دورية أكاديمية
أعرض في EDS

Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants.

التفاصيل البيبلوغرافية
العنوان: Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants.
المؤلفون: Leman R; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. r.leman@baclesse.unicancer.fr.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. r.leman@baclesse.unicancer.fr.; Université Caen-Normandie, Caen, France. r.leman@baclesse.unicancer.fr., Tubeuf H; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France.; Interactive Biosoftware, Rouen, France., Raad S; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Tournier I; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Derambure C; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Lanos R; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Gaildrat P; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Castelain G; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Hauchard J; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Killian A; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Baert-Desurmont S; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Legros A; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France., Goardon N; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Quesnelle C; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France., Ricou A; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Castera L; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Vaur D; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Le Gac G; Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France., Ka C; Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France., Fichou Y; Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France., Bonnet-Dorion F; Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France., Sevenet N; Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France., Guillaud-Bataille M; Service de Génétique, Institut Gustave Roussy, Villejuif, France., Boutry-Kryza N; Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, Lyon, France., Schultz I; Laboratoire d'Oncogénétique, Centre Paul Strauss, Strasbourg, France., Caux-Moncoutier V; Service de Génétique, Institut Curie, Paris, France., Rossing M; Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark., Walker LC; Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand., Spurdle AB; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia., Houdayer C; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Martins A; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France., Krieger S; Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. S.KRIEGER@baclesse.unicancer.fr.; Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. S.KRIEGER@baclesse.unicancer.fr.; Université Caen-Normandie, Caen, France. S.KRIEGER@baclesse.unicancer.fr.; Present address: Laboratoire de biologie et génétique des cancers, Centre François Baclesse, Caen, France. S.KRIEGER@baclesse.unicancer.fr.
المصدر: BMC genomics [BMC Genomics] 2020 Jan 28; Vol. 21 (1), pp. 86. Date of Electronic Publication: 2020 Jan 28.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Introns* , RNA Precursors* , RNA Splice Sites* , RNA Splicing*, Alternative Splicing ; Computational Biology/methods ; Humans ; Nucleotide Motifs ; Position-Specific Scoring Matrices ; RNA Processing, Post-Transcriptional ; ROC Curve ; Reproducibility of Results
مستخلص: Background: Branch points (BPs) map within short motifs upstream of acceptor splice sites (3'ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3'ss.
Results: We used a large set of constitutive and alternative human 3'ss collected from Ensembl (n = 264,787 3'ss) and from in-house RNAseq experiments (n = 51,986 3'ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3'ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%.
Conclusions: Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3'ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.
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معلومات مُعتمدة: 200412859 Fondation de France; Gefluc, # R18064EE Groupement des Entreprises Françaises dans la Lutte contre le Cancer; (#2015/0335 Association Nationale de la Recherche et de la Technologie; 1061779 NHMRC Senior Research Fellowship
فهرسة مساهمة: Keywords: BPP; Benchmark; Branch point; Branchpointer; HSF; LaBranchoR; Prediction; RNA; RNABPS; SVM-BPfinder; Variants
المشرفين على المادة: 0 (RNA Precursors)
0 (RNA Splice Sites)
تواريخ الأحداث: Date Created: 20200130 Date Completed: 20200928 Latest Revision: 20200928
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC6988378
DOI: 10.1186/s12864-020-6484-5
PMID: 31992191
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-020-6484-5