RT-PCR

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Overview

RT-PCR detects NTRK gene fusions expressed at the RNA level [1]. RT-PCR detects a single fusion if the involved exons of both genes are known. However, multiple transcripts can be covered with a type of RT-PCR known as nested RT-PCR.

Recently the Idylla GeneFusion Assay has become available, an RT-PCR-based method that is highly sensitive in detecting most relevant gene fusions, reportedly 25/34 NTRK fusions in different tumour types. It combines RT-PCR detection with Expression Imbalance Analysis, meaning detection of fusion events without knowledge of the fusion partners by analysing expression ratios between the 5’ and 3’ ends of the gene [2, 3, 4].

References

1. Argani P, Fritsch M, Kadkol SS et al. Detection of the ETV6-NTRK3 chimeric RNA of infantile fibrosarcoma/cellular congenital mesoblastic nephroma in paraffin-embedded tissue: application to challenging pediatric renal stromal tumors. Mod Pathol 2000; 13: 29-36.
2. Ukkola I, Nummela P, Kero M, Tammio H, Tuominen J, Kairisto V, Kallajoki M, Haglund C, Peltomäki P, Kytölä S, Ristimäki A. Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers. Virchows Arch. 2022; PMID: 35237889.
3. Sorber L, Van Dorst B, Bellon E, at al. NTRK Gene Fusion Detection in a Pan-Cancer Setting Using the Idylla GeneFusion Assay. J Mol Diagn. 2022 May 10:S1525-1578(22)00117-9. doi: 10.1016/j.jmoldx.2022.03.014. Epub ahead of print. PMID: 35550184.
4. Ukkola I, Nummela P, Kero M, Tammio H, Tuominen J, Kairisto V, Kallajoki M, Haglund C, Peltomäki P, Kytölä S, Ristimäki A. Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers. Virchows Arch. 2022 Apr;480(4):807-817.