title: Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes.
abstract: Comprehensive genetic testing of the breast cancer susceptibility genes BRCA1 and BRCA2 identified approximately 16% of variants of unknown significance (VUS), a significant proportion of which could affect the correct splicing of the genes. Our aim is to establish a workflow for classifying VUS in these complex genes, the first stage of which is splicing analysis. We used a combined approach consisting of five in silico splicing prediction programs and RT-PCR analysis for a set of 26 variants not previously studied at the mRNA level and six variants that had already been studied, four of which were used as positive controls as they were found to affect the splicing of these genes and the other two were used as negative controls. We identified a splicing defect in 8 of the 26 newly studied variants and ruled out splicing alteration in the remaining 18 variants. The results for the four positive and the two negative control variants were consistent with results presented in the literature. Our results strongly suggest that the combination of RNA analysis and in silico programs is an important step towards the classification of VUS. The results revealed a very high correlation between experimental data and in silico programs when using tools for predicting acceptor/donor sites but a lower correlation in the case of tools for identifying ESE elements.
authors: Hereditary Cancer Program, Genetic Diagnosis Unit, Laboratori de Recerca Translacional, Institut Català d'Oncologia, Hospital Duran i Reynals-Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona and Hospital Josep Trueta, IDIBGI, Gran Via 199-203, Girona 08908, Spain.
authors: Mireia
authors: M
authors: Menéndez
authors: Joan
authors: J
authors: Castellsagué
authors: Marc
authors: M
authors: Mirete
authors: Eva
authors: E
authors: Pros
authors: Lídia
authors: L
authors: Feliubadaló
authors: Ana
authors: A
authors: Osorio
authors: Mónica
authors: M
authors: Calaf
authors: Eva
authors: E
authors: Tornero
authors: Jesús
authors: J
authors: del Valle
authors: Juana
authors: J
authors: Fernández-Rodríguez
authors: Francisco
authors: F
authors: Quiles
authors: Mónica
authors: M
authors: Salinas
authors: Angela
authors: A
authors: Velasco
authors: Alex
authors: A
authors: Teulé
authors: Joan
authors: J
authors: Brunet
authors: Ignacio
authors: I
authors: Blanco
authors: Gabriel
authors: G
authors: Capellá
authors: Conxi
authors: C
authors: Lázaro
mesh_terms: D017398:Alternative Splicing; D019313:BRCA1 Protein / Q000235:genetics* / Q000378:metabolism; D024682:BRCA2 Protein / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D003198:Computer Simulation; D005260:Female; D020022:Genetic Predisposition to Disease; D061325:Hereditary Breast and Ovarian Cancer Syndrome / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D024682:BRCA2 Protein; C551750:BRCA2 protein, human; D020033:Protein Isoforms; D012333:RNA, Messenger