BRCA1/2 NGS Somatic Testing in Clinical Practice: A Short Report.

Francesco Pepe,Luigi Insabato,Giancarlo Troncone,Gianluca Russo,Mariantonia Nacchio,Claudio Bellevicine,Umberto Malapelle,Carmine De Angelis,Pierlorenzo Pallante,Elena Vigliar,Sabino De Placido,Pasquale Pisapia

doi:10.3390/genes12121917

Abstract

High-grade serous ovarian carcinoma (HGSOC) is the most common subtype of all ovarian carcinomas. HGSOC harboring BRCA1/2 germline or somatic mutations are sensitive to the poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPi). Therefore, detecting these mutations is crucial to identifying patients for PARPi-targeted treatment. In the clinical setting, next generation sequencing (NGS) has proven to be a reliable diagnostic approach BRCA1/2 molecular evaluation. Here, we review the results of our BRCA1/2 NGS analysis obtained in a year and a half of diagnostic routine practice. BRCA1/2 molecular NGS records of HGSOC patients were retrieved from our institutional archive covering the period from January 2020 to September 2021. NGS analysis was performed on the Ion S5™ System (Thermo Fisher Scientific, Waltham, MA, USA) with the Oncomine™ BRCA Research Assay panel (Thermo Fisher Scientific). Variants were classified as pathogenic or likely pathogenic according to the guidelines of the American College of Medical Genetics and Genomics by using the inspection of Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) and ClinVar (NCBI) databases. Sixty-five HGSOC patient samples were successfully analyzed. Overall, 11 (16.9%) out of 65 cases harbored a pathogenic alteration in BRCA1/2, in particular, six BRCA1 and five BRCA2 pathogenic variations. This study confirms the efficiency and high sensitivity of NGS analysis in detecting BRCA1/2 germline or somatic variations in patients with HGSOC.

Highlights

Our in-house developed next generation sequencing (NGS) workflow successfully analyzed a total of n = 65 High-grade serous ovarian carcinoma (HGSOC) histological samples
As for the technical parameters, NGS analysis generated a median number of reads per sample of
poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPi), which have been shown to improve the survival as well as quality of life patients affected by HGSOC

Summary

Introduction

Ovarian cancer (OC) is the eighth most common cancer type among women worldwide and the leading cause of death for gynecological malignancies [1,2]. OCs are generally classified into Type I and Type II tumors. Whereas the former are generally low-grade and genetically stable tumors, the latter, which predominantly harbor. Tumor Protein P53 (TP53) and Cyclin E1 (CCNE1) gene alterations, are more aggressive and genetically unstable [3]. Among Type II ovarian tumors, high-grade serous ovarian carcinoma (HGSOC) is the most common subtype, accounting for about three quarters of OCs [4,5]. In 96% of cases, HGSOCs carry TP53 somatic mutations.

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Conclusion