INCa-SLC

Adresse postale
Fondation Synergie Lyon Cancer, Bât. Cheney D
28 rue Laënnec 69008 Lyon
Structure(s) :
Non renseignée
Unité :
Non renseignée
Responsable(s) scientifique
Responsable(s) opérationnel
Responsable opérationnel
Non renseigné
Certificat(s)
Non renseigné
Type d'infrastructure
Hébergée
Capacité de stockage
400.00 To
Ferme de calcul
536 cores
Heure de CPU
20 000 H / an
Outils bioinformatiques
10
Nombre d'utilisateurs
15
Description des serveurs

1 serveur Tomcat/MySQL (SampleTracker)


Aucun site web renseigné
Visites annuelles :
Non renseignées
Visites uniques :
500 an
Citations :
30
Dernière mise à jour :
Non renseignée

SampleTracker

Description

Base de données (+ Interfaces Web) de gestion des échantillons tumoraux (et normaux) récoltés dans le cadre des programmes ICGC Sein et Prostate (cf. § Appui).

Conditions d'accès

Accès restreint aux membre de l'ICGC/INCa pour des raisons de confidentialité des données.

Domaines d'activité
  • Biomédical
  • Biologie
Description des expertises

Cette structure a été créée à l'initiative de l'INCa dans le cadre de sa participation à l'"International  Cancer Genome Consortium" (ICGC).

 

Elle a trois missions :
1 collecter ou préparer puis valider les acides nucléiques (ADN normal, ADN tumoral, ARN tumoral,...)  qui   seront   examinés   avec   les   techniques   de  la  génomique:   puce   de  génotypage,   puce d'expression, RNA-­seq, DNA-­‐eq en génomes complets et en éxomes),
2 assurer la liaison avec les centres de génomique (académiques  ou privés) réalisant le séquençage haut-­‐débit,
3 effectuer l'analyse des données de séquence transmises par ces centres de manière à en extraire l'information  (variants  somatiques  et  structuraux,  nombre  de  copie,  niveaux  d'expression  en RNA-­‐seq) utile aux équipes biomédicales.

 

Pour  remplir  sa  mission,  la  plateforme  a  développé  une  application  Internet  permettant  d'assurer  la gestion  de grands  projets  multicentriques  en toute  transparence  pour  les collaborateurs.  Elle  a mis en place  des  procédures  de  contrôle  qualité  des  échantillons  à  analyser.  Elle  dessine  et  automatise  des pipelines d'analyse pour les données de génomique qu'elle reçoit.

Mots clés:
  • Analyse de données de séquençage NGS
  • Méthodologie
  • Alignements de lectures sur des génomes
  • Génomique (DNA-seq)
  • Analyse de génomes
  • Annotation structurale et fonctionnelle des génomes
  • Transcriptomique (RNA-seq)
  • Analyse différentielle de l’expression des gènes
  • Analyses de transcrits et transcrits variants
  • Analyse de variants
  • Panels (amplicons, captures)
  • Exomes
  • Génomes complets
  • Analyse de la régulation de l’expression des gènes
  • Profils de méthylation
  • Biostatistiques
  • Génomique : Puces
  • Biopuces ADN
  • Génotypage
  • CGH
  • Biopuces ARN
  • Expression

Formation professionnelle

Aucun site web renseigné
Personnes formées :
Non renseigné
Temps de formation :
Non renseigné
Pas de nouvelle session prévue

Introduction Unix pour les biologistes

Description

https://www.biosciencesco.fr/formations/bio-informatique/introduction-unix-pour-les-biologistes/

Conditions d'accès

Inscription auprès de la société FC3-­‐Bio, aucun prérequis

Formation universitaire

Aucun site web renseigné
Personnes formées :
20 personnes / an
Temps de formation :
Non renseigné
Pas de nouvelle session prévue

Introduction à l'analyse de séquences nucléiques Du séquençage à l'annotation : aspects théoriques et pratiques

Description

https://www.biosciencesco.fr/formations/bio-informatique/introduction-a-lanalyse-de-sequences-nucleiques-du-sequencage-a-lannotation-aspects-theoriques-et-pratiques/

Conditions d'accès
Non renseigné
Publications internes

Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men. L. Tonon and G. Fromont and S. Boyault and E. Thomas and A. Ferrari and A.-S. Sertier and J. Kielbassa and V. Le Texier and A. Kamoun and N. Elarouci and J. Irani and L. Multigner and I. G. Gut and M. Gut and P. Blanchet and A. De Reynies and G. Cancel-Tassin and A. Viari and O. Cussenot. European urology  75  11--15  (2019)


