Bioinformatics

 
 
 
 
 
Bioinformatics Team_edited.jpg

Presentation

The fondation Imagine, as a partner of the Paris-Descartes University and of the Faculty of Medicine, benefits from the support of the Paris-Descartes Bioinformatics Platform to come-along with the scientists throughout their Imagine labeled projects (support for the experimental design planning, data handling and analysis, biological tools for data integration and interpretation).

The bioinformatics Platform collaborates with the Imagine scientists and genomic platform to develop an original pipeline for genetic linkage studies (from raw SNP microarray data to visualisation and annotation of the candidate genomic regions via an interactive web interface). This pipeline allowed the analysis of 50 linkage projects by year.

Since 2009, the Fondation Imagine followed the “next” generation sequencer evolution and acquired severall machines more and more powerful. The increasing amount of data generated by these technologies created new challenging issues to store, analyze, integrate and visualize pertinent information. To reach this goal, we have developed a new original pipeline to analyze resequencing projects. Our pipeline, Polypipeline is based on public tools (alignment, variation finding) as well as an original database design PolyDB (storage and minning data) and finally a new graphical interface Polyweb (interpretation and visualization). Our tool is completely generic and is independant from the sequencing technology used.

Our team participates also to various projects, either relating to sequencing like chip/seq, rna/seq… or more broadly to biostatistics like transcriptomic, pathway analysis… We can also help the researcher during the design step of her/his experiment to optimize the odds of positive findings.

Staff

Patrick Nitschké_edited.jpg
Patrick Nitschké

Head, IR, Paris Université

patrick.nitschke@inserm.fr

Nicolas Cagnard
Frédéric Tores
Cécile Fourrage
Cécile Masson

IE, Paris Université

cecile.masson@inserm.fr

Emmanuelle Ollivier
Jean-Philippe Jais
Maria-Emilia Puig Lobardi
Fabienne Jabot-Hanin

IR, Paris Université

fabienne.hanin@parisdescartes.fr

Jean-Marc Plaza
Sylvain Hanein
Marc Bras

Localisation 

Institut Imagine

24, Boulevard du Montparnasse 75015 PARIS

2ème étage, Bureaux : 240 / 238 / 236

Serveurs_edited.jpg

Equipement

  • Cluster HP : 320 cores CPU/4TB RAM

  • Serveur d’application : 40 cores et 512 Gb RAM

  • Parallel Cluster File System Beegfs 50 To

  • Disques de stockage (Isilon) 1,8P
     

Fees

NGS analysis

 

The bioinformatics platform provides imagine scientists (researchers and doctors) with a complete software suite allowing them to manage, analyze and visualize resequencing data (gene panels, exomes or complete genomes).

 

This software Polyweb includes:

  • an analysis pipeline (Polypipeline) that relies on

  • most relevant public software and databases to realize

  • sequence alignment, variant invocation and annotation

  • (functional consequence, frequency, associated phenotype...).

  • database developed by the platform (PolyProject) for sample monitoring.

  • two graphical interfaces, PolyQuery and PolyDiag for help in interpreting and visualizing the results.

Polyweb.jpg

Transcriptomics:

Our team supports also different types of "-Seq" studies, providing expertise in methods such as ChIP-Seq or RNA-Seq.

 

More broadly, projects based on matrices (transcriptomics), SNP tables and functional studies (enrichment and channel analyses) are also managed by the platform. 

 

We take care of your analysis projects from quantification to statistical analyses. We have an Ingenuity license that we make available to researchers on a client station to help you in the biological interpretation of your results. A platform engineer is also available to train you on Ingenuity. We can also help you in the posting of your data on the public repository.

Statistical analyses:

Finally, we carry out statistical genetic analyses of groups of patients, commonly known as "burden tests".

