Optimizing Mutation and Fusion Detection in NSCLC by Sequential DNA and RNA Sequencing.

Autor:	Cohen D; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands. Electronic address: d.cohen@lumc.nl., Hondelink LM; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Solleveld-Westerink N; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Uljee SM; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Ruano D; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Cleton-Jansen AM; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., von der Thüsen JH; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Ramai SRS; Department of Pulmonology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Postmus PE; Department of Pulmonology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands., Graadt van Roggen JF; Department of Pathology, Alrijne Hospital, Leiderdorp, The Netherlands., Hoppe BPC; Department of Pulmonology, Alrijne Hospital, Leiderdorp, The Netherlands., Clahsen PC; Department of Pathology, Haaglanden Medical Centre (HMC), Den Haag, The Netherlands., Maas KW; Department of Pulmonology, Haaglanden Medical Centre (HMC), Den Haag, The Netherlands., Ahsmann EJM; Department of Pathology, Groene Hart Hospital (GHZ), Gouda, The Netherlands., Ten Heuvel A; Department of Pulmonology, Groene Hart Hospital (GHZ), Gouda, The Netherlands., Smedts F; Department of Pathology, Reinier de Graaf gasthuis (RdGG), Delft, The Netherlands., van Rossem RN; Department of Pulmonology, Reinier de Graaf gasthuis (RdGG), Delft, The Netherlands., van Wezel T; Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands.
Jazyk:	angličtina
Zdroj:	Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer [J Thorac Oncol] 2020 Jun; Vol. 15 (6), pp. 1000-1014. Date of Electronic Publication: 2020 Jan 31.
DOI:	10.1016/j.jtho.2020.01.019
Abstrakt:	Introduction: Frequently, patients with locally advanced or metastatic NSCLC are screened for mutations and fusions. In most laboratories, molecular workup includes a multitude of tests: immunohistochemistry (ALK, ROS1, and programmed death-ligand 1 testing), DNA sequencing, in situ hybridization for fusion, and amplification detection. With the fast-emerging new drugs targeting specific fusions and exon-skipping events, this procedure harbors a growing risk of tissue exhaustion. Methods: In this study, we evaluated the benefit of anchored, multiplexed, polymerase chain reaction-based targeted RNA sequencing (RNA next-generation sequencing [NGS]) in the identification of gene fusions and exon-skipping events in patients, in which no pathogenic driver mutation was found by DNA-based targeted cancer hotspot NGS (DNA NGS). We analyzed a cohort of stage IV NSCLC cases from both in-house and referral hospitals, consisting 38.5% cytology samples and 61.5% microdissected histology samples, mostly core needle biopsies. We compared molecular findings in a parallel workup (DNA NGS and RNA NGS, cohort 1, n = 198) with a sequential workup (DNA NGS followed by RNA NGS in selected cases, cohort 2, n = 192). We hypothesized the sequential workup to be the more efficient procedure. Results: In both cohorts, a maximum of one oncogenic driver mutation was found per case. This is in concordance with large, whole-genome databases and suggests that it is safe to omit RNA NGS when a clear oncogenic driver is identified in DNA NGS. In addition, this reduced the number of necessary RNA NGS to only 53% of all cases. The tumors of never smokers, however, were enriched for fusions and exon-skipping events (32% versus 4% in former and current smokers, p = 0.00), and therefore benefited more often from the shorter median turnaround time of the parallel approach (15 d versus only 9 d in the parallel workup). Conclusions: We conclude that sequentially combining DNA NGS and RNA NGS is the most efficient strategy for mutation and fusion detection in smoking-associated NSCLC, whereas for never smokers we recommend a parallel approach. This approach was shown to be feasible on small tissue samples including for cytology tests, can drastically reduce the complexity and cost of molecular workup, and also provides flexibility in the constantly evolving landscape of actionable targets in NSCLC. (Copyright © 2020 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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