RESEARCH PROJECT

GENOMAX has a central role as the team is involved in many research programs of the research unit. The GENOMAX team also develops its own projects aiming at developing NGS-based tools or specific research programs. These projects include:

  • Methodological development to study the HLA domain,
  • Exome and RNAseq pipeline developments,
  • Disease gene identification by exome sequencing,
  • Development of multi-omics approaches to analyze complex immunological traits,
  • Deep sequencing of viral genomes,
  • Cancer genome sequencing and mutational hotspot characterization by deep sequencing.

From a global point of view, the mission of the platform is two-fold:

  • It has a strong research focus to lead or support internal projects, but also national and international collaborations.
  • GENOMAX is a fee-for-service service provider. It is an official service provider (CSP) for exome sequencing with the Ampliseq method (ThermoFisher Scientific) since 2013.

The experimental design, the analysis and interpretation of results are performed on an interactive basis between the principal investigators, technicians/engineers and bioinformatician/biostatisticians of the GENOMAX facility.

Our equipment

 Next-generation Sequencing:

  • Ion S5 (ThermoFisher Scientific)
  • Ion PGM (ThermoFisher Scientific)
  • Ion Proton (ThermoFisher Scientific)
  • NextSeq500 (Illumina)
  • NextSeq2000 (Illumina)
  • Equipment for library preparation: Covaris S220, Hydroshear, Library builder, One Touch, Ion Chef (Life Technologies).
  • Informatics cluster: 4 nodes, 48 cores/2.66 GHz Westmere X5650 processor; 24 GB RAM per node; Compute cache per node: drives 2 x 1 TB, RAID 0; local storage: hard drives of  6 X 2 TB, RAID 5 (9.6 TB total); 6 Gbp backplane; QDR (40 GB/sec) Infiniband IPolB cluster private Network ; storage cluster of 48TB (33TB usable)

 Sanger sequencing:

  • 16 capillaries sequencer (ABI3130XL, ThermoFisher Scientific)
  • 96 capillaries sequencer (ABI3730XL, ThermoFisher Scientific)

High Throughput real time PCR :

  • Real time thermocycler Open array NT Cycler (ThermoFisher Scientific)
  • Accufill (ThermoFisher Scientific)

Others :

  • 5 thermocyclers (2x Veriti 96-well, 3x GenAmp 9700) (ThermoFisher Scientific)
  • Q-RT PCR instrument (ABI7000, ThermoFisher Scientific)
  • 2100 Bioanalyzer (Agilent)
  • Nanodrop 2000c (Labtech)

Services provided

  • Whole human genome re-sequencing
  • Whole exome sequencing (capture Sure Select® Agilent, TruSeq® Illumina, Ampliseq® ThermoFisher, Twist Core Exome)
  • de novo sequencing of small genomes
  • Targeted sequencing: gene panels, viruses, bacteria
  • RNA-seq: whole transcriptome and small RNA
  • Copy number variations
  • Chip-seq
  • SNPs genotyping
  • Sanger sequencing
  • Metagenomics

…and other services on demand.

COLLABORATIONS

The group has established multiple collaborations at various levels with:

  • clinical departments: local (e.g. Rheumatology, Immunology, Hematology, Internal medicine,…), national (e.g. Genetics department in Nantes and Dijon, Rheumatolgy department of Bichat hospital in Paris,…), international (e.g. Hematology department of Freiburg and Basel, Hematology/Oncology department of Boston’s Children’s hospital,…)
  • research labs : LSMBO/IPHC Strasbourg, IBMC Strasbourg, EA3072 Strasbourg, INSERM U1012 Paris-Sud, UMR1064 ITUN Nantes, EFS INSERM UMR1232 Nantes, INSERM UMR 1160 Paris St. Louis,….
  • private partners: Prenostics, Ariana Pharma, Novartis, WuxiNextCode, …

FUNDING

  • Cancéropole Grand-Est
    • Feder (Interreg V)
    • Eurométropole de Strasbourg
  • Ministère de l’enseignement supérieur et de la recherche
  • Investissements d’avenir
  • Conseil général du Bas-Rhin
  • Région Grand Est
  • Inserm
  • Université de Strasbourg / IDEX
  • MSD Avenir