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The disadvantages of DNA-based NGS are those common to all NGS techniques as well as those specific to the DNA-based NGS. The disadvantages of DNA-based NGS are summarised in the following table.

Table 22: Disadvantages of DNA-based NGS for Testing for NTRK Gene Fusions


  • Cost (high cost per sample compared with other methods; however, targeted sequencing of a subset of genes or transcripts can reduce costs [1]).
  • Long turnaround time of approximately 1 to 3 weeks (complexity and labour intensity of testing has limited the widespread inclusion of NGS testing in laboratories [2, 3]).
  • Potentially lower sensitivity due to difficulty covering long introns that often harbour breakpoints.
  • DNA-based platforms must tile over introns, requiring more probes, more space on the sequencer, and more starting material [4].
  • Lack of confirmation at the RNA transcription or protein expression level (which is important for novel DNA level rearrangements).
  • May not work well if specimen quality, quantity, or tumour purity is poor.
  • Some panels may not detect all NTRK gene fusions [5, 6].
  • Detection of novel NTRK gene structural rearrangements requires further testing for transcription or translation of a fusion protein [2].
  • The amount of data produced places substantial demands on bioinformatics and information technologies at all stages of the protocol [7].


  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. Archer. Why is it better to use RNA instead of DNA for fusion detection?
  5. Kheder ES, Hong DS. Emerging Targeted Therapy for Tumors with NTRK Fusion Proteins. Clin Cancer Res 2018; 24: 5807-5814.
  6. Cocco E, Scaltriti M, Drilon A. NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol 2018; 15: 731-747.
  7. 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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