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Allain F, Roméjon J, La Rosa P, Jarlier F, Servant N, Hupé P. Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines. Open Res Eur 2022; 1:76. [PMID: 37645091 PMCID: PMC10445886 DOI: 10.12688/openreseurope.13861.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 08/31/2023]
Abstract
With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production has become a challenge such that the data can be processed in real-time and delivered to the end-users as fast as possible. The usage of workflow management systems along with packaging systems and containerization technologies offer an opportunity to tackle this challenge. While very powerful, they can be used and combined in many multiple ways which may differ from one developer to another. Therefore, promoting the homogeneity of the workflow implementation requires guidelines and protocols which detail how the source code of the bioinformatics pipeline should be written and organized to ensure its usability, maintainability, interoperability, sustainability, portability, reproducibility, scalability and efficiency. Capitalizing on Nextflow, Conda, Docker, Singularity and the nf-core initiative, we propose a set of best practices along the development life cycle of the bioinformatics pipeline and deployment for production operations which target different expert communities including i) the bioinformaticians and statisticians ii) the software engineers and iii) the data managers and core facility engineers. We implemented Geniac (Automatic Configuration GENerator and Installer for nextflow pipelines) which consists of a toolbox with three components: i) a technical documentation available at https://geniac.readthedocs.io to detail coding guidelines for the bioinformatics pipeline with Nextflow, ii) a command line interface with a linter to check that the code respects the guidelines, and iii) an add-on to generate configuration files, build the containers and deploy the pipeline. The Geniac toolbox aims at the harmonization of development practices across developers and automation of the generation of configuration files and containers by parsing the source code of the Nextflow pipeline.
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Affiliation(s)
- Fabrice Allain
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
| | - Julien Roméjon
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
| | - Philippe La Rosa
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
| | - Frédéric Jarlier
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
| | - Nicolas Servant
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
| | - Philippe Hupé
- Mines Paris Tech, Fontainebleau, F-77305, France
- Institut Curie, Paris, F-75005, France
- U900, Inserm, Paris, F-75005, France
- PSL Research University, Paris, F-75005, France
- UMR144, CNRS, Paris, F-75005, France
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Coussy F, El-Botty R, Château-Joubert S, Dahmani A, Montaudon E, Leboucher S, Morisset L, Painsec P, Sourd L, Huguet L, Nemati F, Servely JL, Larcher T, Vacher S, Briaux A, Reyes C, La Rosa P, Lucotte G, Popova T, Foidart P, Sounni NE, Noel A, Decaudin D, Fuhrmann L, Salomon A, Reyal F, Mueller C, Ter Brugge P, Jonkers J, Poupon MF, Stern MH, Bièche I, Pommier Y, Marangoni E. BRCAness, SLFN11, and RB1 loss predict response to topoisomerase I inhibitors in triple-negative breast cancers. Sci Transl Med 2021; 12:12/531/eaax2625. [PMID: 32075943 DOI: 10.1126/scitranslmed.aax2625] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022]
Abstract
Topoisomerase I (TOP1) inhibitors trap TOP1 cleavage complexes resulting in DNA double-strand breaks (DSBs) during replication, which are repaired by homologous recombination (HR). Triple-negative breast cancer (TNBC) could be eligible for TOP1 inhibitors given the considerable proportion of tumors with a defect in HR-mediated repair (BRCAness). The TOP1 inhibitor irinotecan was tested in 40 patient-derived xenografts (PDXs) of TNBC. BRCAness was determined with a single-nucleotide polymorphism (SNP) assay, and expression of Schlafen family member 11 (SLFN11) and retinoblastoma transcriptional corepressor 1 (RB1) was evaluated by real-time polymerase chain reaction (RT-PCR) and immunohistochemistry analyses. In addition, the combination of irinotecan and the ataxia telangiectasia and Rad3-related protein (ATR) inhibitor VE-822 was tested in SLFN11-negative PDXs, and two clinical non-camptothecin TOP1 inhibitors (LMP400 and LMP776) were tested. Thirty-eight percent of the TNBC models responded to irinotecan. BRCAness combined with high SLFN11 expression and RB1 loss identified highly sensitive tumors, consistent with the notion that deficiencies in cell cycle checkpoints and DNA repair result in high sensitivity to TOP1 inhibitors. Treatment by the ATR inhibitor VE-822 increased sensitivity to irinotecan in SLFN11-negative PDXs and abolished irinotecan-induced phosphorylation of checkpoint kinase 1 (CHK1). LMP400 (indotecan) and LMP776 (indimitecan) showed high antitumor activity in BRCA1-mutated or BRCAness-positive PDXs. Last, low SLFN11 expression was associated with poor survival in 250 patients with TNBC treated with anthracycline-based chemotherapy. In conclusion, a substantial proportion of TNBC respond to irinotecan. BRCAness, high SLFN11 expression, and RB1 loss are highly predictive of response to irinotecan and the clinical indenoisoquinoline TOP1 inhibitors.
