CARAPITO Raphaël

RESEARCH PROJECT

GENOMAX : High Throughput Sequencing Platform

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.
• Genomics of transplantation

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

Low- and Mid-Throughput Sequencing Platforms

• ABI 3130XL – 16-capillary Sanger sequencer
  Thermo Fisher Scientific
• ABI 3730XL – 96-capillary Sanger sequencer
  Thermo Fisher Scientific
• Ion S5
  Thermo Fisher Scientific
• Ion Chef
  Thermo Fisher Scientific
• NextSeq 500
  Illumina
• NextSeq 2000
  Illumina

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High-Throughput Sequencing Platforms

• NovaSeq X Plus – Short-read sequencing
  Illumina
• Revio – Long-read sequencing
  PacBio

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Automated Library and Sample Preparation Systems

• Covaris S220
• NGS STARlet
  Hamilton

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IT Infrastructure

Development Server

• 32 CPU cores
• 380 GB RAM
• 1,035 PB storage capacity

Analysis Server 1

• 108 CPU cores
• 566 GB RAM
• 1,035 PB storage capacity

Analysis Server 2 (DRAGEN ×2)

• 64 CPU cores
• 503 GB RAM
• 14 TB storage capacity

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Single-Cell & Spatial Transcriptomics

• 10x Genomics platforms
  Single-cell transcriptomics and spatial transcriptomics solutions

Services Provided

(For collaborations or service provision)

Sample Preparation & Sequencing Services

• Sample preparation and biobanking
• Nucleic acid extraction (DNA / RNA)
• Library preparation
• Whole human exome and genome sequencing
• De novo sequencing of small genomes
• Targeted sequencing:
  • Gene panels
  • Viral genomes
  • Bacterial genomes
• RNA sequencing:
  • Whole transcriptome RNA-seq
  • Small RNA sequencing
• Copy number variation (CNV) analysis
• ChIP-seq
• SNP genotyping
• Sanger sequencing
• Metagenomics

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Bioinformatics Services

• Primary bioinformatics analysis
• Secondary bioinformatics analysis

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…and other services available 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, …

TEAM

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