To date, clinical detection of NTRK gene fusions has predominantly utilised DNA- or RNA-based NGS [1-3].
Selection of NGS platforms is critical as not all assays are optimised to detect these fusions [4]. DNA- or protein-based methods are not as commonly used as RNA-based NGS sequencing [5]. RNA-based sequencing appears to be the optimal way to approach NTRK fusions because the splicing out of introns simplifies the technical requirements of adequate coverage and because detection of RNA-level fusions provides direct evidence of functional transcription. However, even though it provides many advantages, RNA-based testing is not perfect [6].
AMP is a more recent platform that allows for rapid enrichment for targeted RNA and DNA NGS [6]. AMP can detect gene fusions, point mutations, insertions, deletions and copy number changes from low amounts of RNA and DNA in formalin-fixed paraffin-embedded samples [6].
Notable limitations that restrict widespread use of NGS platforms are the inability of some panels to detect all types of NTRK gene fusions [4, 7], as well as the cost, complexity and labour intensity of testing [8, 9]. However, as technology advances suitable platforms are becoming increasingly available and established for use in detection of NTRK gene fusions [10, 11].
References
- Cocco E, Scaltriti M, Drilon A. NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol 2018; 15: 731-747.
- Albert CM, Davis JL, Federman N et al. TRK Fusion Cancers in Children: A Clinical Review and Recommendations for Screening. J Clin Oncol 2019; 37: 513-524.
- Penault-Llorca F, Rudzinski ER, Sepulveda AR. Testing algorithm for identification of patients with TRK fusion cancer. J Clin Pathol 2019.72(7): 460-467.
- Cocco E, Scaltriti M, Drilon A. NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol 2018; 15: 731-747.
- Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM. Landscape of gene fusions in epithelial cancers: seq and ye shall find. Genome Med 2015; 7: 129.
- Solomon JP, Linkov I, Rosado A et al.NTRK fusion detection across multiple assays and 33,997 cases: diagnostic implications and pitfalls. Mod Pathol. 2020; 33(1):38-46.
- Zheng Z, Liebers M, Zhelyazkova B et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat Med 2014; 20: 1479-1484.
- Kheder ES, Hong DS. Emerging Targeted Therapy for Tumors with NTRK Fusion Proteins. Clin Cancer Res 2018; 24: 5807-5814.
- 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.
- Chen Y, Chi P. Basket trial of TRK inhibitors demonstrates efficacy in TRK fusion-positive cancers. J Hematol Oncol 2018; 11: 78.
Pfarr N, Kirchner M, Lehmann U, et al. Testing NTRK testing: Wet-lab and in silico comparison of RNA-based targeted sequencing assays. Genes Chromosomes Cancer. 2020 Mar;59(3):178-188.
Kirchner M, Glade J, Lehmann U, et al. NTRK testing: First results of the QuiP-EQA scheme and a comprehensive map of NTRK fusion variants and their diagnostic coverage by targeted RNA-based NGS assays. Genes Chromosomes Cancer. 2020; 59(8):445-453.