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Article

Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes

1
Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
2
Area of Clinical and Molecular Genetics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
3
Medical Oncology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
*
Authors to whom correspondence should be addressed.
Co-first authors.
Co-last authors.
Academic Editor: David Wong
Cancers 2021, 13(13), 3341; https://doi.org/10.3390/cancers13133341
Received: 25 May 2021 / Revised: 25 June 2021 / Accepted: 29 June 2021 / Published: 3 July 2021
(This article belongs to the Special Issue Genetic Variants Associated with Breast and Ovarian Cancer Risk)
There is a significant percentage of hereditary breast and ovarian cancer (HBOC) cases that remain undiagnosed, because no pathogenic variant is detected through massively parallel sequencing of coding exons and exon-intron boundaries of high-moderate susceptibility risk genes. Deep intronic regions may contain variants affecting RNA splicing, leading ultimately to disease, and hence they may explain several cases where the genetic cause of HBOC is unknown. This study aims to characterize intronic regions to identify a landscape of “exonizable” zones and test the efficiency of two in silico tools to detect deep intronic variants affecting the mRNA splicing process.
The contribution of deep intronic splice-altering variants to hereditary breast and ovarian cancer (HBOC) is unknown. Current computational in silico tools to predict spliceogenic variants leading to pseudoexons have limited efficiency. We assessed the performance of the SpliceAI tool combined with ESRseq scores to identify spliceogenic deep intronic variants by affecting cryptic sites or splicing regulatory elements (SREs) using literature and experimental datasets. Our results with 233 published deep intronic variants showed that SpliceAI, with a 0.05 threshold, predicts spliceogenic deep intronic variants affecting cryptic splice sites, but is less effective in detecting those affecting SREs. Next, we characterized the SRE profiles using ESRseq, showing that pseudoexons are significantly enriched in SRE-enhancers compared to adjacent intronic regions. Although the combination of SpliceAI with ESRseq scores (considering ∆ESRseq and SRE landscape) showed higher sensitivity, the global performance did not improve because of the higher number of false positives. The combination of both tools was tested in a tumor RNA dataset with 207 intronic variants disrupting splicing, showing a sensitivity of 86%. Following the pipeline, five spliceogenic deep intronic variants were experimentally identified from 33 variants in HBOC genes. Overall, our results provide a framework to detect deep intronic variants disrupting splicing. View Full-Text
Keywords: spliceogenic deep intronic variants; pseudoexons; cryptic splice sites; splicing regulatory elements; hereditary breast ovarian cancer; in silico prediction tools spliceogenic deep intronic variants; pseudoexons; cryptic splice sites; splicing regulatory elements; hereditary breast ovarian cancer; in silico prediction tools
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MDPI and ACS Style

Moles-Fernández, A.; Domènech-Vivó, J.; Tenés, A.; Balmaña, J.; Diez, O.; Gutiérrez-Enríquez, S. Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes. Cancers 2021, 13, 3341. https://doi.org/10.3390/cancers13133341

AMA Style

Moles-Fernández A, Domènech-Vivó J, Tenés A, Balmaña J, Diez O, Gutiérrez-Enríquez S. Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes. Cancers. 2021; 13(13):3341. https://doi.org/10.3390/cancers13133341

Chicago/Turabian Style

Moles-Fernández, Alejandro, Joanna Domènech-Vivó, Anna Tenés, Judith Balmaña, Orland Diez, and Sara Gutiérrez-Enríquez. 2021. "Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes" Cancers 13, no. 13: 3341. https://doi.org/10.3390/cancers13133341

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