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the sequencing LIGAN platform

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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.
There are several groups inside our team : a group of biologists for the development and application of protocols, a group experienced in bioinformatics for the analysis of data after sequencing, a biostatistical group and a group for the management of computer resources to support bioinformatics analyzes and store the data generated during the projects, and beyond.

Expertise
Whole-exome sequencing
Augmented whole-exome sequencing enabling the accurate detection of CNVs
Targeted DNA-seq (gene panel)
Genotyping by DNA micro-arrays (GWAS)
RNA-seq (coding [mRNA] or non-coding [miRNA/lncRNA])
Counting of RNA molecules (NanoString technology)

RAD-Seq (ready to load)
Expression analysis via mRNA-seq and NanoString technology
Digital PCR
NG-Capture C
Shotgun metagenomics

Ongoing developments
Whole-genome sequencing (in particular computer analyses)

Equipement
Sequencing : 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.
Both teams manipulate their data on a Netapp high-performance storage system of more than one petabyte with multiple redundant controllers across a 10GB network. They can archive their data on an ML6000 DELL library with 130 slots, 2 LTO5 drives and 2 LTO drives.

The efficiency of the platform has been increased year after year with the acquisitions of the latest technologies developed by Illumina®. We were the first in Europe to own and use the HiSeq 4000, and the first in France with the NovaSeq.

Certification / Quality Assurance
ISO 15189 certification in progress

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.

For futher information
http://ligan.good.cnrs.fr/

last update : 01/02/2018


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