Unravelling genetic predisposition to familial breast and ovarian cancer: new susceptibility genes and variant interpretation by in silico approaches

Abstract

Patients with hereditary breast and ovarian cancer (HBOC) in whom a causative pathogenic variant is not identified after genetic analysis may not benefit from prevention, early detection, or precision treatment measures. This negative or inconclusive results are due, among other causes, to the detection of variants of uncertain significance (VUS).The main objective of this thesis is to increase the capacity of genetic diagnosis of patients with HBOC, by focusing on i) the optimisation in the interpretation of exonic and intronic variants that might affect RNA quality or quantity but remain as variants of uncertain significance (VUS) and ii) the identification of new susceptibility genes for HBOC.

The article included in this thesis, Moles-Fernández et al., 2018 (DOI: 10.3389/fgene.2018.00366) explains an optimization in the identification of potentially spliceogenic variants located near to splicing sites, and provides recommendations to use for analysing donor and acceptor sites. Moreover, the creation or activation of cryptic sites along deep intronic regions could alter splicing causing the inclusion of intronic sequences in RNA. In the article, Moles-Fernández et al., 2021 (DOI: 10.3390/cancers13133341), a framework for the identification of deep intronic spliceogenic is provided, after the performance analysis of SpliceAI in silico tool in a dataset of spliceogenic and non-spliceogenic deep intronic variants. In addition, the importance of the splicing regulatory elements balance in the pseudoexon creation is described.

The American College of Medical Genetics (ACMG) variant interpretation guidelines provide general recommendations to classify variants. In the included article Feliubadalò et al., 2021 (DOI: 10.1093/clinchem/hvaa250), ACMG guidelines were adapted to ATM gene. We focused on in silico splicing evidence (PP3/BP4). After reclassification of variants following the adapted guidelines, a reduction of VUS was obtained.

On the other hand, in patients without pathogenic variants identified in HBOC related genes, the phenotype could be due to deleterious variants in genes still not known associated with the disease. For this reason, in Moles-Fernández et al., (article in preparation), the aim was to identify candidate genes through exomes and extended panel analysis and validate their risk association by performing a case-control study. The significant identification of loss-of-function variants in ALKBH3, BLM, CAMKK1, FANCD2, FANCM, NEIL3, PER1, RBL1, RECQL4, WRN and XRCC4 genes in patients with HBOC suggests that they might be breast/ovarian cancer susceptibility genes.