Table 1.
Common commercial targeted and comprehensive sequencing panels for solid tumors.
| Platform/panel parameters | Ion AmpliSeqTM Cancer Hotspot Panel v2 | Ion AmpliSeqTM Comprehensive Cancer Panel | TruSeq Amplicon Cancer Panel | TruSightTM Tumor Sequencing Panel |
|---|---|---|---|---|
| NGS platform, Manufacturer | Ion Torrent, Life Technologies | Ion Proton, Life Technologies | MiSeq or NextSeq, Illumina | MiSeq or NextSeq, Illumina |
| Sample type | FFPE, cytology | FFPE, cytology | FFPE, cytology * | FFPE, cytology |
| DNA input | 10 ng | 40 ng | 250 ng | 30–300 ng |
| Genes in the panel | 50 | 409 | 48 | 26 |
| Library preparation | Multiplexed PCR | Multiplexed PCR | Multiplexed probe-based capture | Multiplexed probe-based capture |
| Amplicon size | 111–187 bp | 125–175 bp | 170–190 bp | 165–195 bp |
| Number of amplicons | 207 | ~16,000 | 212 | 174 |
| Sequencing technique | Semiconductor sequencing | Semiconductor sequencing | Fluorescence based sequencing-by-synthesis | Fluorescence based sequencing-by-synthesis |
| Sequencing quality cutoff | AQ 20 | AQ 20 | Q30 | Q30 |
* only specimens with high cellularity meeting minimum DNA threshold.