Oncotarget

Research Papers:

Sequencing of BRCA1/2-alterations using NGS-based technology: annotation as a challenge

Silvana Ebner _, Ria Winkelmann, Saskia Martin, Jens Köllermann, Peter J. Wild and Melanie Demes

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Oncotarget. 2022; 13:464-475. https://doi.org/10.18632/oncotarget.28213

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Abstract

Silvana Ebner1, Ria Winkelmann1, Saskia Martin1, Jens Köllermann1, Peter J. Wild1,2 and Melanie Demes1,2

1 Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany

2 Wildlab, University Hospital MVZ GmbH, Frankfurt am Main, Germany

Correspondence to:

Silvana Ebner, email: silvana.ebner@kgu.de

Keywords: BRCA1/2; annotation; degree of pathogenicity; next-generation sequencing; NGS

Received: August 25, 2021     Accepted: February 24, 2022     Published: March 03, 2022

Copyright: © 2022 Ebner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ABSTRACT

In this study, the molecular profile of different BRCA-associated tumor types was assessed with regard to the classification and annotation of detected BRCA1/2 variants. The aim was to establish guidelines in order to facilitate the interpretation of BRCA1/2 alterations in routine diagnostics. Annotation of detected variants was evaluated compared to background mutations found in normal tissue samples and manually reviewed according to distinct online databases. This retrospective study included 48 samples (45 tumors, three non-tumors), which were sequenced with the GeneReader (QIAGEN). Thereof ten samples were additionally analyzed with the Ion S5™ (Thermo Fisher) and 20 samples with the MiSeq™ (Illumina®) to compare the different NGS devices, as well as the sequencing results and their quality. The analysis showed that the individual NGS platforms detected different numbers of BRCA1/2 alterations in the respective tumor sample. In addition, the GeneReader revealed variability in the detection and classification of pathogenic alterations within the platform itself as well as in comparison with the other platforms or online databases. The study concluded that the Ion S5™ in combination with the Oncomine™ Comprehensive Assay v3 is most recommendable for current and prospective requirements of molecular analysis in routine diagnostics. In addition to the two BRCA1/2 genes, a broad number of other genes (BRCAness genes and genes involved in the repair pathway) is covered by the panel, which may open up new treatment options for patients depending on the respective eligibility criteria.


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