Publications

1. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C, Rosain J, Bilguvar K, Ye J, Bolze A, Bigio B, Yang R, Arias AA, Zhou Q, Zhang Y, Onodi F, Korniotis S, Karpf L, Philippot Q, Chbihi M, Bonnet-Madin L, Dorgham K, Smith N, Schneider WM, Razooky BS, Hoffmann HH, Michailidis E, Moens L, Han JE, Lorenzo L, Bizien L, Meade P, Neehus AL, Ugurbil AC, Corneau A, Kerner G, Zhang P, Rapaport F, Seeleuthner Y, Manry J, Masson C, Schmitt Y, Schlüter A, Le Voyer T, Khan T, Li J, Fellay J, Roussel L, Shahrooei M, Alosaimi MF, Mansouri D, Al-Saud H, Al-Mulla F, Almourfi F, Al-Muhsen SZ, Alsohime F, Al Turki S, Hasanato R, van de Beek D, Biondi A, Bettini LR, D'Angio' M, Bonfanti P, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Oler AJ, Tompkins MF, Alba C, Vandernoot I, Goffard JC, Smits G, Migeotte I, Haerynck F, Soler-Palacin P, Martin-Nalda A, Colobran R, Morange PE, Keles S, Çölkesen F, Ozcelik T, Yasar KK, Senoglu S, Karabela ŞN, Rodríguez-Gallego C, Novelli G, Hraiech S, Tandjaoui-Lambiotte Y, Duval X, Laouénan C; COVID-STORM Clinicians; COVID Clinicians; Imagine COVID Group; French COVID Cohort Study Group; CoV-Contact Cohort; Amsterdam UMC Covid-19 Biobank; COVID Human Genetic Effort; NIAID-USUHS/TAGC COVID Immunity Group, Snow AL, Dalgard CL, Milner JD, Vinh DC, Mogensen TH, Marr N, Spaan AN, Boisson B, Boisson-Dupuis S, Bustamante J, Puel A, Ciancanelli MJ, Meyts I, Maniatis T, Soumelis V, Amara A, Nussenzweig M, García-Sastre A, Krammer F, Pujol A, Duffy D, Lifton RP, Zhang SY, Gorochov G, Béziat V, Jouanguy E, Sancho-Shimizu V, Rice CM, Abel L, Notarangelo LD, Cobat A, Su HC, Casanova JL.  Imagine COVID Group : Christine Bole-Feysot, Stanislas Lyonnet*, Cécile Masson, Patrick Nitschke, Aurore Pouliet, Yoann Schmitt, Frederic Tores, Mohammed Zarhrate

Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France.

Science. 2020 Oct 23;370 (6515):eabd4570. doi: 10.1126/science.abd4570. PMID: 32972995

2. Autoantibodies against type I IFNs in patients with life-threatening COVID-19.

Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH, Zhang Y, Dorgham K, Philippot Q, Rosain J, Béziat V, Manry J, Shaw E, Haljasmägi L, Peterson P, Lorenzo L, Bizien L, Trouillet-Assant S, Dobbs K, de Jesus AA, Belot A, Kallaste A, Catherinot E, Tandjaoui-Lambiotte Y, Le Pen J, Kerner G, Bigio B, Seeleuthner Y, Yang R, Bolze A, Spaan AN, Delmonte OM, Abers MS, Aiuti A, Casari G, Lampasona V, Piemonti L, Ciceri F, Bilguvar K, Lifton RP, Vasse M, Smadja DM, Migaud M, Hadjadj J, Terrier B, Duffy D, Quintana-Murci L, van de Beek D, Roussel L, Vinh DC, Tangye SG, Haerynck F, Dalmau D, Martinez-Picado J, Brodin P, Nussenzweig MC, Boisson-Dupuis S, Rodríguez-Gallego C, Vogt G, Mogensen TH, Oler AJ, Gu J, Burbelo PD, Cohen JI, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Rossignol P, Mayaux J, Rieux-Laucat F, Husebye ES, Fusco F, Ursini MV, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Castagnoli R, Montagna D, Licari A, Marseglia GL, Duval X, Ghosn J; HGID Lab; NIAID-USUHS Immune Response to COVID Group; COVID Clinicians; COVID-STORM Clinicians; Imagine COVID Group; French COVID Cohort Study Group; Milieu Intérieur Consortium; CoV-Contact Cohort; Amsterdam UMC Covid-19 Biobank; COVID Human Genetic Effort, Tsang JS, Goldbach-Mansky R, Kisand K, Lionakis MS, Puel A, Zhang SY, Holland SM, Gorochov G, Jouanguy E, Rice CM, Cobat A, Notarangelo LD, Abel L, Su HC, Casanova JL.

