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Validating Comprehensive Next-Generation Sequencing Results for Precision Oncology: The NCT/DKTK Molecularly Aided
Amelie Lier1, Roland Penzel1, Christoph Heining1
1Amelie 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, Sebastian Uhrig, Barbara Hutter, Simon Kreutzfeldt, Katrin Pfütze, Esther Herpel, Christof von Kalle, and Stefan Fröhling, National Center for Tumor Diseases Heidelberg; Sebastian Uhrig, Heidelberg University; Simon Kreutzfeldt, Cristiano M. Morais de Oliveira, Christof von Kalle, Peter Schirmacher, Stefan Fröhling, and Albrecht Stenzinger, German Cancer Consortium, Heidelberg; Christoph Heining, Daniela Richter, and Hanno Glimm, National Center for Tumor Diseases Dresden; Christoph Heining, Evelin Schröck, Gunnar Folprecht, and Hanno Glimm, Technische Universität Dresden; Christoph Heining, Daniela Richter, Evelin Schröck, Gunnar Folprecht, and Hanno Glimm, German Cancer Consortium; Gunnar Folprecht, University Hospital, Dresden; Frederick Klauschen, Charité University Hospital; Frederick Klauschen and Mario Lamping, German Cancer Consortium; Damian T. Rieke, Charité Universitätsmedizin Berlin; Damian T. Rieke and Mario Lamping, Charité Comprehensive Cancer Center; Damian T. Rieke, Berlin Institute of Health, Berlin; Philipp J. Jost and Wilko Weichert, Technical University Munich; Philipp J. Jost, Klaus H. Metzeler, and Wilko Weichert, German Cancer Consortium; Klaus H. Metzeler, Ludwig Maximilians University, Munich; Klaus Schulze-Osthoff, University of Tübingen; Klaus Schulze-Osthoff and Hans-Georg Kopp, German Cancer Consortium; Hans-Georg Kopp, Eberhard Karls University, Tübingen; Thomas Kindler, University Cancer Center of Mainz; Thomas Kindler, German Cancer Consortium, Mainz; Christian Brandts, University Cancer Center Frankfurt; Christian Brandts, Goethe University; Christian Brandts, German Cancer Consortium, Frankfurt; Johanna Falkenhorst and Sebastian Bauer, University Hospital Essen, University Duisburg-Essen; Johanna Falkenhorst and Sebastian Bauer, German Cancer Consortium, Essen; Melanie Boerries, Albert-Ludwigs-University; Melanie Boerries and Nikolas von Bubnoff, German Cancer Consortium; and Nikolas von Bubnoff, Medical Center University of Freiburg, Freiburg, Germany.
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.
