Introduction

The NGS platform of the Institut Curie set up in 2007 entered into a major development phase in 2012 thanks to an Equipex grant (ICGex for Institut Curie Genomics Excellence). Since then, the facility has been steadily increasing its throughput and expertise and currently carries out the sequencing and analysis of nearly 70Tb of DNA a year, i.e. more than 500 projects.

In direct contact with clinicians and researchers from both the hospital and the research center, the ICGex platform has a major positioning in cancerology (fundamental and translational research) and offers a broad range of applications to address multiple aspects in cancer genomics.

The facility is open to the scientific community in a collaborative mode and proposes its expertise via the France Genomics national network.

Expertise

The platform offers support for sequencing projects including libraries preparation and sequencing but also direct sequencing of libraries prepared by users.

– In genomics, protocols for whole genome sequencing (WGS) or targeted resequencing of the whole exome (WES) and gene panels are implemented and proposed to the community from genomic DNA or circulating DNA.

– In transcriptomics, RNA sequencing (RNAseq) represents a major application, about ten different protocols are supported to address multiple questions and situation. While the majority of projects concern standard protocols targeting mRNAs or total RNAs (after ribodepletion), protocols adapted to degraded samples (FFPE) and small quantities are also supported.

– In epigenomics, the platform proposes ChIP-seq approaches to characterize histone marks and transcription factor binding sites. The platform is also often asked to sequence ATACseq libraries to identify open regions of chromatin and HiC libraries to study the conformation of chromatin within the nucleus.

– In single cell genomics, the facility set up main applications available on the chromium system (10X Genomics): gene expression 3’ et 5’ (scRNAseq), immune profiling(VDJseq), snATACseq as well as multiome which integrates snRNAseq and snATACseq. Spatial transcriptomics based on Visium technology (10X Genomics) is also offered in collaboration with the hospital’s experimental pathology platform (Pathex).

– Concerning the 3rd generation sequencing, the SMRTseq (Single Molecule Real Time SEQuencing) proposed by Pacific Biosciences (PacBio) is available at the platform The Sequel IIe, allows to produce long sequences (10-20kb) of very high quality (HiFi reads technology). . Full-length RNA sequencing protocols (IsoSeq) have been set up as well as genomic approaches for targeted sequencing (capture or amplicons) and whole genome sequencing.

Equipments