Gustave Roussy's US AMMICa Genomics Platform (INSERM US23 / CNRS UMS3655) aims to characterize cancers and experimental models using innovative genomic approaches.
In 2011, the genomics platform set up a high-throughput sequencing module based on Illumina technology (HiSeq 2000 replaced by a NovaSeq 6000 in 2017, MiSeq and MiniSeq) and all the necessary equipment surrounding these sequencers (robots for pre-analytical preparations and servers).
The analysis of the DNA of tumor cells by comparing it to normal cells to detect genetic abnormalities using WES and WGS techniques will be outsourced whenever possible in order to promote the development of more innovative technologies.
In 2019, a module for single-cell analysis was set up thanks to the acquisition of a Chromium™ Controller from 10X Genomics. This technology has proven to be a powerful tool for discovering new populations of rare cells within tumors, for characterizing changes in gene expression in various cell types, or for discovering subtle transcriptional responses in cells selected from a heterogeneous population. These tumor heterogeneity data aim to better understand the mechanisms of tumor progression, search for new therapeutic targets and guide treatment decisions.
In 2021, the genomics platform acquired the two following instruments:
- A Tapestri from MissionBio, to study mutations and copy number variations (CNV) at the single-cell level (cells or nuclei) (minimum design 20 amplicons and maximum 1000 amplicons of 300 bp) from fresh or frozen tissues.
- A PromethION 48 from Oxford Nanopore which allows the sequencing of ultra-long fragments. From individual cells, long fragment sequencing will make it possible to identify chimeric transcripts and somatic mutations as well as to determine the expressed isoforms. This equipment will also detect epigenetic changes using direct sequencing such as DNA/RNA methylation.
In addition, a technological watch is ensured in order to set up innovative tools for epigenetics and single cell analyses.
The platform offers:
- a definition of experimental design and assistance in the optimization of projects
- advice for the structuring and implementation of projects
- support for sample preparation and quality control
- on reservation, access to Nanodrop, Bioanalyzers, real-time quantitative PCR instruments, Covaris S220
- high-throughput sequencing (NovaSeq6000 & MiSeq Illumina) (RNA-seq, ChIP-seq, ATAC-seq, Cut&Tag, ...)
- single-cell RNA-Seq analysis : from cells : 3’ scRNA-Seq, 5’ scRNA-Seq + TCR +/- BCR, 5’ scRNA-Seq + TCR + CITE-seq, or from nuclei : 3’ scRNA-Seq, scATACseq, 3’ scRNAseq + scATACseq