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.

Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

“…Sequencing was performed on a MiniSeq platform (Illumina) using the MiniSeq Mid Output Kit, 2 × 150 cycles, to obtain reads for both strands. Sequencing results were analyzed using EntroGen Variant Reporter v1.3 and Illumina Variant Studio 3.0 [ 11 ]. Single nucleotide variant (SNV) pathogenic alterations detected by NGS are listed in the supplementary data: Table S2 (see the electronic supplementary material).…”

Whole-exome sequencing and bioinformatic analyses revealed differences in gene mutation profiles in papillary thyroid cancer patients with and without benign thyroid goitre background

“…In contrast to FANCD2 monoubiquitination which has a mild impact on HR, BRCA2 activity is essential for DNA double-strand break (DSB) repair ( 24 ). PALB2 and BRCA s genes have been well-reported due to their high prevalence in breast cancer where patients with PALB2 gene mutation were found to have shorter survival years ( 33 – 35 ). It was also reported that approximately 49.1% of thyroid cancer patients were found to have breast tumours ( 36 ).…”

Detection of BRCA1/2 pathogenic variants in patients with breast and/or ovarian cancer and their families. Analysis of 3,458 cases from Lower Silesia (Poland) according to the diagnostic algorithm of the National Cancer Control Programme

“…Genetic tests for BRCA1/2 genes are also a cost-efficient screening tool for patients with somatic or germline pathogenic variants who can benefit from PARP inhibitor (PARPi) therapy ( Forbes et al, 2019 ; McAlarnen et al, 2021 ; Szczerba et al, 2021 ; Yamamoto and Hirasawa 2021 ). Thus, BRCA1/2 sequencing is more and more commonly ordered by oncologists as a test performed on tDNA not only for patients with ovarian cancer but also for specific patients with prostate cancer and pancreatic cancer in whom such therapy could be considered ( McAlarnen et al, 2021 ; Szczerba et al, 2021 ). For such patients, a consultation with clinical geneticists still should be highly recommended and is crucial to determine whether the pathogenic variant is somatic or germline.…”