Bioinformatics core facility - Lab members

• Head of the bioinformatics core facility: Marc Deloger (marc.deloger@gustaveroussy.fr)

• "Core Service" bioinformaticians (permanent employees): Thibault Dayris, M’boyba Diop, Bastien Job, Gérôme Jules-Clement, Franck Le-Layo.

• "Core Service" bioinformaticians (non-permanent employees) : Marine Aglave, Edi Tihic

Bioinformatics core facility - Activities

• Analysis of (epi)genomic / transcriptomic sequencing data (WGS / WES / TGS, RNA-seq, ChIP / ATAC-seq, Single-Cell, Long Reads)
• Data management (recovery, centralization, organization, labeling, provision / sharing)
• Support to bioinformaticians, biologists, and clinicians from Gustave Roussy
• Publication assistance (material and methods, figures, deposit of data on public databases such as GEO / SRA / EGA / dbGAP)
• Co-supervision of junior bioinformaticians (trainees, PhD students…)

Lab members

Lab head
Prof. Nathalie Chaput-Gras
Email

Lab manager
Dr Lydie Cassard

Assistant professor
Dr Marie Naigeon

Engineer
Jean Jouniaux:

Engineer
Lisa Boselli

Technician
Jonathan Grivel:

Equipments

• 1 MACSQuant 16 Cytometer – Miltenyi Biotec Inc.
• 1 CytoFLEX S base Cytometer – Beckman Coulter
• 2 GALLIOS Cytometer – Beckman Coulter
• MAGPIX Multiplexing System – Luminex B.V.
• MESO QuickPlex SQ 120 – Meso Scale Discovery (LRTI)
• GentleMACS Dissociator - Miltenyi Biotec Inc.
• Vi-CELL XR Cell Analyzer – Beckman Coulter
• xCELLigence RTCA - Agilent

Activities

The Laboratory of Immunomonitoring in Oncology (LIO), created at the end of 2014, is a translational research unit. The main objective of the laboratory is to identify blood or tumor biomarkers that can predict the response or resistance to anti-tumor immunotherapies, as well as the emergence of some immunological adverse effects that may be linked to these treatments. Another objective is to understand the mechanisms of action of anti-tumor immunotherapies.

• Pr Jean Yves Scoazec : Responsable plateforme CRB
• Nathalie Jacques : Cadre hiérarchique plateforme CRB
• Valérie Camara-Clayette : Cadre technique plateforme CRB

CRB-tissus

• Pr Jean Yves Scoazec : Responsable CRB-tissus
• Delphine Arnaud : Technicienne de laboratoire
• Chiraz Ayadi : Technicienne de laboratoire
• Joseph Gutierrez : Technicien de laboratoire
• Christine Machavoine : Technicienne de laboratoire

ET-Extra

• Dr Caroline Pradon : Responsable ET-Extra

Activities of the Biological Resource Centre

The Biological Resource Centre (CRB) is charged with storage of all the patient tissue samples which are considered by clinicians to be useful. All of these patients have signed consent forms and samples of their plasma, serum and whole blood are also stored. In addition the CRB keeps samples of public health importance and those collected in clinical research projects.      

Team members

• Lacroix Ludovic, Biologist/Team leader
• Jacques Nathalie, Laboratory manager
• Saulnier Patrick, Biologist engineer
• Jovelet Cécile, Postdoctoral researcher
• Camara-Clayette Valérie, Biologist engineer 
• Honoré Aurélie, Technician
• Laporte Mélanie, Technician 
• Lecourt Hélène, Technician
• Louis Maxime, Technician
• Motté Nelly, Technician
• Paume Clélia, Technician
• Richon Catherine, Technician

H2 Molecular biopathology equipment

• 2 2100 Bioanalysers (Agilent®)
• 1 NanoDrop® for sample quantification (Ozyme®)
• 1 Liquidator (Mettler Toledo®)
• 2 QUBIT® sample quantification (Labtech®)
• 6 PCR blocks (96 wells)
• 1 ViiA7 PCR Quantification block, 96 wells (Life Technologies®)
• 2 PCR VERITI® blocks (Life Technologies®)
• 1 DNA Extractor EZ1 (Qiagen®)
• 1 48 Capillary array sequencer shared with Biopath (Life Technologies®)
• 2 PGM IonTorrent® + 3 OneTouch, NG sequencing (Life Technologies®)

Molecular biopathology section

This section performs molecular assays (sequencing of more than 350 targets, PCR, qPCR, NGS etc.) in the context of clinical trials or research studies. This section is also involved in testing for mutations in the context of the Gustave Roussy Personalised Medicine programme.

The skill base of the section has been broadened by developing a team to research knowledge transfer in Haematology.
The nature of blood diseases has led to the development of methods of cell selection designed to isolate sub-populations from tumour samples.