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Valtcheva N, Nguyen-Sträuli BD, Wagner U, Freiberger SN, Varga Z, Britschgi C, Dedes KJ, Rechsteiner MP. Setting a diagnostic benchmark for tumor BRCA testing: detection of BRCA1 and BRCA2 large genomic rearrangements in FFPE tissue - A pilot study. Exp Mol Pathol 2021; 123:104705. [PMID: 34637782 DOI: 10.1016/j.yexmp.2021.104705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
PARP inhibitors are used for treatment of tumors lacking function of the double-strand DNA break repair proteins BRCA1 or BRCA2 and are already approved for several cancer types. Thus, it is clinically crucial to determine germline as well as somatic BRCA1/2 mutations in those patients. The amplicon-based Oncomine BRCA1 and BRCA2 Assay is a test routinely used in diagnostics with FFPE specimens. The assay is validated for the detection of mutations, however, data on its performance in detecting large genomic rearrangements in FFPE tissue, is scarce. We cross-validated Oncomine BRCA1 and BRCA2 Assay in blood samples and/or FFPE tissue with multiplex ligation-dependent probe amplification (MLPA) for exon deletions and with OncoScan and an in-house hybridization-based target capture assay (MelArray) with a customized pipeline for the detection of loss of heterozygosity (LOH) and heterozygous versus complete gene loss. The Oncomine BRCA1 and BRCA2 Assay could detect both exon deletion and mono- and bi-allelic losses of the BRCA1/2 genes. We show that the therapeutically relevant large genomic rearrangements are reliably detected with the amplicon-based Oncomine BRCA1 and BRCA2 Assay in FFPE tumor tissue. Based on our data, we suggest tumor BRCA testing as standard diagnostic prescreening prior to germline BRCA testing.
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Affiliation(s)
- Nadejda Valtcheva
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland.
| | - Bich Doan Nguyen-Sträuli
- Department of Gynecology, Comprehensive Cancer Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Sandra N Freiberger
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; University of Zurich, 8091 Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Christian Britschgi
- Department of Medical Oncology and Hematology, Comprehensive Cancer Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Konstantin J Dedes
- Department of Gynecology, Comprehensive Cancer Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Markus P Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
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Hauke J, Hahnen E, Schneider S, Reuss A, Richters L, Kommoss S, Heimbach A, Marmé F, Schmidt S, Prieske K, Gevensleben H, Burges A, Borde J, De Gregorio N, Nürnberg P, El-Balat A, Thiele H, Hilpert F, Altmüller J, Meier W, Dietrich D, Kimmig R, Schoemig-Markiefka B, Kast K, Braicu E, Baumann K, Jackisch C, Park-Simon TW, Ernst C, Hanker L, Pfisterer J, Schnelzer A, du Bois A, Schmutzler RK, Harter P. Deleterious somatic variants in 473 consecutive individuals with ovarian cancer: results of the observational AGO-TR1 study (NCT02222883). J Med Genet 2019; 56:574-580. [PMID: 30979843 DOI: 10.1136/jmedgenet-2018-105930] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/26/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND For individuals with ovarian cancer (OC), therapy options mainly depend on BRCA1/2 germline status. What is the prevalence of deleterious somatic variants, that is, does genetic tumour testing identify subgroups of individuals who also might benefit from targeted therapy? METHODS Paired analysis of tumour-derived versus blood-derived DNA to determine the prevalence of deleterious somatic variants in OC predisposition genes (ATM, BRCA1/2, BRIP1, MSH2/6, PALB2, RAD51C/D and TP53) and the PIK3CA and PTEN genes in individuals with OC (AGO-TR1 study, NCT02222883). Results were complemented by BRCA1, PALB2 and RAD51C promoter methylation analyses and stratified by histological subtype; 473 individuals were included. RESULTS The combined analyses revealed that deleterious germline variants in established OC predisposition genes (all: 125/473, 26.4%; BRCA1/2: 97/473, 20.5%), deleterious somatic variants in established OC predisposition genes excluding TP53 (all: 39/473, 8.2%; BRCA1/2: 30/473, 6.3%) and promoter methylation (all: 67/473, 14.2%; BRCA1: 57/473, 12.1%; RAD51C: 10/473, 2.1%; PALB2: 0/473) were mutually exclusive, with a few exceptions. The same holds true for deleterious somatic PIK3CA and/or PTEN variants (33/473, 7.0%) found to be enriched in endometrioid and clear cell OC (16/35, 45.7%); 84.3 % of the deleterious single-nucleotide/indel germline variants in established OC predisposition genes showed significantly higher variant fractions (VFs) in the tumour-derived versus blood-derived DNA, indicating a loss of the wild-type alleles. CONCLUSION Tumour sequencing of the BRCA1, BRCA2, PIK3CA and PTEN genes along with BRCA1 and RAD51C promoter methylation analyses identified large subgroups of germline mutation-negative individuals who may be addressed in interventional studies using PARP or PI3K/AKT/mTOR inhibitors. TRIAL REGISTRATION NUMBER NCT02222883.
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Affiliation(s)
- Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stephanie Schneider
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Alexander Reuss
- Coordinating Center for Clinical Trials, Philipps-University of Marburg, Marburg, Germany
| | - Lisa Richters
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stefan Kommoss
- Department of Women's Health, University Hospital Tuebingen, Tuebingen, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederik Marmé
- National Center for Tumor Disease, Department of Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Sandra Schmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Katharina Prieske
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Alexander Burges
- Department of Gynecology, University Hospital Munich-Großhadern, Munich, Germany
| | - Julika Borde
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Nikolaus De Gregorio
- Department of Gynecology and Obstetrics, University Hospital, Universität Ulm, Ulm, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Ahmed El-Balat
- Department of Gynecology, University of Frankfurt, Frankfurt, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Felix Hilpert
- Department of Gynecology, University of Kiel, Kiel, Germany.,Onkologisches Therapiezentrum, Krankenhaus Jerusalem, Hamburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Werner Meier
- Department of Gynecology and Obstetrics, University Hospital Duesseldorf, Duesseldorf, Germany
| | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Rainer Kimmig
- Department of Gynecology, University of Essen, Essen, Germany
| | | | - Karin Kast
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Partner Site Dresden, Heidelberg, Germany
| | - Elena Braicu
- Department of Gynecology and Gynecological Oncology, Charité, Berlin, Germany
| | - Klaus Baumann
- Department of Gynecology, Gynecologic Endocrinology and Oncology, University of Gießen and Marburg GmbH, Marburg, Germany.,Department of Gynecology and Obstetrics, Klinikum Ludwigshafen, Ludwigshafen, Germany
| | - Christian Jackisch
- Department of Gynecology and Obstetrics, Sana Klinikum, Offenbach, Germany
| | | | - Corinna Ernst
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Lars Hanker
- Department of Gynecology & Obstetrics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Andreas Schnelzer
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,Department of Obstetrics and Gynecology, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
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