Presentation

The genomics core facility was created in 2008 to provide high-throughput sequencing and gene expression services to the Necker research community mainly on a fee-for-service basis. The facility performs all the molecular biology steps required to produce raw data form the DNA and RNA samples provided by the users. The Experimental design and the analysis and interpretation of results are performed on an interactive basis with investigators and the bioinformatics facility (Imagine Foundation/Paris Descartes University).

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Localisation 

Imagine - Institut des maladies génétiques - 3e étage

24 Boulevard du Montparnasse, 75015 Paris

 

Offices : 333-334, Labs : 335-336-337

Staff

 
 
Christine Bole-Feysot 5.jpg
Christine Bôle-Feysot, PhD

Manager, IR, Inserm

christine.bole@inserm.fr

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Annarita Miccio, PhD

Scientific adviser

annarita.miccio@inserm.fr

Mélanie Parisot
Cecile Rouillon
Mohammed Zarhrate
Yohann Schmitt
 
 

Equipement

Genomic core facility has acquired its first next generation sequencer in 2010 and has increased and adapted its sequencing capabilities over the time.

Since 2019, the genomic platform is using a NovaSeq6000 (Illumina, short read technology) and an iSeq100 (Illumina) used mainly for libraries quality checks)​

Other equipment: DNA shearing: Covaris E220, Capillary electrophoresis: Fragment Analyzer (Proteigene), Tape Station 2200 (Agilent Technologies), Nucleic acids measurement: Xpose spectrophotometer (Trinean), QuBit fluorimeter (Invitrogen), real time PCR StepOnePlus (Life Technologies)

Services

The core facility provides:

  • A help to the experimental design

  • The quality check of DNAs and RNAs samples

  • The library construction, clonal amplification and sequencing with next generation sequencers

  • The quality check and sequencing of various types of NGS libraries

  • The primary data analysis and transfer to the bioinformatics facility for further data analysis

Proposed applications:

  • Exome Sequencing (standard, cancer)

  • Whole Genome Sequencing

  • Targeted re-sequencing using panels of genes of interest (capture by hybridization approach)

  • Amplicon-Sequencing (approach by ligation, including quality controls performed following CRISPR-Cas9 mediated mutagenesis, revertant analysis)

  • Transcriptomic analysis by RNA sequencing:    

standard analyses: mRNAseq Profiling (15-20 million reads), mRNAseq Transcriptome (50 million reads)

on demand: mRNAseq Transcriptome - small amount of total RNA (<50 ng/µl, 50 million reads), total RNAseq

  • Single cell RNAseq libraries sequencing

  • Other applications of next generation sequencing on demand: sequencing of ChIP-Seq libraries (sequencing of immunoprecipitated chromatin), sequencing of ATAC-Seq libraries (Assay for Transposase-Accessible Chromatin sequencing to analyse the chromatin region accessible to transcription regulators)…

Publications

 

Improving the diagnostic efficiency of primary immunodeficiencies with targeted next-generation sequencing. Fusaro M, Rosain J, Grandin V, Lambert N, Hanein S, Fourrage C, Renaud N, Gil M, Chevalier S, Chahla WA, Bader-Meunier B, Barlogis V, Blanche S, Boutboul D, Castelle M, Comont T, Diana JS, Fieschi C, Galicier L, Hermine O, Lefèvre-Utile A, Malphettes M, Merlin E, Oksenhendler E, Pasquet M, Suarez F, André I, Béziat V, De Saint Basile G, De Villartay JP, Kracker S, Lagresle-Peyrou C, Latour S, Rieux-Laucat F, Mahlaoui N, Bole C, Nitschke P, Hulier-Ammar E, Fischer A, Moshous D, Neven B, Alcais A, Vogt G, Bustamante J, Picard C.J Allergy Clin Immunol. 2021 Feb;147(2):734-737.

