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Mareschal S, Ruminy P, Alcantara M, Villenet C, Figeac M, Dubois S, Bertrand P, Bouzelfen A, Viailly PJ, Penther D, Tilly H, Bastard C, Jardin F. Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. Bioinformatics 2018; 33:2977-2985. [PMID: 28481978 DOI: 10.1093/bioinformatics/btx309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Motivation Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyze such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. Results The cghRA framework combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas. New algorithms for copy-number calling, polymorphism detection and minimal common region prioritization were also developed and validated. While their performances will only be demonstrated with aCGH, these algorithms could actually prove useful to any copy-number analysis, whatever the technique used. Availability and implementation R package and source for Linux, MS Windows and MacOS are freely available at http://bioinformatics.ovsa.fr/cghRA. Contact mareschal@ovsa.fr or fabrice.jardin@chb.unicancer.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylvain Mareschal
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Ruminy
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Marion Alcantara
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Céline Villenet
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France
| | - Martin Figeac
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France.,Cellule de Bioinformatique du Plateau Commun de Séquençage, CHRU de Lille, 59000 Lille, France
| | - Sydney Dubois
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Bertrand
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Abdelilah Bouzelfen
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Pierre-Julien Viailly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Dominique Penther
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Hervé Tilly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France
| | - Christian Bastard
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Fabrice Jardin
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
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Grond-Ginsbach C, Chen B, Krawczak M, Pjontek R, Ginsbach P, Jiang Y, Abboud S, Arnold ML, Bersano A, Brandt T, Caso V, Debette S, Dichgans M, Geschwendtner A, Giacalone G, Martin JJ, Metso AJ, Metso TM, Grau AJ, Kloss M, Lichy C, Pezzini A, Traenka C, Schreiber S, Thijs V, Touzé E, Del Zotto E, Tatlisumak T, Leys D, Lyrer PA, Engelter ST. Genetic Imbalance in Patients with Cervical Artery Dissection. Curr Genomics 2017; 18:206-213. [PMID: 28367076 PMCID: PMC5345335 DOI: 10.2174/1389202917666160805152627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 07/15/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022] Open
Abstract
Background: Genetic and environmental risk factors are assumed to contribute to the susceptibility to cervical artery dissection (CeAD). To explore the role of genetic imbalance in the etiology of CeAD, copy number variants (CNVs) were identified in high-density microarrays samples from the multicenter CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) study and from control subjects from the CADISP study and the German PopGen biobank. Microarray data from 833 CeAD patients and 2040 control subjects (565 subjects with ischemic stroke due to causes different from CeAD and 1475 disease-free individuals) were analyzed. Rare genic CNVs were equally frequent in CeAD-patients (16.4%; n=137) and in control subjects (17.0%; n=346) but differed with respect to their genetic content. Compared to control subjects, CNVs from CeAD patients were enriched for genes associated with muscle organ development and cell differentiation, which suggests a possible association with arterial development. CNVs affecting cardiovascular system development were more common in CeAD patients than in control subjects (p=0.003; odds ratio (OR) =2.5; 95% confidence interval (95% CI) =1.4-4.5) and more common in patients with a familial history of CeAD than in those with sporadic CeAD (p=0.036; OR=11.2; 95% CI=1.2-107). Conclusion: The findings suggest that rare genetic imbalance affecting cardiovascular system development may contribute to the risk of CeAD. Validation of these findings in independent study populations is warranted.
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Affiliation(s)
| | - Bowang Chen
- Department of Biology, South University of Science and Technology of China, Shenzhen, China
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Philip Ginsbach
- School of Informatics, University of Edinburgh, United Kingdom
| | - Yanxiang Jiang
- Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Shérine Abboud
- Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie-Luise Arnold
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna Bersano
- Cerebrovascular Unit IRCCS Foundation C.Besta Neurological Institute, via Celoria 11, Milan, Italy
| | - Tobias Brandt
- Clinics for Neurologic Rehabilitation, Kliniken Schmieder, Heidelberg, Germany
| | - Valeria Caso
- Stroke Unit, Perugia University Hospital, Perugia, Italy
| | | | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians Universität, Munich, Germany;; Munich Cluster of Systems Neurology (SyNergy), Munich Germany
| | - Andreas Geschwendtner
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians Universität, Munich, Germany
| | - Giacomo Giacalone
- Department of Neurology, Milan, San Raffaele University Hospital, Milan, Italy
| | | | - Antti J Metso
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tiina M Metso
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Armin J Grau
- Department of Neurology, Klinikum Ludwigshafen, Ludwigshafen, Germany
| | - Manja Kloss
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Lichy
- Department of Neurology, Klinikum Memmingen, Memmingen, Germany
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Christopher Traenka
- Department of Neurology and Stroke Center, Basel University Hospital, Basel, Switzerland
| | - Stefan Schreiber
- Department of Internal Medicine, University Hospital Schleswig Holstein, Kiel, Germany
| | - Vincent Thijs
- Vesalius Research Center, Experimental Neurology - Laboratory of Neurobiology, Leuven, Belgium
| | - Emmanuel Touzé
- Paris Descartes University, INSERM UMR S894, Department of Neurology, Sainte-Anne Hospital, Paris, France;; University of Caen Basse Normandie, INSERM U919, Department of Neurology, CHU Côte de Nacre, Caen, France
| | - Elisabetta Del Zotto
- Department of Recovery and Functional Rehabilitation, IRCCS Don Gnocchi Foundation, Milan, Italy
| | - Turgut Tatlisumak
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland;; Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden;; Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Didier Leys
- INSERM U 1171. University hospital of Lille. Department of Neurology. Lille, France
| | - Philippe A Lyrer
- Department of Neurology and Stroke Center, Basel University Hospital, Basel, Switzerland
| | - Stefan T Engelter
- Department of Neurology and Stroke Center, Basel University Hospital, Basel, Switzerland;; Neurorehabilitation Unit, University Center for Medicine of Aging and Rehabilitation, Felix Platter-Spital, Basel, Switzerland
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