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  1. OncologyPRO
  2. Oncology in Practice
  3. Anti-Cancer Agents and Biological Therapy
  4. Targeting NTRK Gene Fusions
  5. Importance of Testing Cancers for NTRK Gene Fusions
  6. General Challenges of Testing for Cancers With NTRK Gene Fusion
  7. Next-Generation Sequencing (NGS)
  8. RNA-based NGS

RNA-based NGS

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Disadvantages

The disadvantages of RNA-based NGS are those common to all NGS techniques as well as those specific to the RNA-based NGS.

The disadvantages of RNA-based NGS are summarised in the following table.

Disadvantages of RNA-based NGS for Testing for NTRK Gene Fusions

Disadvantages

  • Cost (high cost per sample compared with other methods; however, targeted sequencing of a subset of genes or transcripts can reduce costs [1])
  • Turnaround time of approximately 1 to 3 weeks (complexity and labour intensity of testing has limited the widespread inclusion in laboratories [2, 3])
  • Labile nature of RNA: RNA quality in formalin-fixed paraffin-embedded tissue may be too poor for clinical testing, especially in older blocks [4, 5]
  • The amount of data produced places substantial demands on bioinformatics and information technologies at all stages of the protocol [6]

References

  1. Beadling C, Wald AI, Warrick A et al. A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing. J Mol Diagn 2016; 18: 165-175.
  2. Zehir A, Benayed R, Shah RH et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23: 703-713.
  3. Chen Y, Chi P. Basket trial of TRK inhibitors demonstrates efficacy in TRK fusion-positive cancers. J Hematol Oncol 2018; 11: 78.
  4. Choi Y, Won YJ, Lee S et al. Cytoplasmic TrkA Expression as a Screen for Detecting NTRK1 Fusions in Colorectal Cancer. Transl Oncol 2018; 11: 764-770.
  5. Murphy DA, Ely HA, Shoemaker R et al. Detecting Gene Rearrangements in Patient Populations Through a 2-Step Diagnostic Test Comprised of Rapid IHC Enrichment Followed by Sensitive Next-Generation Sequencing. Appl Immunohistochem Mol Morphol 2017; 25: 513-523.
  6. Rizzo JM, Buck MJ. Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prev Res (Phila) 2012; 5: 887-900.

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