Imagine COVID Group : Christine Bole-Feysot, Stanislas Lyonnet*, Cécile Masson, Patrick Nitschke, Aurore Pouliet, Yoann Schmitt, Frederic Tores, Mohammed Zarhrate Imagine Institute, Université de Paris, INSERM UMR 1163, Paris, France.

Science. 2020 Oct 23;370(6515):eabd4585. doi: 10.1126/science.abd4585. PMID: 32972996.

 

3. Bi-allelic Variations of SMO in Humans Cause a Broad Spectrum of Developmental Anomalies Due to Abnormal Hedgehog Signaling.

Le TL, Sribudiani Y, Dong X, Huber C, Kois C, Baujat G, Gordon CT, Mayne V, Galmiche L, Serre V, Goudin N, Zarhrate M, Bole-Feysot C, Masson C, Nitschké P, Verheijen FW, Pais L, Pelet A, Sadedin S, Pugh JA, Shur N, White SM, El Chehadeh S, Christodoulou J, Cormier-Daire V, Hofstra RMW, Lyonnet S, Tan TY, Attié-Bitach T, Kerstjens-Frederikse WS, Amiel J, Thomas S. Am J Hum Genet. 2020 Jun 4;106(6):779-792. doi: 10.1016/j.ajhg.2020.04.010.  PMID: 32413283

4. Tumor invasion in draining lymph nodes is associated with Treg accumulation in breast cancer patients.

Núñez NG, Tosello Boari J, Ramos RN, Richer W, Cagnard N, Anderfuhren CD, Niborski LL, Bigot J, Meseure D, De La Rochere P, Milder M, Viel S, Loirat D, Pérol L, Vincent-Salomon A, Sastre-Garau X, Burkhard B, Sedlik C, Lantz O, Amigorena S, Piaggio E.

Nat Commun. 2020 Jun 29;11(1):3272. doi: 10.1038/s41467-020-17046-2. PMID: 32601304

 

5. Early-onset autoimmunity associated with SOCS1 haploinsufficiency.

Hadjadj J, Castro CN, Tusseau M, Stolzenberg MC, Mazerolles F, Aladjidi N, Armstrong M, Ashrafian H, Cutcutache I, Ebetsberger-Dachs G, Elliott KS, Durieu I, Fabien N, Fusaro M, Heeg M, Schmitt Y, Bras M, Knight JC, Lega JC, Lesca G, Mathieu AL, Moreews M, Moreira B, Nosbaum A, Page M, Picard C, Ronan Leahy T, Rouvet I, Ryan E, Sanlaville D, Schwarz K, Skelton A, Viallard JF, Viel S, Villard M, Callebaut I, Picard C, Walzer T, Ehl S, Fischer A, Neven B, Belot A, Rieux-Laucat F.

Nat Commun. 2020 Oct 21;11(1):5341. doi: 10.1038/s41467-020-18925-4. PMID: 33087723

 

6. Clonal tracking in gene therapy patients reveals a diversity of human hematopoietic differentiation programs.

Six E, Guilloux A, Denis A, Lecoules A, Magnani A, Vilette R, Male F, Cagnard N, Delville M, Magrin E, Caccavelli L, Roudaut C, Plantier C, Sobrino S, Gregg J, Nobles CL, Everett JK, Hacein-Bey-Abina S, Galy A, Fischer A, Thrasher AJ, André I, Cavazzana M, Bushman FD.

