IGR

Adress
UMS INSERM 23/CNRS 3655 AMMICA
114 rue Edouard Vaillant 94800 Villejuif
Structure(s)
INSERM, CNRS
Unit:
AMMICA, UMS 23 / CNRS 3655
Regional Center
ApliBio, Ile-de-France
Scientific leader
Gautheret Daniel
Technical leader
Meurice Guillaume
Certificat(s)
Not documented
Infrastructure
Propriétaire
Effective storage
420.00 To
Cluster: cores number
450 cores
Data collections number
15
Bioinformatic tools number
90
Users number (last year)
25
Servers description
- Cluster de calcul dédié à l’analyse de données de séquencage
- Serveur Galaxy
- Serveur d’applications

      - Shiny
      - Redmine
- Serveur dédié à l’analyse de données microarray


Access conditions

- Serveur Galaxy : Demande de compte auprès de la plate-forme. Ouvert à toute équipe exterieure à Gustave Roussy sur demande (adresse IP).
- Cluster de calcul : accessible exclusivement aux bioinformaticiens du site GR.

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

DEVA

Description

Detection of variants from NGS data. Pipeline for variant detection adapted to exon capture from clinical DNA samples. Special options for germline or somatic variants are provided. Interface is available in command line or Galaxy system. Output from mutliple samples can be visualized and filtered using web-based interface.

Access conditions

Accès : web server, https://galaxy.gustaveroussy.fr/galaxyprod

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

VCF2HTML

Description

A visualization and filtering tool for multiple VCF (variant) datasets.

Access conditions

Script documenté sur demande.

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

SCA

Description

SCA (Similarity Core Analysis) is a computational framework for extracting the core molecular features, such as mRNA or miRNA signatures, common to tumors and corresponding cell lines.

Access conditions

Programme fourni sur demande.

Domains of activity
  • Biomedical
  • Biology
Description of expertise domains
● Bioanalyses
Conception, définition de design expérimentaux en génomique (microarrays, NGS). Analyse de données génomiques (microarray et NGS)
- Microarray :
- Gene Expression (Agilent, Affymetrix)
- CGH array
- microRNA array
- NGS (DNA-seq):
- Détection de SNP (WES, WGS, TS)
- Détection de variants structuraux (LOH, CNV)
- ChipSeq
- NGS (RNA-seq) :
- Analyse différentielle
- recherche de transcrit de fusion
- recherche de splicing alternatif
- detection de SNP par RNA-seq

 

● Conseil / Support
Elaboration de cahier des charges pour des projets de recherche à composante "bioinformatique" : définition du projet bioinformatique, définition des compétences requises, rédaction de fiche de poste, recrutement de bioinformaticien, estimation du coût global. La plateforme peut se positionner en partenaire du projet ou en prestataire de service.

 

● Formations
Organisation de formations généraliste en interne. Organisation de formations spécifiques, sur demande, dans les locaux des demandeurs (utilisation d’un logiciel, explication de méthodologie bioinformatique, statistiques)

 

● R&D
Développement /Maintenance de pipelines d’analyse.
Développement à facon d’outils d’annotation / de visualisation de données NGS Développement de DB de données génomiques
Participation au developpement de DB en médecine personnalisée

Keywords:
  • NGS data analysis
  • Transcriptomics (RNA-seq)
  • Differential gene expression analysis
  • Variant calling
  • Panels (amplicons, captures)
  • Exomes
  • Whole genomes
  • Analysis of gene expression regulation
  • Chip-seq
  • Methylation profiles
  • Metagenomics, metatranscriptomics
  • Genomics: Chips
  • DNA chips
  • CGH
  • Functionnal
  • RNA chips
  • Expression

Formation professionnelle

No website documented
Trainees:
120 trainees / year
Training time:
Not documented
No upcoming session scheduled

Bioinformatique, NGS et Cancer

Description

Co-organisation Atelier Cancéropole Ile de France « Bioinformatique, NGS et Cancer» (avril 2014 et Nov 2014)

Access conditions

http://www.canceropole-idf.fr/fr/ngs

No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Ecole NGS Aviesan Roscoff

Description

(nov 2013, oct 2014): responsabilité de l’atelier RNA-seq (Marc Deloger), intervention atelier CNV (Bastien Job).

Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation interne pipeline DEVA detection de variants par NGS

Description
Not documented
Access conditions
Not documented
No website documented
Trainees:
Not documented
Training time:
Not documented
No upcoming session scheduled

Formation interne pipeline RNASeq

Description
Not documented
Access conditions
Not documented

Formation universitaire

No website documented
Trainees:
20 trainees / year
Training time:
Not documented
No upcoming session scheduled

IFSBM

Description
UFR médecine Paris-Sud (mai 2015). Big data en médecine. Acquisition et analyse des données de haut débit dans le but de détecter des variants génomiques (CGH, exome, génome), étudier les profils d’expression ou le statut épigénétique des cellules (expression array, RNA-seq, ChiP-seq, medip-seq).