A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. A. Ferrari and A. Vincent-Salomon and X. Pivot and A.-S. Sertier and E. Thomas and L. Tonon and S. Boyault and E. Mulugeta and I. Treilleux and G. MacGrogan and L. Arnould and J. Kielbassa and V. Le Texier and H. Blanche and J.-F. Deleuze and J. Jacquemier and M.-C. Mathieu and F. Penault-Llorca and F. Bibeau and O. Mariani and C. Mannina and J.-Y. Pierga and O. Trédan and T. Bachelot and H. Bonnefoi and G. Romieu and P. Fumoleau and S. Delaloge and M. Rios and J.-M. Ferrero and C. Tarpin and C. Bouteille and F. Calvo and I. G. Gut and M. Gut and S. Martin and S. Nik-Zainal and M. R. Stratton and I. Pauporté and P. Saintigny and D. Birnbaum and A. Viari and G. Thomas. Nature communications  7  12222  (2016)

 


A phenotypic and mechanistic perspective on heterogeneity of HER2-positive breast cancers. A. Ferrari and A.-S. Sertier and A. Vincent-Salomon and X. Pivot and I. Pauporté and P. Saintigny and D. Birnbaum and A. Viari. Molecular & cellular oncology  3  e1232186  (2016)

Publications externes

Neoepitopes-based vaccines: challenges and perspectives. V. Alcazer and P. Bonaventura and L. Tonon and S. Wittmann and C. Caux and S. Depil. European journal of cancer (Oxford, England : 1990)  108  55--60  (2019)


The circular RNome of primary breast cancer. M. Smid and S. M. Wilting and K. Uhr and F. G. Rodríguez-González and V. de Weerd and W. J. C. Prager-Van der Smissen and M. van der Vlugt-Daane and A. van Galen and S. Nik-Zainal and A. Butler and S. Martin and H. R. Davies and J. Staaf and M. J. van de Vijver and A. L. Richardson and G. MacGrogan and R. Salgado and G. G. G. M. van den Eynden and C. A. Purdie and A. M. Thompson and C. Caldas and P. N. Span and F. C. G. J. Sweep and P. T. Simpson and S. R. Lakhani and S. Van Laere and C. Desmedt and A. Paradiso and J. Eyfjord and A. Broeks and A. Vincent-Salomon and A. P. Futreal and S. Knappskog and T. King and A. Viari and A.-L. Børresen-Dale and H. G. Stunnenberg and M. Stratton and J. A. Foekens and A. M. Sieuwerts and J. W. M. Martens. Genome research (2019)


Nouvelles approches vaccinales en cancérologie. S. Depil and P. Bonaventura and V. Alcazer and L. Tonon. Bulletin du cancer  105 Suppl 1  S113--S120  (2018)


Integrated analysis highlights APC11 protein expression as a likely new independent predictive marker for colorectal cancer. Y. Drouet and I. Treilleux and A. Viari and S. Léon and M. Devouassoux-Shisheboran and N. Voirin and C. de la Fouchardière and B. Manship and A. Puisieux and C. Lasset and C. Moyret-Lalle. Scientific reports  8  7386  (2018)


A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts. S. Huet and B. Tesson and J.-P. Jais and A. L. Feldman and L. Magnano and E. Thomas and A. Traverse-Glehen and B. Albaud and M. Carrère and L. Xerri and S. M. Ansell and L. Baseggio and C. Reyes and K. Tarte and S. Boyault and C. Haioun and B. K. Link and P. Feugier and A. Lopez-Guillermo and H. Tilly and P. Brice and S. Hayette and F. Jardin and F. Offner and P. Sujobert and D. Gentien and A. Viari and E. Campo and J. R. Cerhan and G. Salles. The lancet oncology  19  549--561  (2018)

 

Immunological and classical subtypes of oral premalignant lesions. J.-P. Foy and C. Bertolus and S. Ortiz-Cuaran and M.-A. Albaret and W. N. Williams and W. Lang and S. Destandau and G. D. Souza and E. Sohier and J. Kielbassa and E. Thomas and S. Deneuve and P. Goudot and A. Puisieux and A. Viari and L. Mao and C. Caux and S. M. Lippman and P. Saintigny. Oncoimmunology  7  e1496880  (2018)


A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes. J.-P. Foy and L. Bazire and S. Ortiz-Cuaran and S. Deneuve and J. Kielbassa and E. Thomas and A. Viari and A. Puisieux and P. Goudot and C. Bertolus and N. Foray and Y. Kirova and P. Verrelle and P. Saintigny. BMC medicine  15  165  (2017)


Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency. H. Davies and S. Morganella and C. A. Purdie and S. J. Jang and E. Borgen and H. Russnes and D. Glodzik and X. Zou and A. Viari and A. L. Richardson and A.-L. Børresen-Dale and A. Thompson and J. E. Eyfjord and G. Kong and M. R. Stratton and S. Nik-Zainal. Cancer research  77  4755--4762  (2017)