Blood. 2020 Apr 9;135(15):1219-1231. doi: 10.1182/blood.2019002350. PMID: 32040546

 

7. Human C-terminal CUBN variants associate with chronic proteinuria and normal renal function.

Bedin M, Boyer O, Servais A, Li Y, Villoing-Gaudé L, Tête MJ, Cambier A, Hogan J, Baudouin V, Krid S, Bensman A, Lammens F, Louillet F, Ranchin B, Vigneau C, Bouteau I, Isnard-Bagnis C, Mache CJ, Schäfer T, Pape L, Gödel M, Huber TB, Benz M, Klaus G, Hansen M, Latta K, Gribouval O, Morinière V, Tournant C, Grohmann M, Kuhn E, Wagner T, Bole-Feysot C, Jabot-Hanin F, Nitschké P, Ahluwalia TS, Köttgen A, Andersen CBF, Bergmann C, Antignac C,Simons M

J Clin Invest. 2020 Jan 2;130(1):335-344. doi: 10.1172/JCI129937. PMID: 31613795

 

8.      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.. Allergy Clin Immunol. 2020 Jun 10:S0091-6749(20)30816-2.

 

9. Gene Mutations in a Large Cohort of Predominantly Caucasian Patients with Hidradenitis Suppurativa. Low Prevalence of GSC.

Duchatelet S, Miskinyte S, Delage M, Ungeheuer MN, Lam T, Benhadou F, Del Marmol V, Vossen ARJV, Prens EP, Cogrel O, Beylot-Barry M, Girard C, Vidil J, Join-Lambert O, Parisot M, Nitschké P, Hanein S, Fraitag S, Van der Zee HH, Bessis D, Damiani G, Altomare A, Liao YH, Nikolakis G, Zouboulis CC, Nassif A, Hovnanian A. J Invest Dermatol. 2020 Oct;140(10):2085-2088.e14.

 

10. A novel pathogenic variant in DYNC1H1 causes various upper and lower motor neuron anomalies.

Viollet LM, Swoboda KJ, Mao R, Best H, Ha Y, Toutain A, Guyant-Marechal L, Laroche-Raynaud C, Ghorab K, Barthez MA, Pedespan JM, Hernandorena X, Lia AS, Deleuze JF, Masson C, Nelson I, Nectoux J, Si Y.

Eur J Med Genet. 2020 Dec;63(12):104063. doi: 10.1016/j.ejmg.2020.104063. Epub 2020 Sep 16. PMID: 32947049

              

11. Fetal megacystis-microcolon: Genetic mutational spectrum and identification of PDCL3 as a novel candidate gene.

Billon C, Molin A, Poirsier C, Clemenson A, Dauge C, Grelet M, Sigaudy S, Patrier S, Goldenberg A, Layet V, Tantau J, Fleury C, Liard A, Diguet A, Fritih R, Verspyck E, Rendu J, Boutaud L, Tessier A, Thomas S, Razavi F, Achaiaa A, Elkhartoufi N, Hakkakian L, Magnin E, Bôle-Feysot C, Masson C, Ville Y, Roth P, Prieur F, Bessieres B, Bonniere M, Attie-Bitach T.

Clin Genet. 2020 Sep;98(3):261-273. doi: 10.1111/cge.13801. PMID: 32621347

 

12.  Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype.

Weber L, Frati G, Felix T, Hardouin G, Casini A, Wollenschlaeger C, Meneghini V, Masson C, De Cian A, Chalumeau A, Mavilio F, Amendola M, Andre-Schmutz I, Cereseto A, El Nemer W, Concordet JP, Giovannangeli C, Cavazzana M, Miccio A.

Sci Adv. 2020 Feb 12;6(7):eaay9392. doi: 10.1126/sciadv.aay9392. PMID: 32917636 

 

13.  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 WWY, Abdo C, Winter S, Chevalier S, Levy R, Masson C, Schmitt Y, Bole-Feysot 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 S, Ma CS.