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Affiliation(s)
- Florence Coussy
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France.,Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Rania El-Botty
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | | | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Elodie Montaudon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, UMR3306, 91405 Orsay, France
| | - Ludivine Morisset
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Pierre Painsec
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Léa Huguet
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fariba Nemati
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jean-Luc Servely
- BioPôle Alfort, Ecole Nationale Vétérinaire d'Alfort, 94704 Maisons Alfort, France.,INRA, PHASE Department, 37380 Nouzilly, France
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Adrien Briaux
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Cécile Reyes
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Philippe La Rosa
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Georges Lucotte
- INSERM, U900, 75005 Paris, France.,Institut Curie, PSL Research University, 75005 Paris, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Pierre Foidart
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Nor Eddine Sounni
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Agnès Noel
- Laboratory of Tumor and Developmental Biology, Groupe Interdisciplinaire de Génoprotéomique Appliqué-Cancer (GIGA-Cancer), University of Liège, Liège 4000, Belgium
| | - Didier Decaudin
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.,Medical Oncology Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laetitia Fuhrmann
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Anne Salomon
- Department of Pathology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Fabien Reyal
- Surgery Department, Institut Curie, PSL Research University, 75005 Paris, France.,U932, Immunity and Cancer, INSERM, Institut Curie, 75005 Paris, France
| | - Christopher Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Petra Ter Brugge
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, 1066 CX, Netherlands
| | - Marie-France Poupon
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, 75005 Paris, France.,INSERM U830, 75005 Paris, France
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL Research University, 75005 Paris, France
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL Research University, 75005 Paris, France.
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Renault AL, Mebirouk N, Fuhrmann L, Bataillon G, Cavaciuti E, Le Gal D, Girard E, Popova T, La Rosa P, Beauvallet J, Eon-Marchais S, Dondon MG, d'Enghien CD, Laugé A, Chemlali W, Raynal V, Labbé M, Bièche I, Baulande S, Bay JO, Berthet P, Caron O, Buecher B, Faivre L, Fresnay M, Gauthier-Villars M, Gesta P, Janin N, Lejeune S, Maugard C, Moutton S, Venat-Bouvet L, Zattara H, Fricker JP, Gladieff L, Coupier I, Chenevix-Trench G, Hall J, Vincent-Salomon A, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers. Breast Cancer Res 2018; 20:28. [PMID: 29665859 PMCID: PMC5905168 DOI: 10.1186/s13058-018-0951-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/05/2018] [Indexed: 01/23/2023] Open
Abstract
Background The ataxia telangiectasia mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear histopathological and molecular features of breast tumours occurring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumour signature may help in patient management. Methods To characterise hallmarks of ATM-associated tumours, we performed systematic pathology review of tumours from 21 participants from ataxia-telangiectasia families and 18 participants from HBOC families, as well as copy number profiling on a subset of 23 tumours. Morphology of ATM-associated tumours was compared with that of 599 patients with no BRCA1 and BRCA2 mutations from a hospital-based series, as well as with data from The Cancer Genome Atlas. Absolute copy number and loss of heterozygosity (LOH) profiles were obtained from the OncoScan SNP array. In addition, we performed whole-genome sequencing on four tumours from ATM loss-of-function variant carriers with available frozen material. Results We found that ATM-associated tumours belong mostly to the luminal B subtype, are tetraploid and show LOH at the ATM locus at 11q22–23. Unlike tumours in which BRCA1 or BRCA2 is inactivated, tumours arising in ATM deleterious variant carriers are not associated with increased large-scale genomic instability as measured by the large-scale state transitions signature. Losses at 13q14.11-q14.3, 17p13.2-p12, 21p11.2-p11.1 and 22q11.23 were observed. Somatic alterations at these loci may therefore represent biomarkers for ATM testing and harbour driver mutations in potentially ‘druggable’ genes that would allow patients to be directed towards tailored therapeutic strategies. Conclusions Although ATM is involved in the DNA damage response, ATM-associated tumours are distinct from BRCA1-associated tumours in terms of morphological characteristics and genomic alterations, and they are also distinguishable from sporadic breast tumours, thus opening up the possibility to identify ATM variant carriers outside the ataxia-telangiectasia disorder and direct them towards effective cancer risk management and therapeutic strategies. Electronic supplementary material The online version of this article (10.1186/s13058-018-0951-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne-Laure Renault
