LIGAN platform – Personnalized Medicine
Presentation
Located in EGID building on the site of the Lille University Hospital, the LIGAN-PM platform is dedicated to next-generation sequencing and other state-of-the-art genomic technologies. Our sequencing and genotyping systems are primarily dedicated to precision medicine. However, the platform is opened to all applications related to genetics and genomics regardless of species. This platform includes several sequencing systems (MiSeq, NextSeq, NovaSeq), various robots for library preparation, a platform dedicated to genotyping and other state-of-the-art systems of genetics and genomics (such as NanoString).
The platform includes several groups of people :
- A group dedicated to biobank, for sample reception, DNA/RNA extraction, and sample storage.
- A group dedicated to next-generation sequencing (NGS) for the development and application of protocols.
- A group dedicated to genotyping (via DNA arrays) for the analyses of methylation and genome-wide association studies (GWAS).
- A group dedicated to bioinformatics.
- A group dedicated to biostatistics.
- A group dedicated to the management of computing resources.
- A group dedicated to the quality management system.
Website : http://ligan.good.cnrs.fr
Highlights
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The platform has been labelled ISO15189 (Medical Laboratory) allowing us to perform genetic diagnosis based on whole-exome sequencing or whole-genome sequencing. The platform has primarily been funded by an Equipement d’Excellence award (EquipEx). Beyond genetic diagnosis, the platform is opened to any requests related to genetics or genomics of academic or private laboratories.
Members
Amélie BONNEFOND
DR Inserm, head of the platform and head of post-analytics
Frederic ALLEGAERT
AI, Biobank
Souhila AMANZOUGARENE
IE, Bioinformatics
Anne-Sophie ANTOINE
AI, Assistant LIGAN
Alaa BADREDDINE
IE, Bioinformatics
Lionel BERBERIAN
IE, Bioinformatics
Mathilde BOISSEL
IE, Biostatistics
Raphaël BOUTRY
AI, Sequencing
Mickaël CANOUIL
IE, Biostatistics
IE, RH
Aurélie DECHAUME
IE, Sequencing
Fabien DELAHAYE
Postdoc, skills in single-cell
Marion DELBARRE
IE, quality management system ISO1589 and sequencing
Mehdi DERHOURHI
IR, Bioinformatics
Julien DEROP
IE, quality management system ISO1589, sequencing, sequencing and head of services
Emmanuelle DURAND
IE, Sequencing
Philippe FROGUEL
PU-PH, CHU Lille, unit director
Corentin GIRARD
AI, quality management system ISO1589
Mélanie HOCQUET
Secretary, RH
Nicolas KUREZOBA
Technician, Purchasing
Anne-Sophie LEDOUX
IE, Informatics
Hélène LOISELLE
AI, Sequencing
Vincent MASSY
IE, Informatics
Lijiao NING
IE, Biostatistics
Bénédicte TOUSSAINT
IE, Sequencing
Emmanuel VAILLANT
IE, Sequencing
Nicolas VANEECHOUTTE
IE, Informatics
Vincent VATIN
AI, Purchasing
Martine VAXILAIRE
DR Pasteur Lille, co-head of post-analytics
Publications
Bonnefond A, Boissel M, Bolze A, Durand E, Toussaint B, Vaillant E, Gaget S, Graeve F, Dechaume A, Allegaert F, Guilcher DL, Yengo L, Dhennin V, Borys JM, Lu JT, Cirulli ET, Elhanan G, Roussel R, Balkau B, Marre M, Franc S, Charpentier G, Vaxillaire M, Canouil M, Washington NL, Grzymski JJ, Froguel P.
Pathogenic variants in actionable MODY genes are associated with type 2 diabetes.
Nat Metab. 2020 Oct;2(10):1126-1134.
Baron M, Maillet J, Huyvaert M, Dechaume A, Boutry R, Loiselle H, Durand E, Toussaint B, Vaillant E, Philippe J, Thomas J, Ghulam A, Franc S, Charpentier G, Borys JM, Lévy-Marchal C, Tauber M, Scharfmann R, Weill J, Aubert C, Kerr-Conte J, Pattou F, Roussel R, Balkau B, Marre M, Boissel M, Derhourhi M, Gaget S, Canouil M, Froguel P, Bonnefond A.
Loss-of-function mutations in MRAP2 are pathogenic in hyperphagic obesity with hyperglycemia and hypertension.
Nat Med. 2019 Nov;25(11):1733-1738.
Saeed S, Bonnefond A, Tamanini F, Mirza MU, Manzoor J, Janjua QM, Din SM, Gaitan J, Milochau A, Durand E, Vaillant E, Haseeb A, De Graeve F, Rabearivelo I, Sand O, Queniat G, Boutry R, Schott DA, Ayesha H, Ali M, Khan WI, Butt TA, Rinne T, Stumpel C, Abderrahmani A, Lang J, Arslan M, Froguel P.
Loss-of-function mutations in ADCY3 cause monogenic severe obesity.
Nat Genet. 2018 Feb;50(2):175-179.
Juge PA, Borie R, Kannengiesser C, Gazal S, Revy P, Wemeau-Stervinou L, Debray MP, Ottaviani S, Marchand-Adam S, Nathan N, Thabut G, Richez C, Nunes H, Callebaut I, Justet A, Leulliot N, Bonnefond A, Salgado D, Richette P, Desvignes JP, Lioté H, Froguel P, Allanore Y, Sand O, Dromer C, Flipo RM, Clément A, Béroud C, Sibilia J, Coustet B, Cottin V, Boissier MC, Wallaert B, Schaeverbeke T, Dastot le Moal F, Frazier A, Ménard C, Soubrier M, Saidenberg N, Valeyre D, Amselem S; FREX consortium, Boileau C, Crestani B, Dieudé P.
Shared genetic predisposition in rheumatoid arthritis-interstitial lung disease and familial pulmonary fibrosis.
Eur Respir J. 2017 May 11;49(5):160231
Louis-Dit-Picard H, Barc J, Trujillano D, Miserey-Lenkei S, Bouatia-Naji N, Pylypenko O, Beaurain G, Bonnefond A, Sand O, Simian C, Vidal-Petiot E, Soukaseum C, Mandet C, Broux F, Chabre O, Delahousse M, Esnault V, Fiquet B, Houillier P, Bagnis CI, Koenig J, Konrad M, Landais P, Mourani C, Niaudet P, Probst V, Thauvin C, Unwin RJ, Soroka SD, Ehret G, Ossowski S, Caulfield M; International Consortium for Blood Pressure (ICBP), Bruneval P, Estivill X, Froguel P, Hadchouel J, Schott JJ, Jeunemaitre X.
Shared genetic predisposition in rheumatoid arthritis-interstitial lung disease and familial pulmonary fibrosis.
Nat Genet. 2012 Mar 11;44(4):456-60, S1-3.
Keywords
Next-generation sequencing ; Genotyping ; DNA array ; ISO1589 ; Bioinformatics ; Biostatistics ; Genetic diagnosis ; Rare disorder ; Genomics ; Epigenetics ; Epitranscriptomics ; Whole-genome sequencing ; Whole-exome sequencing ; RNA-seq ; ChIP-seq ; HiC ; Methylation ; Single-cell ; Genome-wide association studies