J Clin Invest. 2020 Dec 8:142434. doi: 10.1172/JCI142434. PMID: 33290277

              

14. From Dysgammaglobulinemia to Autosomal-Dominant Activation-Induced Cytidine Deaminase Deficiency: Unraveling an Inherited Immunodeficiency after 50 Years.

Fadlallah J, Chentout L, Boisson B, Pouliet A, Masson C, Morin F, Durandy A, Casanova JL, Oksenhendler E, Kracker S.

J Pediatr. 2020 Aug;223:207-211.e1. doi: 10.1016/j.jpeds.2020.03.024. PMID: 32423680

 

15. High Diagnostic Yield of Targeted Next-Generation Sequencing in a Cohort of Patients with Congenital Hypothyroidism Due to Dyshormonogenesis

Athanasia STOUPA, Ghada Al Hage Chehade, Rim Chaabane, Dulanjalee Kariyawasam, Gabor Szinnai, Sylvain Hanein, Christine Bole-Feysot, Cecile Fourrage, Patrick Nitschke, Caroline Thalassinos, Graziella Pinto, Mouna Mnif, Sabine Baron, Marc De Kerdanet, Rachel Reynaud, Pascal Barat, Mongia Hachicha, Neila Belguith, Michel Polak, Aurore CARRE

Frontiers in Endocrinology, section Thyroid Endocrinology  | doi: 10.3389/fendo.2020.545339

 

16. Loss-of-Function Mutations in NR4A2 Cause Dopa-Responsive Dystonia Parkinsonism.

Wirth T, Mariani LL, Bergant G, Baulac M, Habert MO, Drouot N, Ollivier E, Hodžić A, Rudolf G, Nitschke P, Rudolf G, Chelly J, Tranchant C, Anheim M, Roze E.

Mov Disord. 2020 May;35(5):880-885. doi: 10.1002/mds.27982. Epub 2020 Jan 10. PMID: 31922365

 

17.  Increased diagnostic yield in complex dystonia through exome sequencing.

Wirth T, Tranchant C, Drouot N, Keren B, Mignot C, Cif L, Lefaucheur R, Lion-François L, Méneret A, Gras D, Roze E, Laroche C, Burbaud P, Bannier S, Lagha-Boukbiza O, Spitz MA, Laugel V, Bereau M, Ollivier E, Nitschke P, Doummar D, Rudolf G, Anheim M, Chelly

J. Parkinsonism Relat Disord. 2020 May;74:50-56. doi: 10.1016/j.parkreldis.2020.04.003. Epub 2020 Apr 20. PMID: 32334381

 

18. NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Høyeraal-Hreidarsson syndrome.

Benyelles M, O'Donohue MF, Kermasson L, Lainey E, Borie R, Lagresle-Peyrou C, Nunes H, Cazelles C, Fourrage C, Ollivier E, Marcais A, Gamez AS, Morice-Picard F, Caillaud D, Pottier N, Ménard C, Ba I, Fernandes A, Crestani B, de Villartay JP, Gleizes PE, Callebaut I, Kannengiesser C, Revy P.

Hum Mol Genet. 2020 Apr 15;29(6):907-922. doi: 10.1093/hmg/ddaa011. PMID: 31985013

 

19. MeCP2 is involved in random mono-allelic expression for a subset of human autosomal genes.

Brousseau M, Nectoux J, Saintpierre B, Lebrun N, Cagnard N, Izac B, Ollivier E, Letourneur F, Bienvenu T. Biochim Biophys Acta Mol Basis Dis. 2020 Jun 1;1866(6):165730. doi: 10.1016/j.bbadis.2020.165730. PMID: 32070770

 

20.  Unique inflammatory signature in haemophilic arthropathy: miRNA changes due to interaction between blood and fibroblast-like synoviocytes.

Mignot S, Cagnard N, Albaud B, Bally C, Siavellis J, Hermine O, Frenzel L.

J Cell Mol Med. 2020 Nov 7;24(24):14453-66. doi: 10.1111/jcmm.16068. PMID: 33159500