Next-Generation Sequencing (NGS) gained greater importance and interest in hereditary tumours, and in particular breast, ovarian, and colon cancer syndromes. This technology increased the chance of detecting germline DNA mutations in cancer-related genes, guiding patients’ management, and surveillance strategies in their families. NGS-based multi-gene panels (MGP) are the methods of choice for the diagnosis of such syndromes, because they allow targeting the sequencing to selected relevant genes for many patients simultaneously, reaching high coverage and sensitivity. That means increasing the number of variants with a lower variant allele frequency than the heterozygous threshold identified and therefore more unexpected genomic results with higher complexity in their interpretation.
In this research work, we investigated this phenomenon in patients tested with multi-gene panels for hereditary cancer syndromes. Actually, there are no standard guidelines for the analysis of such variants in the NGS diagnostic pipelines. Furthermore, only a few papers are reported in the literature, at the moment.
The study aimed to examine the prevalence and characteristics of low-frequency variants in patients who underwent an NGS hereditary-cancer test at the Clinical Genomics Laboratory, Azienda Ospedaliero Universitaria of Modena from October 2017 to October 2021.
Nine out of 1896 patients (0.47%) patients carried a variant with low allele frequency classified as pathogenic in ATM, CHEK2, MSH2, BRCA1, or TP53 genes. Seven patients turned out to have blood-confined variants, which means Clonal Haematopoiesis of Indeterminate Potential (CHIP). Two patients, instead, were identified with constitutional mosaicism in BRCA1 and TP53 genes, respectively. For one of them, the variant was also found in one of the daughters.
Mosaicism resulted to be rare in the studied cohort, but reaching a proper diagnosis had strong clinical implications for the patients and their offspring.