Secondary findings in genes related to cancer phenotypes in Turkish exome sequencing data from 2020 individuals

Abstract

Big data generated from exome sequencing (ES) and genome sequencing (GS) analyses can be used to detect actionable and high‐penetrance variants that are not directly associated with the primary diagnosis of patients but can guide their clinical follow‐up and treatment. Variants that are classified as pathogenic/likely pathogenic and are clinically significant but not directly associated with the primary diagnosis of patients are defined as secondary findings (SF). The aim of this study was to examine the frequency and variant spectrum of cancer‐related SF in 2020 Turkish ES data and to discuss the importance of the presence of cancer‐related SF in at‐risk family members in terms of genetic counseling and follow‐up. A total of 2020 patients from 2020 different families were evaluated by ES. SF were detected in 28 unrelated cases (1.38%), and variants in BRCA2 (11 patients) and MLH1 (4 patients) genes were observed most frequently. A total of 21 different variants were identified, with 4 of them (c.9919_9932del and c.3653del in the BRCA2 gene, c.2002A>G in the MSH2 gene, c.26_29del in the TMEM127 gene) being novel variations. In three different families, c.1189C>T (p.Gln397*) variation in BRCA2 gene was detected, suggesting that this may be a common variant in the Turkish population. This study represents the largest cohort conducted in the Turkish population, examining the frequency and variant spectrum of cancer‐related SF. With the identification of frequent variations and the detection of novel variations, the findings of this study have contributed to the variant spectrum. Genetic testing conducted in family members is presented as real‐life data, showcasing the implications in terms of counseling, monitoring, and treatment through case examples.