Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation Sequencing

Abstract

Background: Methods for identifying gene fusion events, such as fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and transcriptome analysis, are either single gene approaches or require bioinformatics expertise not generally available in clinical laboratories. We analytically validated a customized next-generation sequencing (NGS) panel targeting fusion events in 34 genes involving soft-tissue sarcomas.

Methods: Specimens included 87 formalin-fixed paraffin-embedded (FFPE) tissues with known gene fusion status. Isolated total nucleic acid was used to identify fusion events at the RNA level. The potential fusions were targeted by gene-specific primers, followed by primer extension and nested PCR to enrich for fusion candidates with subsequent bioinformatics analysis.

Results: The study generated results using the following quality metrics for fusion detection: (a) ≥100 ng total nucleic acid, (b) RNA average unique start sites per gene-specific primer control ≥10, (c) quantitative PCR assessing input RNA quality had a crossing point <30, (d) total RNA percentage ≥30%, and (e) total sequencing fragments ≥500 000.

Conclusions: The test validation study demonstrated analytical sensitivity of 98.7% and analytical specificity of 90.0%. The NGS-based panel generated highly concordant results compared to alternative testing methods.

Keywords: bone and soft-tissue neoplasms; formalin-fixed paraffin-embedded (FFPE) tissue; gene fusion; neurotrophin receptor tyrosine kinase (NTRK); next-generation sequencing.