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Noura Mebirouk
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | | | | | - Eve Cavaciuti
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Dorothée Le Gal
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Elodie Girard
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Tatiana Popova
- Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,INSERM U830, Paris, France
| | - Philippe La Rosa
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juana Beauvallet
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Séverine Eon-Marchais
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Marie-Gabrielle Dondon
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | | | | | - Walid Chemlali
- Unité de Pharmacogénomique, Institut Curie, Paris, France
| | - Virginie Raynal
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | - Martine Labbé
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Ivan Bièche
- Unité de Pharmacogénomique, Institut Curie, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | | | - Pascaline Berthet
- Unité de Pathologie Gynécologique, Centre François Baclesse, Caen, France
| | - Olivier Caron
- Service d'Oncologie Génétique, Gustave Roussy, Villejuif, France
| | | | - Laurence Faivre
- Institut GIMI, CHU de Dijon, Hôpital d'Enfants, Dijon, France.,Oncogénétique, Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | - Marc Fresnay
- Département d'Hématologie et d'Oncologie Médicale, CLCC Antoine Lacassagne, Nice, France
| | | | - Paul Gesta
- Service d'Oncogénétique Régional Poitou-Charentes, Centre Hospitalier Georges-Renon, Niort, France
| | - Nicolas Janin
- Service de Génétique, Clinique Universitaire Saint-Luc, Brussels, Belgium
| | - Sophie Lejeune
- Service de Génétique Clinique Guy Fontaine, Hôpital Jeanne de Flandre, Lille, France
| | - Christine Maugard
- Laboratoire de Diagnostic Génétique, UF1422 Oncogénétique Moléculaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Oncogénétique Evaluation familiale et suivi, UF6948 Oncogénétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sébastien Moutton
- Laboratoire Maladies Rares: Génétique et Métabolisme, CHU de Bordeaux-GH Pellegrin, Bordeaux, France
| | | | - Hélène Zattara
- Département de Génétique, Hôpital de la Timone, Marseille, France
| | | | | | - Isabelle Coupier
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France.,Unité d'Oncogénétique, ICM Val d'Aurelle, Montpellier, France
| | | | | | | | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Janet Hall
- UMR INSERM 1052, Lyon, France.,CNRS 5286, Lyon, France.,Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - Dominique Stoppa-Lyonnet
- INSERM U830, Paris, France.,Service de Génétique, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Nadine Andrieu
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines Paris Tech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Fabienne Lesueur
- INSERM, U900, Paris, France. .,Institut Curie, Paris, France. .,Mines Paris Tech, Fontainebleau, France. .,PSL Research University, Paris, France.
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Laé M, La Rosa P, Mandel J, Reyal F, Hupé P, Terrier P, Couturier J. Whole-genome profiling helps to classify phyllodes tumours of the breast. J Clin Pathol 2016; 69:1081-1087. [DOI: 10.1136/jclinpath-2016-203684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/21/2016] [Accepted: 04/28/2016] [Indexed: 11/03/2022]
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Servant N, Roméjon J, Gestraud P, La Rosa P, Lucotte G, Lair S, Bernard V, Zeitouni B, Coffin F, Jules-Clément G, Yvon F, Lermine A, Poullet P, Liva S, Pook S, Popova T, Barette C, Prud'homme F, Dick JG, Kamal M, Le Tourneau C, Barillot E, Hupé P. Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial. Front Genet 2014; 5:152. [PMID: 24910641 PMCID: PMC4039073 DOI: 10.3389/fgene.2014.00152] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/08/2014] [Indexed: 11/13/2022] Open
Abstract
Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of (i) warranting the integration and the traceability of data, (ii) ensuring the correct processing and analyses of genomic data, and (iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.