  

Somatic reversion of pathogenic DOCK8 variants alters lymphocyte differentiation and function to effectively cure DOCK8 deficiency. Pillay BA, Fusaro M, Gray PE, Statham AL, Burnett L, Bezrodnik L, Kane A, Tong W, Abdo C, Winter S, Chevalier S, Levy R, Masson C, Schmitt Y, Bole C, Malphettes M, Macintyre E, De Villartay JP, Ziegler JB, Smart JM, Peake J, Aghamohammadi A, Hammarström L, Abolhassani H, Picard C, Fischer A, Latour S, Neven B, Tangye SG, Ma CS.J Clin Invest. 2021 Feb 1;131(3):e142434.

 

Heterozygous FGFR1 mutation may be responsible for an incomplete form of osteoglophonic dysplasia, characterized only by radiolucent bone lesions and teeth retentions. Marzin P, Baujat G, Gensburger D, Huber C, Bole C, Panuel M, Finidori G, De la Dure M, Cormier-Daire V.Eur J Med Genet. 2020 Feb;63(2):103729.

 

Novel de novo ZBTB20 mutations in three cases with Primrose syndrome and constant corpus callosum anomalies. Alby C, Boutaud L, Bessières B, Serre V, Rio M, Cormier-Daire V, de Oliveira J, Ichkou A, Mouthon L, Gordon CT, Bonnière M, Mechler C, Nitschke P, Bole C, Lyonnet S, Bahi-Buisson N, Boddaert N, Colleaux L, Roth P, Ville Y, Vekemans M, Encha-Razavi F, Attié-Bitach T, Thomas S.Am J Med Genet A. 2018 May;176(5):1091-1098.

 

 

BAFF and CD4+ T cells are major survival factors for long-lived splenic plasma cells in a B-cell-depletion context. Thai LH, Le Gallou S, Robbins A, Crickx E, Fadeev T, Zhou Z, Cagnard N, Mégret J, Bole C, Weill JC, Reynaud CA, Mahévas M.Blood. 2018 Apr 5;131(14):1545-1555. doi: 10.1182/blood-2017-06-789578. Epub 2018 Jan 29.PMID: 29378696 

 

Recurrent RTTN mutation leading to severe microcephaly, polymicrogyria and growth restriction.Cavallin M, Bery A, Maillard C, Salomon LJ, Bole C, Reilly ML, Nitschké P, Boddaert N, Bahi-Buisson N.Eur J Med Genet. 2018 Dec;61(12):755-758.

 

 

No correlation between mtDNA amount and methylation levels at the CpG island of POLG exon 2 in wild-type and mutant human differentiated cells. Steffann J, Pouliet A, Adjal H, Bole C, Fourrage C, Martinovic J, Rolland-Galmiche L, Rotig A, Tores F, Munnich A, Bonnefont JP.J Med Genet. 2017 May;54(5):324-329. doi: 10.1136/jmedgenet-2016-104335. Epub 2017 Jan 9.PMID: 28069933

 

WDR81 mutations cause extreme microcephaly and impair mitotic progression in human fibroblasts and Drosophila neural stem cells. Cavallin M, Rujano MA, Bednarek N, Medina-Cano D, Bernabe Gelot A, Drunat S, Maillard C, Garfa-Traore M, Bole C, Nitschké P, Beneteau C, Besnard T, Cogné B, Eveillard M, Kuster A, Poirier K, Verloes A, Martinovic J, Bidat L, Rio M, Lyonnet S, Reilly ML, Boddaert N, Jenneson-Liver M, Motte J, Doco-Fenzy M, Chelly J, Attie-Bitach T, Simons M, Cantagrel V, Passemard S, Baffet A, Thomas S, Bahi-Buisson N.Brain. 2017 Oct 1;140(10):2597-2609.


Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. Capel E, Zomer AL, Nussbaumer T, Bole C, Izac B, Frapy E, Meyer J, Bouzinba-Ségard H, Bille E, Jamet A, Cavau A, Letourneur F, Bourdoulous S, Rattei T, Nassif X, Coureuil M.mBio. 2016 Aug 2;7(4):e01173-16.