Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes

Rita D. Brandão, Klaas Mensaert, Irene López-Perolio, Demis Tserpelis, Markos Xenakis, Vanessa Lattimore, Logan C. Walker, Anders Kvist, Ana Vega, Sara Gutiérrez-Enríquez, Orland Díez, Miguel de la Hoya, Amanda B. Spurdle, Tim De Meyer, Marinus J. Blok

Research output: Contribution to journalArticlepeer-review

17 Citations (SciVal)

Abstract

A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary electrophoresis and were compared to a non-targeted RNA-seq approach. We also compared splicing events from lymphoblastoid cell-lines with those from breast and ovarian fimbriae tissues. The potential of targeted RNA-seq to detect pathogenic changes in RNA-splicing was validated by the inclusion of samples with previously well characterized BRCA1/2 genetic variants. In our study, we update the catalogue of normal splicing events for BRCA1/2, provide an extensive catalogue of normal RAD51C and RAD51D alternative splicing, and list splicing events found for eight other genes. Additionally, we show that our approach allowed the identification of aberrant splicing events due to the presence of BRCA1/2 genetic variants and distinguished between complete and partial splicing events. In conclusion, targeted-RNA-seq can be very useful to classify variants based on their putative pathogenic impact on splicing.

Original languageEnglish
Pages (from-to)401-414
JournalInternational Journal of Cancer
Volume145
Issue number2
Early online date2019 Jan 8
DOIs
Publication statusPublished - 2019

Subject classification (UKÄ)

  • Cancer and Oncology
  • Medical Genetics

Keywords

  • alternative splicing
  • BRCA1/2
  • inherited breast/ovarian cancer syndrome
  • lynch syndrome
  • targeted RNA-seq

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