science meeting on 27 and 28 September 2017 in Turin, the ministers of higher education and research in these countries identified two projects, including the International Mouse Phenotyping Consortium (IMPC), as models of international scientific collaboration.

The group of senior officials (GSO) proactively works to identify opportunities for international collaboration among Research Infrastructures that are proposed by its members: it has identified five Case Studies in 2015 and has carried out an analysis on their potential as Research Infrastructures for global collaboration. A specific roadmap for implementation has been identified for two of the Case Studies, including the IMPC.

The updated GSO Framework contains a refined definition of global Excellence-driven Access to global research infrastructures that recognises scientific merit as the principal criterion of access. The GSO is also currently addressing the global Open Research Data issue including the key criteria for data management, data quality control and access to data, and sketching a preliminary set of potential guidelines for implementation by global research infrastructures that builds on the results and good practices of, among others, the Research Data Alliance.

Within the IPMC, which brings together 18 international laboratories, PHENOMIN takes part to a large-scale project: to address the challenge of developing an encyclopedia of mammalian gene function. The IMPC envisages a ten year programme to undertake a broad-based, systematic genome-wide phenotyping project of knockout mice generated from the embryonic stem cell mutant resources. It is the responsibility to PHENOMIN to generate 266 mouse lines, thanks to the technology such as CRISPR/Cas9 for instance, all to be characterized.

At the same time, PHENOMIN also pursues the objective of supporting researchers and identifying drug candidates thanks to the murine models of human pathologies.

GSO Case studies reports

G7 Press release

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