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Affiliation(s)
- Nicolas Servant
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Julien Roméjon
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Pierre Gestraud
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Philippe La Rosa
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Georges Lucotte
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Séverine Lair
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | | | - Bruno Zeitouni
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Fanny Coffin
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Gérôme Jules-Clément
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; INSERM U932, Paris France
| | - Florent Yvon
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Alban Lermine
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Patrick Poullet
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Stéphane Liva
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Stuart Pook
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Tatiana Popova
- Institut Curie, Paris France ; INSERM U830, Paris France
| | - Camille Barette
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Institut Curie, Informatic Department, Paris France
| | - François Prud'homme
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Institut Curie, Informatic Department, Paris France ; Institut Curie, Sequencing Facility ICGex, Paris France
| | | | - Maud Kamal
- Institut Curie, Translational Research Department, Paris France
| | - Christophe Le Tourneau
- INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; Department of Medical Oncology, Institut Curie, Paris France
| | - Emmanuel Barillot
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France
| | - Philippe Hupé
- Institut Curie, Paris France ; INSERM U900, Paris France ; Mines ParisTech, Fontainebleau France ; CNRS UMR144, Paris France
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Rigaill G, Hupé P, Almeida A, La Rosa P, Meyniel JP, Decraene C, Barillot E. ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. ACTA ACUST UNITED AC 2008; 24:768-74. [PMID: 18252739 DOI: 10.1093/bioinformatics/btn048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
MOTIVATION Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000-500 000 SNPs along the genome. Their high density facilitates the precise localization of genomic alterations and makes them a powerful tool for studies of cancers and copy number polymorphism. Like other microarray technologies it is influenced by non-relevant sources of variation, requiring correction. Moreover, the amplitude of variation induced by non-relevant effects is similar or greater than the biologically relevant effect (i.e. true copy number), making it difficult to estimate non-relevant effects accurately without including the biologically relevant effect. RESULTS We addressed this problem by developing ITALICS, a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. We compared our normalization method with other existing and available methods, and found that ITALICS outperformed these methods for several in-house datasets and one public dataset. These results were validated biologically by quantitative PCR. AVAILABILITY The R package ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) has been submitted to Bioconductor.
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Affiliation(s)
- Guillem Rigaill
- Institut Curie, Service de Bioinformatique, INSERM, U900, CNRS UMR144, Institut Curie, Translational Research Department, 26 rue d'Ulm, Paris F-75248, France
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Abstract
Assessing variations in DNA copy number is crucial for understanding constitutional or somatic diseases, particularly cancers. The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. We report the availability of a web tool for analysing array-CGH data. CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visualization and biological interpretation. The user typically performs the following bioinformatics steps of a CGH array project within CAPweb: the secure upload of the results of CGH array image analysis and of the array annotation (genomic position of the probes); first level analysis of each array, including automatic normalization of the data (for correcting experimental biases), breakpoint detection and status assignment (gain, loss or normal); validation or deletion of the analysis based on a summary report and quality criteria; visualization and biological analysis of the genomic profiles and results through a user-friendly interface. CAPweb is accessible at .
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Affiliation(s)
- Stéphane Liva
- Institut Curie, Service Bioinformatique 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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La Rosa P, Viara E, Hupé P, Pierron G, Liva S, Neuvial P, Brito I, Lair S, Servant N, Robine N, Manié E, Brennetot C, Janoueix-Lerosey I, Raynal V, Gruel N, Rouveirol C, Stransky N, Stern MH, Delattre O, Aurias A, Radvanyi F, Barillot E. VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics 2006; 22:2066-73. [PMID: 16820431 DOI: 10.1093/bioinformatics/btl359] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Microarray-based CGH (Comparative Genomic Hybridization), transcriptome arrays and other large-scale genomic technologies are now routinely used to generate a vast amount of genomic profiles. Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses. This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses. RESULTS We have developed a graphical user interface for visualization and first level analysis of molecular profiles. It is currently in use at the Institut Curie for cancer research projects involving CGH arrays, transcriptome arrays, SNP (single nucleotide polymorphism) arrays, loss of heterozygosity results (LOH), and Chromatin ImmunoPrecipitation arrays (ChIP chips). The interface offers the possibility of studying these different types of information in a consistent way. Several views are proposed, such as the classical CGH karyotype view or genome-wide multi-tumor comparison. Many functionalities for analyzing CGH data are provided by the interface, including looking for recurrent regions of alterations, confrontation to transcriptome data or clinical information, and clustering. Our tool consists of PHP scripts and of an applet written in Java. It can be run on public datasets at http://bioinfo.curie.fr/vamp AVAILABILITY The VAMP software (Visualization and Analysis of array-CGH,transcriptome and other Molecular Profiles) is available upon request. It can be tested on public datasets at http://bioinfo.curie.fr/vamp. The documentation is available at http://bioinfo.curie.fr/vamp/doc.