 

UFR médecine Paris-Sud (janvier 2015) Méthodologie en biologie moléculaire et cellulaire et analyse d’article

Access conditions
Not documented
Users distribution
International
0 %
National
5 %
Regional
0 %
Local
95%
Explanation about this distribution:

La plateforme est soutenue financièrement par des crédits Gustave Roussy

Platform's own projects

Not Documented

Collaborations
National projets
- INCA PAIR Mélanome. Partenaires: R. Ballotti (U. Nice), A. de la Fouchardière (Unicancer Lyon), B. Bressac (Gustave Roussy) + PF Bioinformatique (2014-17).

 

- INSERM Plan Cancer. “Molecular signature of radiation-induced thyroid cancers” . Partenaires: S. Chevillard (CEA Fontenay), L. Lacroix (Gustave Roussy), M Schlumberger (Gustave Roussy) + PF Bioinformatique. (2014-2016)

 

- INCA SIRIC MMO “Molecular Medicine in Oncology”. (2012-2017). Projet Gustave Roussy impliquant la plateforme de Bioinformatique et les laboratoires de recherche.

International and European projects
Not documented
Projects with industry

- 17e FUI (Fond Unique Interministériel): Projet ICE “Interpretation of Clinical Exome”. Partenaires: Sté Integragen, Sté Sogeti High Tech, INSERM, Gustave Roussy. (2014-2017).

Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

Groupe de travail :
AAP INCA NGS : Volet 1 et volet 2. Participation à l’animation d’un groupe de travail dédié à la mise en place des technologie NGS dans un contexte clinique (en partenariat avec Institut Curie)

Internal publications
External publications
"A prognostic signature of defective p53-dependent G1 checkpoint function in melanoma cell lines.", Pigment Cell Melanoma Res, vol. 25, issue 4, pp. 514-26, 2012 Jul.
"Prognostic impact of vitamin B6 metabolism in lung cancer.", Cell Rep, vol. 2, issue 2, pp. 257-69, 2012 Aug 30.
"[Cytogenomic studies of hydatiform moles and gestational choriocarcinoma].", Bull Cancer, vol. 99, issue 9, pp. 827-43, 2012 Sep.
"Independent transcriptional reprogramming and apoptosis induction by cisplatin.", Cell Cycle, vol. 11, issue 18, pp. 3472-80, 2012 Sep 15.
"An immunosurveillance mechanism controls cancer cell ploidy.", Science, vol. 337, issue 6102, pp. 1678-84, 2012 Sep 28.
"Clonal architecture of chronic myelomonocytic leukemias.", Blood, vol. 121, issue 12, pp. 2186-98, 2013 Mar 21.
"Atlas of genetics and cytogenetics in oncology and haematology in 2013.", Nucleic Acids Res, vol. 41, issue Database issue, pp. D920-4, 2013 Jan.
"Proteolysis of cystatin C by cathepsin D in the breast cancer microenvironment.", FASEB J, vol. 26, issue 12, pp. 5172-81, 2012 Dec.
"Genome-wide high-resolution aCGH analysis of gestational choriocarcinomas.", PLoS One, vol. 7, issue 1, pp. e29426, 2012.
"Acquired initiating mutations in early hematopoietic cells of CLL patients.", Cancer Discov, vol. 4, issue 9, pp. 1088-101, 2014 Sep.
"Chk1 as a new therapeutic target in triple-negative breast cancer.", Breast, vol. 23, issue 3, pp. 250-8, 2014 Jun.
"β-catenin inhibitor ICAT modulates the invasive motility of melanoma cells.", Cancer Res, vol. 74, issue 7, pp. 1983-95, 2014 Apr 1.
"Integrated molecular portrait of non-small cell lung cancers.", BMC Med Genomics, vol. 6, pp. 53, 2013.
"Retinoic acid receptor alpha amplifications and retinoic acid sensitivity in breast cancers.", Clin Breast Cancer, vol. 13, issue 5, pp. 401-8, 2013 Oct.
"Developmental changes in human megakaryopoiesis.", J Thromb Haemost, vol. 11, issue 9, pp. 1730-41, 2013 Sep.
"Cisplatin resistance associated with PARP hyperactivation.", Cancer Res, vol. 73, issue 7, pp. 2271-80, 2013 Apr 1.
"Gene copy number variations in breast cancer of Sub-Saharan African women.", Breast, vol. 22, issue 3, pp. 295-300, 2013 Jun.
Publications with the hosting laboratory
cea
cnrs
inra
inria
inserm
logo_elixir
logo-investissements