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Disadvantages

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.

Disadvantages of DNA-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]).
  • 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].

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. Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel). 2020 Jul 27;10(8):521.
  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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