Table 1 A comparison of frequently used analysis methods to detect gene fusions with the ASPYRE assay ([22,23,24] and manufacturer’s guidelines)
From: Ultra-sensitive molecular detection of gene fusions from RNA using ASPYRE
NGS | ASPYRE | RT-PCR | IHC | FISH | |
|---|---|---|---|---|---|
Method performance characteristics | Highly variable performance due to need to sequence large intronic regions | < 6 copies/6 µL (Analytical sensitivity) | Extremely high diagnostic sensitivity | Variable performance; subject to interobserver variability | Variable performance; subject to interobserver variability |
Multiplexing | 1000+ | 37 | < 10 | 1 3’ gene | 1 3’ gene |
Prior knowledge of 5’ & 3’ fused genes required | No | Yes | Yes | No | No |
Instrument complexity | High | Low | Low | Moderate | Moderate |
Laboratory workflow complexity | High | Medium | Medium | Medium | High |
Data analysis complexity | High | Low | Low | Medium | Medium |
Time to result | > 7 days | 1–2 days | 1–2 days | 2–3 days | 2–3 days |
Material required | 10–55 ng | 1–10 ng | > 10 ng | 2 slides per stain | 2 slides |
Cost | High | Low | Medium | Low | Medium |