Abstract
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes. Our pipeline identified 14 new alternative splices in BRCA1 and BRCA2 in addition to detecting the majority of known alternative spliced transcripts therein. We provide here the first global splicing pattern analysis for the other nine genes, which will enable a comprehensive interpretation of splicing defects caused by VUS in HBOC. Previously known splicing alterations were consistently detected, occasionally with a more complex splicing pattern than expected. We also found that splicing in the 11 genes is similar in blood and breast tissue, supporting the utility and simplicity of blood splicing assays. Our pipeline is ready to be integrated into standard molecular diagnosis for HBOC, but it could equally be adapted for an integrative analysis of any multigene disorder.
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Acknowledgements
We thank the members of our department of biopathology for their input, the high-throughput sequencing platform of Basse-Normandie SéSAME (Sequencing for Health, Agronomy, the Sea and the Environment) and the Clinical Research of the Centre François Baclesse. We also thank the members of the Evidence-Based Network for the Interpretation of Germ-Line Mutant Alleles consortium (ENIGMA) for their interactions during this study. This work was supported by grants from the Institut National du Cancer (INCa); the French Cancéropôle Nord-Ouest (CNO); and the Ligue Régionale du Calvados Contre le Cancer. We thank the Brazilian agency Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for providing a postdoctoral fellowship for ASS.
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Davy, G., Rousselin, A., Goardon, N. et al. Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet 25, 1147–1154 (2017). https://doi.org/10.1038/ejhg.2017.116
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DOI: https://doi.org/10.1038/ejhg.2017.116
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