Oncotarget

Priority Research Papers:

BRCA somatic and germline mutation detection in paraffin embedded ovarian cancers by next-generation sequencing

Andrea Mafficini, Michele Simbolo, Alice Parisi, Borislav Rusev, Claudio Luchini, Ivana Cataldo, Elena Piazzola, Nicola Sperandio, Giona Turri, Massimo Franchi, Giampaolo Tortora, Chiara Bovo, Rita T. Lawlor, _ Aldo Scarpa

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Oncotarget. 2016; 7:1076-1083. https://doi.org/10.18632/oncotarget.6834

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Abstract

Andrea Mafficini1,*, Michele Simbolo1,*, Alice Parisi2, Borislav Rusev1,2, Claudio Luchini1,2, Ivana Cataldo1, Elena Piazzola2, Nicola Sperandio1, Giona Turri2, Massimo Franchi3, Giampaolo Tortora4, Chiara Bovo5, Rita T. Lawlor1,2 and Aldo Scarpa1,2

1 ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy

2 Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy

3 Department of Gynecology, University and Hospital Trust of Verona, Verona, Italy

4 Comprehensive Cancer Centre, University and Hospital Trust of Verona, Verona, Italy

5 Board of Directors, University and Hospital Trust of Verona, Verona, Italy

* Shared first authors

Correspondence to:

Rita T. Lawlor , email:

Keywords: BRCA1-BRCA2, ovarian carcinoma, next generation sequencing, PARP inhibitor, olaparib

Received: November 10, 2015 Accepted: December 29, 2015 Published: January 07, 2016

Abstract

BRCA mutated ovarian cancers respond better to platinum-based therapy and to the recently approved PARP-inhibitors. There is the need for efficient and timely methods to detect both somatic and germline mutations using formalin-fixed paraffin-embedded (FFPE) tissues and commercially available technology. We used a commercial kit exploring all exons and 50bp exon-intron junctions of BRCA1 and BRCA2 genes, and semiconductor next-generation sequencing (NGS) on DNA from 47 FFPE samples of high-grade serous ovarian cancers. Pathogenic mutations were found in 13/47 (28%) cancers: eight in BRCA1 and five in BRCA2. All BRCA1 and two BRCA2 mutations were germline; three BRCA2 mutations were somatic. All mutations were confirmed by Sanger sequencing. To evaluate the performance of the NGS panel, we assessed its capability to detect the 6,953 variants described for BRCA1 and BRCA2 in ClinVar and COSMIC databases using callability analysis. 6,059 (87.1%) variants were identified automatically by the software; 829 (12.0%) required visual verification. The remaining 65 (0.9%) variants were uncallable, and would require 15 Sanger reactions to be resolved. Thus, the sensitivity of the NGS-panel was 99.1%. In conclusion, NGS performed with a commercial kit is highly efficient for detection of germline and somatic mutations in BRCA genes using routine FFPE tissue.


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