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

Danielle Cohen1, Liesbeth M Hondelink1, Nienke Solleveld-Westerink1

  • 1Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands.

Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer
|February 5, 2020
PubMed
Summary

For non-small cell lung cancer (NSCLC), a sequential DNA and RNA next-generation sequencing (NGS) approach is efficient for smokers. Never-smokers benefit from a parallel DNA and RNA NGS strategy for detecting gene fusions and exon-skipping events.

Keywords:
DNA sequencingMolecular diagnosticsNSCLCNext-generation sequencingRNA sequencing

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Area of Science:

  • Oncology
  • Molecular Biology
  • Genetics

Background:

  • Locally advanced or metastatic non-small cell lung cancer (NSCLC) patients often undergo molecular screening for mutations and fusions.
  • Current molecular workup involves multiple tests, risking tissue exhaustion due to emerging targeted therapies.

Purpose of the Study:

  • To evaluate the efficiency of targeted RNA next-generation sequencing (NGS) for identifying gene fusions and exon-skipping events in NSCLC.
  • To compare parallel (DNA and RNA NGS) versus sequential (DNA NGS followed by RNA NGS) molecular workup strategies.

Main Methods:

  • Analyzed stage IV NSCLC cases using both parallel and sequential DNA and RNA NGS workflows.
  • Included cytology and microdissected histology samples, primarily core needle biopsies.
  • Compared molecular findings between the two workup approaches.

Main Results:

  • Identifying an oncogenic driver via DNA NGS allows omitting RNA NGS in most cases, reducing RNA NGS necessity to 53%.
  • Tumors from never-smokers showed a higher enrichment of fusions and exon-skipping events (32%) compared to smokers (4%).
  • The parallel approach offered a shorter turnaround time (9 days) for never-smokers compared to the sequential approach (15 days).

Conclusions:

  • A sequential DNA and RNA NGS strategy is most efficient for smoking-associated NSCLC.
  • A parallel DNA and RNA NGS approach is recommended for never-smokers.
  • This optimized molecular workup is feasible for small samples, reduces complexity and cost, and adapts to evolving therapeutic targets.