Rna sequencing role in the genetic diagnosis of hereditary breast and ovarian cancer

Abstract

Hereditary breast and ovarian cancer (HBOC) is a syndrome defined by an increased risk of developing breast cancer (BC) and/or ovarian cancer (OC), mainly due to germline pathogenic variants in BRCA1 and BRCA2. While clinical genetic testing typically focuses on DNA coding regions, RNA sequencing (RNA-seq) offers a potential improvement in patient diagnosis the study of the expression of these regions. The goal of this study was to evaluate whether splicing and expression analysis of whole blood RNA, tested using Illumina sequencing, can provide a genetic diagnosis of HBOC in patients with high suspicion for the disorder, where conventional DNA testing has yielded inconclusive results. Consequently, the expression of 15 genes associated with HBOC was examined through RNA-seq in 45 patients who tested negative for BRCA1 and BRCA2 mutations. This study employed various bioinformatic approaches to assess the impact of transcriptomics on a cohort of HBOC patients, focusing on patient-specific alterations, using RNA from blood samples: Differential Expression Analysis (DEA), Outlier in RNA-seq Finder (OUTRIDER), Differential Exon Usage (DEU), SUPPA, and Find Rare Splicing Events in RNA-seq Data (FRASER). The results revealed 2 aberrantly expressed genes detected by OUTRIDER, 24 local splicing events identified by SUPPA, and 14 significant findings discovered by FRASER. After performing this study, we can conclude that bioinformatics approaches, such as transcriptomics, are powerful but require laboratory validation. This initial exploration should be followed by additional computational and experimental analyses.