For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies.

BC Cancer Agency Vancouver British Columbia Canada

Cancer Genetics and Genomics Laboratory Department of Pathology and Laboratory Medicine BC Cancer Agency Vancouver British Columbia Canada

Cancer Research Program Research Institute of the McGill University Health Centre McGill University Montreal Quebec Canada

Center for Medical Genetics Ghent University Hospital Ghent Belgium

Department of Basic Medical Sciences Ghent University Ghent Belgium

Department of Cancer Epidemiology and Genetics Masaryk Memorial Cancer Institute Brno Czech Republic

Department of Internal Medicine Hematology and Oncology University Hospital Brno Brno Czech Republic

Familial Cancer Program University of Vermont Medical Center Burlington Vermont United States

Fundación Pública Galega de Medicina Xenómica SERGAS Grupo de Medicina Xenómica CIBERER IDIS Santiago de Compostela Spain

Molecular Oncology Laboratory CIBERONC Hospital Clinico San Carlos IdISSC Madrid Spain

Provincial Medical Genetics Program Eastern Health St John's Newfoundland and Labrador Canada

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