Table 2.
Sequencing performance metrics
| Total mapped reads (CV) | Average amplicon coverage depth (CV) | Percent of all amplicons ≥ ×500 | Percent of target amplicons ≥ ×500 | |
|---|---|---|---|---|
| Total (n78) | ||||
| Tissue type | ||||
| Lung (n22) | 390,884 (0.89) | 1,545 (0.83) | 61 | 64.3 |
| GIST (n10) | 507,137 (0.35) | 1,861 (0.35) | 81 | 88.8 |
| Melanoma (n18) | 396,993 (0.32) | 1,447 (0.33) | 82.6 | 85.6 |
| CRC (n28) | 441,153 (0.72) | 1,613 (0.73) | 73.7 | 81.7 |
| p value | 0.120 | 0.175 | 0.186 | 0.033a |
| Specimen type | ||||
| Cell block (n6) | 469,270 (1.06) | 2,166 (0.8) | 61.2 | 62.8 |
| Biopsy (n13) | 374,194 (0.79) | 1,371 (0.8) | 59 | 69.2 |
| Resection (n57) | 430,195 (0.59) | 1,569 (0.59) | 77.3 | 81.9 |
| p value | 0.840 | 0.613 | 0.664 | 0.692 |
Sequencing performance metrics (total mapped reads, average amplicon coverage, percentage of all amplicons ≥ 500X, percentage of target amplicons ≥ 500X). Metrics are presented by tissue type and specimen type. Mean values are reported. A significant difference in % target amplicons at 500X between tissue type was identified; however, adjustment for false discovery rate (FDR) using Bonferoni correction deemed this not significant (Kruskal-Wallis p = 0.033; n78). There was however a trend in NSCLC samples having a lower percentage of amplicons at ≥ 500X than the other tissue types
ap value significant at 0.05. For specimen type analysis 2 samples, one fine needle aspirate and one polyp were excluded from statistical analysis due to limited numbers of samples of this type. Coefficient of variation stated for total mapped reads and average amplicon coverage