GENOMICS
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).
SERVICES
THE CORE FACILITY PROVIDES
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A help to the experimental design
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The quality check of DNAs and RNAs samples
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The library construction, clonal amplification and sequencing
with next generation sequencers
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The quality check and sequencing of various types of NGS libraries
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The primary data analysis and transfer to the bioinformatics facility
for further data analysis
PROPOSED APPLICATIONS
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Exome Sequencing (standard, cancer)
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Whole Genome Sequencing
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Targeted re-sequencing using panels of genes of interest
(capture by hybridization approach)
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Amplicon-Sequencing (approach by ligation, including quality controls performed following CRISPR-Cas9 mediated mutagenesis, revertant analysis)
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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
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Single cell RNAseq libraries sequencing
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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)…
EQUIPMENT
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)
STAFF
Yakov VITRENKO
Head
Annarita MICCIO, PhD
Scientific Advisor
Mélanie PARISOT
Cécile ROUILLON
Yohann SCHMITT
Mohammed ZARHRATE
Fatou CAMARA
Christine BÔLE-FEYSOT, PhD
Marie JAZZARA
PUBLICATIONS
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.
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.
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.
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.
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.
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
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.
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.