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Affiliation(s)
- Philippe La Rosa
- Institut Curie, Service Bioinformatique, 26 rue d'Ulm, Paris 75248 cedex 05, France
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Elfilali A, Lair S, Verbeke C, La Rosa P, Radvanyi F, Barillot E. ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res 2006; 34:D613-6. [PMID: 16381943 PMCID: PMC1347385 DOI: 10.1093/nar/gkj022] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcriptome microarrays have become one of the tools of choice for investigating the genes involved in tumorigenesis and tumor progression, as well as finding new biomarkers and gene expression signatures for the diagnosis and prognosis of cancer. Here, we describe a new database for Integrated Tumor Transcriptome Array and Clinical data Analysis (ITTACA). ITTACA centralizes public datasets containing both gene expression and clinical data. ITTACA currently focuses on the types of cancer that are of particular interest to research teams at Institut Curie: breast carcinoma, bladder carcinoma and uveal melanoma. A web interface allows users to carry out different class comparison analyses, including the comparison of expression distribution profiles, tests for differential expression and patient survival analyses. ITTACA is complementary to other databases, such as GEO and SMD, because it offers a better integration of clinical data and different functionalities. It also offers more options for class comparison analyses when compared with similar projects such as Oncomine. For example, users can define their own patient groups according to clinical data or gene expression levels. This added flexibility and the user-friendly web interface makes ITTACA especially useful for comparing personal results with the results in the existing literature. ITTACA is accessible online at .
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Affiliation(s)
- Adil Elfilali
- Institut Curie, Service Bioinformatique26 rue d'Ulm, Paris, 75248 cedex 05, France
- Institut Curie, CNRS UMR 14426 rue d'Ulm, Paris, 75248 cedex 05, France
| | - Séverine Lair
- Institut Curie, Service Bioinformatique26 rue d'Ulm, Paris, 75248 cedex 05, France
- Institut Curie, CNRS UMR 14426 rue d'Ulm, Paris, 75248 cedex 05, France
| | - Catia Verbeke
- Institut Curie, Service Bioinformatique26 rue d'Ulm, Paris, 75248 cedex 05, France
- Institut Curie, CNRS UMR 14426 rue d'Ulm, Paris, 75248 cedex 05, France
| | - Philippe La Rosa
- Institut Curie, Service Bioinformatique26 rue d'Ulm, Paris, 75248 cedex 05, France
| | - François Radvanyi
- Institut Curie, CNRS UMR 14426 rue d'Ulm, Paris, 75248 cedex 05, France
| | - Emmanuel Barillot
- Institut Curie, Service Bioinformatique26 rue d'Ulm, Paris, 75248 cedex 05, France
- To whom correspondence should be addressed.
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Janoueix-Lerosey I, Hupé P, Maciorowski Z, La Rosa P, Schleiermacher G, Pierron G, Liva S, Barillot E, Delattre O. Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma. Cell Cycle 2005; 4:1842-6. [PMID: 16294040 DOI: 10.4161/cc.4.12.2257] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Neuroblastoma (NB) is a frequent paediatric extra cranial solid tumor characterized by the occurrence of unbalanced chromosome translocations, frequently, but not exclusively, involving chromosomes 1 and 17. We have used a 1 Mb resolution BAC array to further refine the mapping of breakpoints in NB cell lines. Replication timing profiles were evaluated in 7 NB cell lines, using DNAs from G1 and S phases flow sorted nuclei hybridised on the same array. Strikingly, these replication timing profiles were highly similar between the different NB cell lines. Furthermore, a significant level of similarity was also observed between NB cell lines and lymphoblastoid cells. A segmentation analysis using the Adaptative Weights Smoothing procedure was performed to determine regions of coordinate replication. More than 50% of the breakpoints mapped to early replicating regions, which account for 23.7% of the total genome. The breakpoints frequency per 10(8) bases was therefore 10.84 for early replicating regions, whereas it was only 2.94 for late replicating regions, these difference being highly significant (p < 10(-4)). This strong association was also observed when chromosomes 1 and 17, the two most frequent translocation partners in NB were excluded from the statistical analysis. These results unambiguously establish a link between unbalanced translocations, whose most likely mechanism of occurrence relies on break-induced replication, and early replication of the genome.
