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

Ewelina Szczerba,Marzena Anna Lewandowska,Janusz Kowalewski,Marcin Misiek,Katarzyna Kamińska,Tomasz Mierzwa

doi:10.3390/genes12040519

Ewelina Szczerba, Marzena Anna Lewandowska + Show 4 more

Open Access

https://doi.org/10.3390/genes12040519

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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.

Highlights

Breast cancer is the most common cancer in women worldwide [1]
The median age was 43 years at the time of diagnosis (75 patients with breast cancer enrolled in the study were negative for the 5 most common BRCA1 mutations)
Pathogenic variants were detected predominantly in patients diagnosed with breast cancer who were under 46 years of age (n = 8), and this prevalence observed in the studied subpopulation of 25–69 years of age was statistically significant (Mann–Whitney U test, α = 0.05) (Table 1)

Summary

Introduction

Breast cancer is the most common cancer in women worldwide [1]. Women carrying BRCA mutations have an increased risk of breast cancer and/or ovarian cancer development, with a probability of 45–75% and 18–40%, respectively [2,3,4,5]. Hereditary ovarian/breast cancer (HOBC) is frequently caused by founder mutations in the BRCA1 and BRCA2 genes. Founder mutations were historically present with high frequencies in small, geographically or culturally isolated groups and are derived from one or more ancestors [6]. A founder effect can be observed in a population characterized by lower genetic diversity, which might be caused by the parental population suffering a dramatic decrease or bottleneck. The parental population could give rise to a larger population in which new variants could occur spontaneously or be transferred from other populations [7]

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