The sequencing LIGAN platform
Introduction
Located at EGID site on the Lille CHRU site, the Ligan-PM platform is dedicated to a plethora of next-generation sequencing protocols (whole-exome sequencing, whole-genome sequening, RNA-seq) and to other cutting-edge technologie for personalized medicine. We have developed many protocols adapted to human genetic disease in order to perform accurate molecular diagnosis of human genetic diseases and to reach personalized medicine.
LIGAN-PM is a scientific collaboration facility with high expertise in human genetics and a high speed NGS service platform opened to public and private organizations.
Projects are focused on diabetes, obesity, associated metabolic diseases and rare diseases but the plateform accepts all types of scientific projects as long as they remain within the field of expertise and the means allow.
The team is composed of several groups a group dedicated to new generation sequencing (NGS) for the development and application of protocols, a group dedicated to genotyping by DNA chip, a group experienced in bioinformatics for the analysis of data after sequencing, a group dedicated to biostatistics, a group dedicated to the management of IT resources in order to manage bioinformatics analyses and to store the data generated during the duration of the project, and beyond that, a group dedicated to customer relations and a group dedicated to quality (NF EN ISO 15189).
Expertise
- WGS, WES sequencing
- Improved NGS exome sequencing with enriched capture to detect CNVs
- Targeted NGS DNA sequencing (gene panel)
- NGS sequencing of coding (mRNA) or non-coding (miRNA/lncRNA) RNA
- NGS shotgun metagenomics sequencing
- NGS ChIP-seq sequencing (histone, transcription factors...)
- NGS HiC sequencing
- Counting of coding and non-coding RNA molecules (NanoString technology)
- Digital PCR
- Genotyping by DNA chip (GWAS study)
Equipments
- Sequencing NGS: 2MiSeq Illumina, 1 NextSeq 500 Illumina, 2 HiSeq 2500 Illumina, 1 HiSeq 4000 Illumina, 1 NovaSeq 6000 Illumina
- Genotyping / expression: IScan Illumina, 3730xl DNA analysis, Biomark Fluidigm, NCounter NanoString, Viia 7 LifeTechnologies
- Robotics: 1 DuoSTARlet, 2 STAR Hamilton, 2 Bravo Agilent,
- Other: Covaris E220, LabChip GX PerkinElmer, Pyromark Q24 and Q48, Light Cycler Roche, Access Array Fluidigm QX200 Droplet Digital PCR Bio-Rad
Computer tools
- The NGS team has 3 NAS storage spaces of 30TB each (receiving sequencing data directly from the sequencing equipments)
- The Bioinfo team has 10 DELL R9XX quad-processor computing servers (each with a minimum of 512GB of RAM). The set counts more than 1000 cores, runs on an ubuntu server system and is grouped in a docker cluster.
- The Biostatistics team has 2 DELL R920 four-processor computing servers (each with 512GB of RAM). The set counts 220 cores, under proxmox 4 cut in containers under Linux 7 scientist.
Developments
- development of a targeted 3D chromatin conformation analysis (SONICC) [new method]
- optimisation of whole genome sequencing via new library preparations (in particular to improve the uniformity of sequence quantities between individuals) [computational optimisation]
- optimisation of whole genome sequencing analysis time through the use of graphics cards (GPU) [computational optimisation]
- new analytical method] automation via Sciclone of the last library choice for exome/whole genome sequencing
Main achievements
- Bonnefond A, et al. Pathogenic variants in actionable MODY genes are associated with type 2 diabetes. Nat Metab. (2020) 2(10):1126-1134.
- Baron M, et al. Loss-of-function mutations in MRAP2 are pathogenic in hyperphagic obesity with hyperglycemia and hypertension. Nat Med. (2019) 25(11):1733-1738.
- 3/ Montagne L, et al. CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability. Mol Metab. (2018)13:1-9
- Canouil M, et al. Epigenome-Wide Association Study Reveals Methylation Loci Associated With Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome. Diabetes Care. (2021) dc202960.
- Saeed S, et al. Loss-of-function mutations in ADCY3 cause monogenic severe obesity. Nat Genet. (2018) 50(2):175-179.
Last update Nov 2021
Certification / Quality Assurance
ISO 15189 certification in progress
Labels
IBiSA platform
Partnerships
In addition to our own research projects and services, LIGAN-PM is a partner of two RHUs: iMAP and PreciNASH; LIGAN-PM is a partner of the Transimmunom labex; the unit is involved in several IMI projects: DIRECT, RHAPSODY.
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