Next Generation Sequencing

Next generation sequencing technology has now reached tremendous throughput and accuracy that enable researchers to conduct large-scale genomic projects at affordable cost and in less time.

The NGS Platform of the Institut Curie has greatly evolved since 2012 mainly with the financial support of the ICGEx grant obtained in the frame of the EQUIPEX « investissement d’avenir » piloted by the ANR (ANR-10-EQPX-03). This grant allowed to purchase high throughput NGS sequencers, to fully equip a dedicated lab at the 7th floor of the hospital and expand the staff in charge of running sequencing projects.

 Aims

• Provide state of the art services in sequencing for the different research teams of the Institut Curie.
• Offer technical and scientific support in experimental design and sequencing strategies.
• Be flexible to best respond to scientific needs (technical development and implementation).

Activity

Under the supervision of Olivier Delattre and Alain Nicolas, the NGS platform provides state of the art services in sequencing. This includes the organization of pre-run meetings where the choice of the most appropriate technical strategy is defined in order to best address the biological question of collaborators. Multiple sequencing protocols have been developed and routinely used at the platform in order to cover most commonly used applications in genetics and epigenetics (Genome, Exome and targeted resequencing, RNA sequencing, ChIP-seq …). Furthermore, we are also willing to co-develop more specific protocols according to the need of research teams of the Institute.

Once the technical aspects are defined, samples are provided by collaborators and libraries compatible with the dedicated sequencing devices (Illumina or PacBio) are then prepared by the NGS team. After sequencing, raw data are transferred to the bioinformatics team (U900) for quality controls and basic analysis. At the end, sequence data are provided to research teams with comprehensive analysis and quality reports.

The platform is not restricted to fundamental research, we are also involved in multiple translational research projects in collaboration with U830, the translational research department and the Curie Hospital.

Networking

• Active member of the national infrastructure France Génomique, a French consortium of NGS platforms dedicated to the mutualisation of NGS resources that benefit to French research teams
• Member of the European Core For Life network, which brings together several platforms of different technologies. The Core for Life Genomics Work Group provides networking opportunities enabling the sharing of experiences and knowledge.

Training

• Organisation of the genomic module for the Master 2 degree « Ingénieur de plateforme » of Université de Paris.
• Oral presentation on NGS for the Licence Pro Génomique of ENCPB (Paris).
• Oral presentation in « International Courses » organized by the training unit of the Institute.
• Oral presentation on NGS for the EPF Engineering school (Sceaux).
• Oral presentation in Bioinformatic training organized by the U900.
• Oral presentation on NGS for the Master 2 degree of the « Ecole doctorale de Cancérologie de Paris » (Saclay).

Services

• Availability of a dedicated interface for NGS projects submission and follow up
• Library preparations for multiple sequencing applications :
  • Whole genome, whole exome and targeted resequencing
  • Transcriptome analysis (RNAseq for mRNA and total RNA)
  • Epigenetics with ChIP-seq for histone modifications or protein binding analysis. Analysis of open regions of chromatin from single cell (single-cell ATAC-seq)
  • Single cell mRNA sequencing (3’ seq technology and Spatial Transcriptomic of 10X Genomics)
• Development of analysis pipelines for routine applications
• Bioinformatics supports through collaboration with the bioinformatics platform (U900)

 Equipment

• One high throughput sequencer from Illumina : 1 NovaSeq 6000 dedicated to applications requiring a large amount of data (human genome and exome sequencing, transcriptome analysis …).
• Two benchtop sequencers from Illumina : 2 MiSeq used for projects requiring a low depth of sequencing and for custom libraries validation.
• One Long Read sequencer from PacBio : 1 Sequel II allowing the sequencing of long fragments (>10kb) and repeated regions.
• One Chromium from 10X Genomics enabling single cell analysis, including transcriptomics.
• 1 LabChip GXII Touch, 1 BioAnalyzer, 1 Femto Pulse, 1 CFX96 real-time PCR system et 1 Pippin Pulse used to assess samples and libraries quality.

All equipments have been funded by ICGex. Except the Novaseq cofunded by ITMO Cancer and Hôpital Curie. The Chromium from 10X Genomics has been funded by SiRIC.

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Next actions for 2021

• Implementation of the Visium Spatial Gene Expression technology from 10X Genomics.
• Implémentation of the HiFi reads application with the Sequel II from Pacific Biosciences (reads with >Q20 quality and several kb length).
• Setting-up of a Quality approach in order to obtain ISO 9001 certification.