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Round-Robin Comparison of RET Rearrangement Detection in ctDNA: A Novel Method for Limited Clinical Samples.

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Commercial next-generation sequencing (NGS) assays show variable sensitivity for detecting RET rearrangements in non-small cell lung cancer (NSCLC) plasma. Performance varied across three labs, indicating a need for assay optimization in ctDNA analysis.

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Area of Science:

  • Oncology
  • Molecular Diagnostics
  • Genomics

Background:

  • Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) is standard for advanced non-small cell lung cancer (NSCLC).
  • Assay sensitivity for detecting gene fusions, such as RET rearrangements, can vary significantly.
  • Accurate detection of RET fusions is critical for targeted therapy selection in NSCLC.

Purpose of the Study:

  • To evaluate the performance of three commercial NGS assays in detecting RET rearrangements in plasma ctDNA.
  • To compare the sensitivity and concordance of these assays across different laboratories.
  • To assess the agreement of fusion breakpoint calls between plasma ctDNA and tumor tissue.

Main Methods:

  • A round-robin study using banked plasma from 60 NSCLC patients with known RET fusions from the LIBRETTO-431 trial.
  • Plasma samples were tested using Guardant360, FoundationOne Liquid CDx, and ctDx-First assays.
  • Pairwise comparisons were conducted, and concordance with tumor tissue genotyping was analyzed.

Main Results:

  • Successful sequencing rates were 100%, 92.5%, and 90% for Guardant360, FoundationOne Liquid CDx, and ctDx-First, respectively.
  • RET fusion detection rates in plasma were 60%, 63.9%, and 67.6% across the assays.
  • Concordance of fusion partners between plasma and tissue ranged from 81% to 89%.

Conclusions:

  • ctDNA assays are useful for detecting RET translocations alongside tissue testing.
  • Opportunities exist to further optimize the performance of NGS assays for ctDNA analysis.
  • Standardization and validation are key for reliable clinical application of ctDNA testing.