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La Rosa P, Liva S, Hupé P, Pierron G, Neuvial P, Brito I, Viara E, Lair S, Servant N, Robine N, Manié E, Brennetot C, Jannoueix I, Gruel N, Rouveirol C, Stransky N, Stern MH, Radvanyi F, Delattre O, Aurias A, Barillot E. P23: CAP: a Web-based platform for CGH-array management and analysis. Eur J Med Genet 2005. [DOI: 10.1016/j.ejmg.2005.10.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hupé P, Rouveirol C, Brito I, Neuvial P, La Rosa P, Viara E, Stransky N, Pierron G, Manié E, Brennetot C, Jannoueix I, Gruel N, Aurias A, Delattre O, Radvanyi F, Barillot E. O11: Analysis of array CGH experiments: methods for the identification of informative genomic alterations. Eur J Med Genet 2005. [DOI: 10.1016/j.ejmg.2005.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chumakov I, Blumenfeld M, Guerassimenko O, Cavarec L, Palicio M, Abderrahim H, Bougueleret L, Barry C, Tanaka H, La Rosa P, Puech A, Tahri N, Cohen-Akenine A, Delabrosse S, Lissarrague S, Picard FP, Maurice K, Essioux L, Millasseau P, Grel P, Debailleul V, Simon AM, Caterina D, Dufaure I, Malekzadeh K, Belova M, Luan JJ, Bouillot M, Sambucy JL, Primas G, Saumier M, Boubkiri N, Martin-Saumier S, Nasroune M, Peixoto H, Delaye A, Pinchot V, Bastucci M, Guillou S, Chevillon M, Sainz-Fuertes R, Meguenni S, Aurich-Costa J, Cherif D, Gimalac A, Van Duijn C, Gauvreau D, Ouellette G, Fortier I, Raelson J, Sherbatich T, Riazanskaia N, Rogaev E, Raeymaekers P, Aerssens J, Konings F, Luyten W, Macciardi F, Sham PC, Straub RE, Weinberger DR, Cohen N, Cohen D, Ouelette G, Realson J. Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia. Proc Natl Acad Sci U S A 2002; 99:13675-80. [PMID: 12364586 PMCID: PMC129739 DOI: 10.1073/pnas.182412499] [Citation(s) in RCA: 684] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A map of 191 single-nucleotide polymorphism (SNPs) was built across a 5-Mb segment from chromosome 13q34 that has been genetically linked to schizophrenia. DNA from 213 schizophrenic patients and 241 normal individuals from Canada were genotyped with this marker set. Two 1,400- and 65-kb regions contained markers associated with the disease. Two markers from the 65-kb region were also found to be associated to schizophrenia in a Russian sample. Two overlapping genes G72 and G30 transcribed in brain were experimentally annotated in this 65-kb region. Transfection experiments point to the existence of a 153-aa protein coded by the G72 gene. This protein is rapidly evolving in primates, is localized to endoplasmic reticulum/Golgi in transfected cells, is able to form multimers and specifically binds to carbohydrates. Yeast two-hybrid experiments with the G72 protein identified the enzyme d-amino acid oxidase (DAAO) as an interacting partner. DAAO is expressed in human brain where it oxidizes d-serine, a potent activator of N-methyl-D-aspartate type glutamate receptor. The interaction between G72 and DAAO was confirmed in vitro and resulted in activation of DAAO. Four SNP markers from DAAO were found to be associated with schizophrenia in the Canadian samples. Logistic regression revealed genetic interaction between associated SNPs in vicinity of two genes. The association of both DAAO and a new gene G72 from 13q34 with schizophrenia together with activation of DAAO activity by a G72 protein product points to the involvement of this N-methyl-d-aspartate receptor regulation pathway in schizophrenia.
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