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Int J Cancer. 2019 Jan 17. doi: 10.1002/ijc.32133. [Epub ahead of print]

Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics: Analysis of the first 3,000 Heidelberg cases.

Author information

1
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
2
Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.
3
Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany.
4
National Center for Tumor Diseases (NCT), Heidelberg, Germany.
5
German Cancer Consortium (DKTK), Heidelberg partner site, Germany.
6
Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
7
Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.
8
Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
9
German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.
10
Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.
11
Department of Cardiology and Pneumology, Hospital Esslingen, Esslingen, Germany.
12
Department of Thoracic Oncology, Lungenklinik Löwenstein, Löwenstein, Germany.
13
Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.
14
Department of Pneumology and Critical Care Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.

Abstract

Tyrosine kinase inhibitors currently confer the greatest survival gain for nonsmall cell lung cancer (NSCLC) patients with actionable genetic alterations. Simultaneously, the increasing number of targets and compounds poses the challenge of reliable, broad and timely molecular assays for the identification of patients likely to benefit from novel treatments. Here, we demonstrate the feasibility and clinical utility of comprehensive, NGS-based genetic profiling for routine workup of advanced NSCLC based on the first 3,000 patients analyzed in our department. Following automated extraction of DNA and RNA from formalin-fixed, paraffin-embedded tissue samples, parallel sequencing of DNA and RNA for detection of mutations and gene fusions, respectively, was performed using PCR-based enrichment with an ion semiconductor sequencing platform. Overall, 807 patients (27%) were eligible for currently approved, EGFR-/BRAF-/ALK- and ROS1-directed therapies, while 218 additional cases (7%) with MET, ERBB2 (HER2) and RET alterations could potentially benefit from experimental targeted compounds. In addition, routine capturing of comutations, e.g. TP53 (55%), KEAP1 (11%) and STK11 (11%), as well as the precise typing of fusion partners and involved exons in case of actionable translocations including ALK and ROS1, are prognostic and predictive tools currently gaining importance for further refinement of therapeutic and surveillance strategies. The reliability, low dropout rates (<5%), minimal tissue requirements, fast turnaround times (6 days on average) and lower costs of the diagnostic approach presented here compared to sequential single-gene testing, highlight its practicability in order to support individualized decisions in routine patient care, enrollment in molecularly stratified clinical trials, as well as translational research.

KEYWORDS:

drug target; gene fusion; lung adenocarcinoma; next-generation sequencing

PMID:
30653256
DOI:
10.1002/ijc.32133

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