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Lier A, Penzel R, Heining C, Horak P, Fröhlich M, Uhrig S, Budczies J, Kirchner M, Volckmar AL, Hutter B, Kreutzfeldt S, Endris V, Richter D, Wolf S, Pfütze K, Neumann O, Buchhalter I, Morais de Oliveira CM, Singer S, Leichsenring J, Herpel E, Klauschen F, Jost PJ, Metzeler KH, Schulze-Osthoff K, Kopp HG, Kindler T, Rieke DT, Lamping M, Brandts C, Falkenhorst J, Bauer S, Schröck E, Folprecht G, Boerries M, von Bubnoff N, Weichert W, Brors B, Lichter P, von Kalle C, Schirmacher P, Glimm H, Fröhling S, Stenzinger A. Validating Comprehensive Next-Generation Sequencing Results for Precision Oncology: The NCT/DKTK Molecularly Aided Stratification for Tumor Eradication Research Experience. JCO Precis Oncol 2018; 2:1-13. [DOI: 10.1200/po.18.00171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Purpose Rapidly evolving genomics technologies, in particular comprehensive next-generation sequencing (NGS), have led to exponential growth in the understanding of cancer biology, shifting oncology toward personalized treatment strategies. However, comprehensive NGS approaches, such as whole-exome sequencing, have limitations that are related to the technology itself as well as to the input source. Hence, clinical implementation of comprehensive NGS in a quality-controlled diagnostic workflow requires both the standardization of sequencing procedures and continuous validation of sequencing results by orthogonal methods in an ongoing program to enable the determination of key test parameters and continuous improvement of NGS and bioinformatics pipelines. Patients and Methods We present validation data on 220 patients who were enrolled between 2013 and 2016 in a multi-institutional, genomics-guided precision oncology program (Molecularly Aided Stratification for Tumor Eradication Research) of the National Center for Tumor Diseases Heidelberg and the German Cancer Consortium. Results More than 90% of clinically actionable genomic alterations identified by combined whole-exome sequencing and transcriptome sequencing were successfully validated, with varying frequencies of discordant results across different types of alterations (fusions, 3.7%; single-nucleotide variants, 2.6%; amplifications, 1.1%; overexpression, 0.9%; deletions, 0.6%). The implementation of new computational methods for NGS data analysis led to a substantial improvement of gene fusion calling over time. Conclusion Collectively, these data demonstrate the value of a rigorous validation program that partners with comprehensive NGS to successfully implement and continuously improve cancer precision medicine in a clinical setting.
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Affiliation(s)
- Amelie Lier
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Roland Penzel
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christoph Heining
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Horak
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Martina Fröhlich
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Sebastian Uhrig
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Jan Budczies
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Martina Kirchner
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Anna-Lena Volckmar
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Barbara Hutter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Simon Kreutzfeldt
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Volker Endris
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Daniela Richter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stephan Wolf
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Katrin Pfütze
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Olaf Neumann
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Ivo Buchhalter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Cristiano M. Morais de Oliveira
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stephan Singer
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Jonas Leichsenring
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Esther Herpel
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Frederick Klauschen
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Philipp J. Jost
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Klaus H. Metzeler
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Klaus Schulze-Osthoff
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Hans-Georg Kopp
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Thomas Kindler
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Damian T. Rieke
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Mario Lamping
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christian Brandts
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Johanna Falkenhorst
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Sebastian Bauer
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Evelin Schröck
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Gunnar Folprecht
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Melanie Boerries
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Nikolas von Bubnoff
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Wilko Weichert
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Benedikt Brors
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Lichter
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Christof von Kalle
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Peter Schirmacher
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Hanno Glimm
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Stefan Fröhling
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
| | - Albrecht Stenzinger
- Amelie Lier, Roland Penzel, Peter Horak, Jan Budczies, Martina Kirchner, Anna-Lena Volckmar, Simon Kreutzfeldt, Volker Endris, Olaf Neumann, Ivo Buchhalter, Cristiano M. Morais de Oliveira, Stephan Singer, Jonas Leichsenring, Esther Herpel, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, Heidelberg University Hospital; Christoph Heining, Daniela Richter, Stephan Wolf, Katrin Pfütze, Benedikt Brors, Peter Lichter, and Hanno Glimm, German Cancer Research Center; Peter Horak
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Hirsch B, Endris V, Lassmann S, Weichert W, Pfarr N, Schirmacher P, Kovaleva V, Werner M, Bonzheim I, Fend F, Sperveslage J, Kaulich K, Zacher A, Reifenberger G, Köhrer K, Stepanow S, Lerke S, Mayr T, Aust DE, Baretton G, Weidner S, Jung A, Kirchner T, Hansmann ML, Burbat L, von der Wall E, Dietel M, Hummel M. Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics. Virchows Arch 2018; 472:557-565. [PMID: 29374318 PMCID: PMC5924673 DOI: 10.1007/s00428-017-2288-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022]
Abstract
The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.
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Affiliation(s)
- B Hirsch
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - V Endris
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - S Lassmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - W Weichert
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - N Pfarr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - P Schirmacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - V Kovaleva
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - M Werner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - I Bonzheim
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - F Fend
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - J Sperveslage
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - K Kaulich
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - A Zacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - G Reifenberger
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - K Köhrer
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Stepanow
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Lerke
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - T Mayr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - D E Aust
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - G Baretton
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - S Weidner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - A Jung
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - T Kirchner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - M L Hansmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Dr. Senckenberg Institute of Pathology, University Hospital, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - L Burbat
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - E von der Wall
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Dietel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Hummel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
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