Identification and Validation of Noncanonical RET Fusions in Non-Small-Cell Lung Cancer through DNA and RNA Sequencing

J Mol Diagn. 2022 Apr;24(4):374-385. doi: 10.1016/j.jmoldx.2021.12.004. Epub 2022 Jan 19.

Abstract

RET fusion has emerged as a targetable driver in non-small-cell lung cancer. A comparative analysis on RET fusions at DNA [DNA sequencing (DNA-seq)] and RNA [RNA sequencing (RNA-seq)] levels was performed in this study. Archived tumor samples from 54 non-small-cell lung cancer patients with DNA-level noncanonical RET fusions were selected for RNA-seq. RNA-seq identified RET fusion transcripts in 41 of 44 samples passing quality control. In the subset of cases harboring RET 3'-end fusions and predicted to produce in-frame proteins (group A; n = 33), RNA-seq identified the same 3'-end fusions in 32 (96.9%). A total of 26 of 32 also had a reciprocal RET 5'-end fusion detected by DNA-seq that was not transcribed. In the subset with DNA-level out-of-frame RET fusions (group B; n = 9), RNA-seq identified in-frame RET fusion transcripts in 8 cases (88.9%). In the subset only identified with a RET 5'-end fusion by DNA-seq (group C; n = 2), RNA-seq detected the corresponding 3'-end fusion in one case. The discordant DNA- and RNA-level fusions observed in group B may be mediated by complex genomic rearrangement events and transcriptional or post-transcriptional processes. In conclusion, DNA-seq demonstrates a high concordance of 96.9% on detecting in-frame RET fusion, but shows a low concordance on detecting out-of-frame RET fusion and RET 5'-end fusion compared with RNA-seq.

MeSH terms

  • Carcinoma, Non-Small-Cell Lung* / genetics
  • Carcinoma, Non-Small-Cell Lung* / pathology
  • DNA, Neoplasm* / genetics
  • Humans
  • Lung Neoplasms* / diagnosis
  • Lung Neoplasms* / genetics
  • Oncogene Proteins, Fusion* / genetics
  • Proto-Oncogene Proteins c-ret* / genetics
  • RNA, Neoplasm / genetics
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA

Substances

  • DNA, Neoplasm
  • Oncogene Proteins, Fusion
  • RNA, Neoplasm
  • Proto-Oncogene Proteins c-ret
  • RET protein, human