Table 2.
Instrument and selection method used by reporting laboratories
| Sequencing Platform | # of labs (%) | # of labs (%)* that did not detect expected mutation | Selection Method for Targeted Sequencing | # of labs (%) | # of labs (%)* that did not detect expected mutation | |
|---|---|---|---|---|---|---|
| Ion Torrent PGM | 49 (44.1) | 4 (33.3) | Ion AmpliSeq Cancer Hotspot Panel v2 | 40 (36.0) | 2 (16.7) | |
| Illumina MiSeq | 34 (30.6) | 4** (33.3) | Custom Enrichment Approach | 34 (30.6) | 5 (41.7) | |
| Illumina HiSeq 2500 | 11 (9.9) | 2 (16.7) | Illumina TruSight Tumor Sequencing Panel | 12 (10.8) | 2 (16.7) | |
| Ion Torrent Proton | 5 (4.5) | Illumina TruSeq Amplicon Cancer Panel | 9 (8.1) | 2** (16.7) | ||
| Illumina NextSeq 500 | 4 (3.6) | 1 (8.3) | Ion AmpliSeq Comprehensive Cancer Panel | 3 (2.7) | ||
| Illumina MiSeqDx | 4 (3.6) | 1 (8.3) | Ion AmpliSeq Colon and Lung Cancer Research Panel | 3 (2.7) | ||
| Illumina HiSeq 3000/4000 | 3 (2.7) | Ion AmpliSeq Oncomine Comprehensive Assay | 2 (1.8) | |||
| Ion Torrent S5/S5 XL | 1 (0.9) | Ion AmpliSeq Oncomine Focus Assay | 2 (1.8) | |||
| RainDance ThunderBolts Cancer Panel | 2 (1.8) | |||||
| Total | 111 | 12 | Multiplicom Tumor Hotspot MASTR Plus Assay | 1 (0.9) | ||
| QIAGEN Human Tumor Actionable Mutations Panel | 1 (0.9) | |||||
| Not Applicable – exome sequencing | 2 (1.8) | 1 (8.3) | ||||
| Total | 111 | 12 |
*
Percentage is based on the 12 laboratories that did not detect the expected mutation.
**
Includes results from the laboratory that correctly detected the presence of a variant in a gene, but reported it as a different variant from expected (i.e., the laboratory did not report detection of the EGFR p.G719S variant, but instead reported detection of the EGFR p.G719C variant). This laboratory did not have any other false-positive or false-negative results, and this error likely represents a post-analytical (reporting) error.