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An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice |
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| Authors: | Miika Ahdesmäki Sally Luke Paul M. Waring Andrew Wallace Ronnie Wright Benno Röthlisberger Katja Ludin Sabine Merkelbach‐Bruse Carina Heydt Marjolijn J.L. Ligtenberg Arjen R. Mensenkamp David Gonzalez de Castro Thomas Jones Ana Vivancos Olga Kondrashova Patrick Pauwels Christine Weyn Eric Hahnen Jan Hauke Richie Soong Zhongwu Lai Brian Dougherty T. Hedley Carr Justin Johnson John Mills J. Carl Barrett |
| Affiliation: | 1. Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UKGillian Ellison and Miika Ahdesm?ki contributed equally to this work.;2. R&D Information, AstraZeneca, Cambridge, UK;3. Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia;4. Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK;5. Kantonsspital Aarau, Institut für Labormedizin, Abteilung für Medizinische Genetik, Aarau, Switzerland;6. Institute of Pathology, University Hospital Cologne, Cologne, Germany;7. Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands;8. Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands;9. Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK;10. The Centre for Molecular Pathology, The Royal Marsden NHS FT, Sutton, UK;11. Laboratory 2.01, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain;12. Center for Oncological Research (CORE), Pathology Department, University Hospital Antwerp (UZA), Edegem, Belgium;13. Center for Hereditary Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany;14. Cancer Science Institute of Singapore, and Department of Pathology, National University of Singapore, Singapore, Singapore;15. Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, IMED Oncology, Waltham, Massachusetts;16. Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts;17. Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK;18. Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Macclesfield, UK |
| Abstract: | Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with poly ADP ribose polymerase (PARP) inhibitors. Tumor BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin‐fixed paraffin embedded (FFPE), the tumor genome is complex, and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumors to compare different approaches to identify clinically important variants within FFPE tumor DNA samples. This was not a proficiency study but an inter‐laboratory comparison to identify common issues. Each laboratory received the same tumor DNA samples ranging in genotype, quantity, quality, and variant allele frequency (VAF). Each laboratory performed their preferred next‐generation sequencing method to report on the variants. No false positive results were reported in this small study and the majority of methods detected the low VAF variants. A number of variants were not detected due to the bioinformatics analysis, variant classification, or insufficient DNA. The use of hybridization capture or short amplicon methods are recommended based on a bioinformatic assessment of the data. The study highlights the importance of establishing standards and standardization for tBRCA testing particularly when the test results dictate clinical decisions regarding life extending therapies. |
| Keywords: | diagnostic FFPE NGS PARP tBRCA |