Implementation of amplicon parallel sequencing leads to improvement of diagnosis and therapy of lung cancer patients

Koenig K, Peifer M, Fassunke J, Ihle MA, Kuenstlinger H, Heydt C, Stamm K, Ueckeroth F, Vollbrecht C, Bos M, Gardizi M, Scheffler M, Nogova L, Leenders F, Albus K, Meder L, Becker K, Florin A, Rommerscheidt-Fuss U, Altmueller J, Kloth M, Nuernberg P, Henkel T, Bikar SE, Sos ML, Geese WJ, Strauss L, Ko YD, Gerigk U, Odenthal M, Zander T, Wolf J, Merkelbach-Bruse S, Buettner R, Heukamp LC (2015)

Publication Type: Journal article

Publication year: 2015

Journal

Journal of Thoracic Oncology Lippincott, Williams & Wilkins

Book Volume: 10

Pages Range: 1049-1057

Journal Issue: 7

DOI: 10.1097/JTO.0000000000000570

Abstract

Introduction: The Network Genomic Medicine Lung Cancer was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer performing molecular analyses of more than 3500 patients annually. Because sequential analysis of the relevant driver mutations on fixated samples is challenging in terms of workload, tissue availability, and cost, we established multiplex parallel sequencing in routine diagnostics. The aim was to analyze all therapeutically relevant mutations in lung cancer samples in a high-throughput fashion while significantly reducing turnaround time and amount of input DNA compared with conventional dideoxy sequencing of single polymerase chain reaction amplicons. Methods: In this study, we demonstrate the feasibility of a 102 amplicon multiplex polymerase chain reaction followed by sequencing on an Illumina sequencer on formalin-fixed paraffin-embedded tissue in routine diagnostics. Analysis of a validation cohort of 180 samples showed this approach to require significantly less input material and to be more reliable, robust, and cost-effective than conventional dideoxy sequencing. Subsequently, 2657 lung cancer patients were analyzed. Results: We observed that comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, we identified driver mutations at the expected prevalence. Furthermore we found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas. Conclusion: Overall, our data demonstrate the utility of systematic sequencing analysis in a clinical routine setting and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

Authors with CRIS profile

Lydia Meder

Involved external institutions

Universitätsklinikum Köln DE Germany (DE) Medizinisches Versorgungszentrum (MVZ) Labor Dr. Quade & Kollegen GmbH DE Germany (DE) Targos Molecular Pathology GmbH DE Germany (DE) Universität zu Köln DE Germany (DE) Cologne Center for Genomics DE Germany (DE) GENterprise, Gesellschaft für Genanalyse und Biotechnologie mbH DE Germany (DE) Bristol-Myers Squibb US United States (USA) (US)

How to cite

APA:

Koenig, K., Peifer, M., Fassunke, J., Ihle, M.A., Kuenstlinger, H., Heydt, C.,... Heukamp, L.C. (2015). Implementation of amplicon parallel sequencing leads to improvement of diagnosis and therapy of lung cancer patients. Journal of Thoracic Oncology, 10(7), 1049-1057. https://doi.org/10.1097/JTO.0000000000000570

MLA:

Koenig, Katharina, et al. "Implementation of amplicon parallel sequencing leads to improvement of diagnosis and therapy of lung cancer patients." Journal of Thoracic Oncology 10.7 (2015): 1049-1057.

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