The immune microenvironment of HPV-negative oral squamous cell carcinoma from never-smokers and never-drinkers patients suggests higher clinical benefit of IDO1 and PD1/PD-L1 blockade. J.-P. Foy and C. Bertolus and M.-C. Michallet and S. Deneuve and R. Incitti and N. Bendriss-Vermare and M.-A. Albaret and S. Ortiz-Cuaran and E. Thomas and A. Colombe and C. Py and N. Gadot and J.-P. Michot and J. Fayette and A. Viari and B. Van den Eynde and P. Goudot and M. Devouassoux-Shisheboran and A. Puisieux and C. Caux and P. Zrounba and S. Lantuejoul and P. Saintigny. Annals of oncology : official journal of the European Society for Medical Oncology / ESMO  28  1934--1941  (2017)


BCL2 mutations do not confer adverse prognosis in follicular lymphoma patients treated with rituximab. S. Huet and E. Szafer-Glusman and B. Tesson and L. Xerri and W. J. Fairbrother and K. Mukhyala and C. Bolen and E. Punnoose and L. Tonon and C. Chassagne-Clément and P. Feugier and A. Viari and F. Jardin and G. Salles and P. Sujobert. American journal of hematology  92  515--519  (2017)


EZH2 alterations in follicular lymphoma: biological and clinical correlations. S. Huet and L. Xerri and B. Tesson and S. Mareschal and S. Taix and L. Mescam-Mancini and E. Sohier and M. Carrère and J. Lazarovici and O. Casasnovas and L. Tonon and S. Boyault and S. Hayette and C. Haioun and B. Fabiani and A. Viari and F. Jardin and G. Salles. Blood cancer journal  7  e555  (2017)


HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. H. Davies and D. Glodzik and S. Morganella and L. R. Yates and J. Staaf and X. Zou and M. Ramakrishna and S. Martin and S. Boyault and A. M. Sieuwerts and P. T. Simpson and T. A. King and K. Raine and J. E. Eyfjord and G. Kong and Å. Borg and E. Birney and H. G. Stunnenberg and M. J. van de Vijver and A.-L. Børresen-Dale and J. W. M. Martens and P. N. Span and S. R. Lakhani and A. Vincent-Salomon and C. Sotiriou and A. Tutt and A. M. Thompson and S. Van Laere and A. L. Richardson and A. Viari and P. J. Campbell and M. R. Stratton and S. Nik-Zainal. Nature medicine  23  517--525  (2017)


A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. D. Glodzik and S. Morganella and H. Davies and P. T. Simpson and Y. Li and X. Zou and J. Diez-Perez and J. Staaf and L. B. Alexandrov and M. Smid and A. B. Brinkman and I. H. Rye and H. Russnes and K. Raine and C. A. Purdie and S. R. Lakhani and A. M. Thompson and E. Birney and H. G. Stunnenberg and M. J. van de Vijver and J. W. M. Martens and A.-L. Børresen-Dale and A. L. Richardson and G. Kong and A. Viari and D. Easton and G. Evan and P. J. Campbell and M. R. Stratton and S. Nik-Zainal. Nature Genetics  49  341--348  (2017)


[Contribution and challenges of Big Data in oncology]. P. Saintigny and J.-P. Foy and A. Ferrari and P. Cassier and A. Viari and A. Puisieux. Bulletin du cancer  104  281--287  (2017)


Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Y. S. Ju and I. Martincorena and M. Gerstung and M. Petljak and L. B. Alexandrov and R. Rahbari and D. C. Wedge and H. R. Davies and M. Ramakrishna and A. Fullam and S. Martin and C. Alder and N. Patel and S. Gamble and S. O'Meara and D. D. Giri and T. Sauer and S. E. Pinder and C. A. Purdie and Å. Borg and H. Stunnenberg and M. van de Vijver and B. K. T. Tan and C. Caldas and A. Tutt and N. T. Ueno and L. J. Van 't Veer and J. W. M. Martens and C. Sotiriou and S. Knappskog and P. N. Span and S. R. Lakhani and J. E. Eyfjörd and A.-L. Børresen-Dale and A. Richardson and A. M. Thompson and A. Viari and M. E. Hurles and S. Nik-Zainal and P. J. Campbell and M. R. Stratton. Nature  543  714--718  (2017)


Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. M. Smid and F. G. Rodríguez-González and A. M. Sieuwerts and R. Salgado and W. J. C. Prager-Van der Smissen and M. v. d. Vlugt-Daane and A. van Galen and S. Nik-Zainal and J. Staaf and A. B. Brinkman and M. J. van de Vijver and A. L. Richardson and A. Fatima and K. Berentsen and A. Butler and S. Martin and H. R. Davies and R. Debets and M. E. M.-V. Gelder and C. H. M. van Deurzen and G. MacGrogan and G. G. G. M. van den Eynden and C. Purdie and A. M. Thompson and C. Caldas and P. N. Span and P. T. Simpson and S. R. Lakhani and S. Van Laere and C. Desmedt and M. Ringnér and S. Tommasi and J. Eyford and A. Broeks and A. Vincent-Salomon and P. A. Futreal and S. Knappskog and T. King and G. Thomas and A. Viari and A. Langerød and A.-L. Børresen-Dale and E. Birney and H. G. Stunnenberg and M. Stratton and J. A. Foekens and J. W. M. Martens. Nature communications  7  12910  (2016


Landscape of somatic mutations in 560 breast cancer whole-genome sequences. S. Nik-Zainal and H. Davies and J. Staaf and M. Ramakrishna and D. Glodzik and X. Zou and I. Martincorena and L. B. Alexandrov and S. Martin and D. C. Wedge and P. Van Loo and Y. S. Ju and M. Smid and A. B. Brinkman and S. Morganella and M. R. Aure and O. C. Lingjærde and A. Langerød and M. Ringnér and S.-M. Ahn and S. Boyault and J. E. Brock and A. Broeks and A. Butler and C. Desmedt and L. Dirix and S. Dronov and A. Fatima and J. A. Foekens and M. Gerstung and G. K. J. Hooijer and S. J. Jang and D. R. Jones and H.-Y. Kim and T. A. King and S. Krishnamurthy and H. J. Lee and J.-Y. Lee and Y. Li and S. McLaren and A. Menzies and V. Mustonen and S. O'Meara and I. Pauporté and X. Pivot and C. A. Purdie and K. Raine and K. Ramakrishnan and F. G. Rodríguez-González and G. Romieu and A. M. Sieuwerts and P. T. Simpson and R. Shepherd and L. Stebbings and O. A. Stefansson and J. Teague and S. Tommasi and I. Treilleux and G. G. Van den Eynden and P. Vermeulen and A. Vincent-Salomon and L. Yates and C. Caldas and L. van't Veer and A. Tutt and S. Knappskog and B. K. T. Tan and J. Jonkers and Å. Borg and N. T. Ueno and C. Sotiriou and A. Viari and P. A. Futreal and P. J. Campbell and P. N. Span and S. Van Laere and S. R. Lakhani and J. E. Eyfjord and A. M. Thompson and E. Birney and H. G. Stunnenberg and M. J. van de Vijver and J. W. M. Martens and A.-L. Børresen-Dale and A. L. Richardson and G. Kong and G. Thomas and M. R. Stratton. Nature  534  47--54  (2016


A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. T. S. Alioto and I. Buchhalter and S. Derdak and B. Hutter and M. D. Eldridge and E. Hovig and L. E. Heisler and T. A. Beck and J. T. Simpson and L. Tonon and A.-S. Sertier and A.-M. Patch and N. Jäger and P. Ginsbach and R. Drews and N. Paramasivam and R. Kabbe and S. Chotewutmontri and N. Diessl and C. Previti and S. Schmidt and B. Brors and L. Feuerbach and M. Heinold and S. Gröbner and A. Korshunov and P. S. Tarpey and A. P. Butler and J. Hinton and D. Jones and A. Menzies and K. Raine and R. Shepherd and L. Stebbings and J. W. Teague and P. Ribeca and F. C. Giner and S. Beltran and E. Raineri and M. Dabad and S. C. Heath and M. Gut and R. E. Denroche and N. J. Harding and T. N. Yamaguchi and A. Fujimoto and H. Nakagawa and V. Quesada and R. Valdés-Mas and S. Nakken and D. Vodák and L. Bower and A. G. Lynch and C. L. Anderson and N. Waddell and J. V. Pearson and S. M. Grimmond and M. Peto and P. Spellman and M. He and C. Kandoth and S. Lee and J. Zhang and L. Létourneau and S. Ma and S. Seth and D. Torrents and L. Xi and D. A. Wheeler and C. López-Otín and E. Campo and P. J. Campbell and P. C. Boutros and X. S. Puente and D. S. Gerhard and S. M. Pfister and J. D. McPherson and T. J. Hudson and M. Schlesner and P. Lichter and R. Eils and D. T. W. Jones and I. G. Gut. Nature communications  6  10001  (2015)

 

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants and A. D. Ewing and K. E. Houlahan and Y. Hu and K. Ellrott and C. Caloian and T. N. Yamaguchi and J. C. Bare and C. P'ng and D. Waggott and V. Y. Sabelnykova and M. R. Kellen and T. C. Norman and D. Haussler and S. H. Friend and G. Stolovitzky and A. A. Margolin and J. M. Stuart and P. C. Boutros. Nature Methods  12  623--630  (2015)

Publications avec le laboratoire d'hébergement
Remerciements

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