BRCA1/2 Mutation Detection in the Tumor Tissue from Selected Polish Patients with Breast Cancer Using Next Generation Sequencing

Abstract

(1) Background: Although, in the mutated BRCA detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare BRCA1/2 variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the BRCA1/2 genes. (3) Results: We detected nine pathogenic variants in 8 out of 75 selected patients (10.7%). We identified one somatic and eight germline variants. We also used different bioinformatic NGS software programs to analyze NGS FASTQ files and established that tertiary analysis performed with different tools was more likely to give the same outcome if we analyzed files received from secondary analysis using the same method. (4) Conclusions: Our study emphasizes (i) the importance of an NGS validation process with a bioinformatic procedure included; (ii) the importance of screening both somatic and germline pathogenic variants; (iii) the urgent need to identify additional susceptible genes in order to explain the high percentage of non-BRCA-related hereditary cases of breast cancer.

Keywords: BRCA 1/2 genes; TNBC patients; bioinformatic NGS software; hereditary breast cancer; next-generation sequencing; somatic BRCA variant.

Figure 1

5 BRCA1 recurrent mutations in the Polish population (blue dots) and pathogenic variants detected in the BRCA1 and BRCA2 genes (red dots). Five known mutations in BRCA1: c. 68_69delAG, c.181T>G, c.3700_3704delGTAAA, c.4035delA, c.5266dupC. Nine pathogenic variants detected in the study group: c.1687C>T (BRCA1), c. 4752C>G (BRCA1), c.5186C>A (BRCA1), c.5242A>T (BRCA1), c.5645C>A (BRCA2), c.7758G>A (BRCA2), c.8191C>T (BRCA2) and c.9097dupA (BRCA2). BRCA1 domains: zf—zinc finger C3-HC4; CRCT-assoc.—serine-rich domain associated with BRCT; EIN-3—ethylene-insensitive 3; BRCT—BRCA1 C terminus domain. BRCA2 domains: BRCA2-helical; BRCA2-OB1—oligonucleotide/oligosaccharide binding domain 1; BRCA2-OB3—oligonucleotide/oligosaccharide-binding domain 3.