Table 2.
List of all assessed variants and the results obtained from ddPCR analysis of tumour cell DNA (one sample/patient) and cfDNA in plasma from each patient. Each patient had at least one plasma sample and two variants were analysed for each sample and shown in separate rows. If multiple plasma samples were available from a patient, the results are shown as additional rows
| ID | Variant | Tumour cell DNA | False positive rate | Plasma cfDNA | Total cfDNA | ||||
|---|---|---|---|---|---|---|---|---|---|
| Mutant VAF (%) | VAF (%) | Mutant VAF (%) |
Mutant Copies/mL |
WT Copies/mL |
Variant result | Sample result | Copies/mL | ||
| PP-1 | KMT2D c.15517G > T | 7 | 0 | 0 | 0 | 4177 | Negative | Negative | 9329 |
| KMT2D c.6562delG | 5 | 0.05 | 0 | 0 | 5152 | Negative | |||
| KMT2D c.15517G > T | 0 | 0 | 1396 | Negative | Negative | 3105 | |||
| KMT2D c.6562delG | 0 | 0 | 1709 | Negative | |||||
| PP-2 | KDM6A c.1663C > T | 5 | 0 | 0 | 0 | 483 | Negative | Negative | 1422 |
| TERT C228T | 4 | 0.07 | 0.04 | 0 | 939 | Negative | |||
| KDM6A c.1663C > T | 0 | 0 | 777 | Negative | Negative | 2262 | |||
| TERT C228T | 0 | 0 | 1485 | Negative | |||||
| PP-3 | KDM6A c.3373dupA | 20 | 0.03 | 0 | 0 | 753 | Negative | Negative | 3502 |
| FGFR3 c.1118A > G | 17 | 0 | 0 | 0 | 2749 | Negative | |||
| PP-5 | HRAS c.351G > C | 9 | 0 | 0 | 0 | 2105 | Negative | Negative | 4557 |
| TERT C228T | 6 | 0 | 0 | 0 | 2452 | Negative | |||
| PP-6 | TP53 c.326 T > C | 19 | 0 | 4 | 217 | 5767 | Positive | Positive | 12477 |
| PIK3CA c.1633G > C | 7 | 0 | 1 | 83 | 6410 | Positive | |||
| PP-4 | KMT2C c.4432C > T | 22 | 0.02 | 0.03 | 1 | 2079 | Negative | Positive | 4744 |
| TERT C228T | 20 | 0.02 | 24 | 645 | 2020 | Positive | |||
| PP-8 | TSC1 c.2507C > G | 24 | 0 | 1 | 14 | 1037 | Positive | Positive | 2052 |
| TERT C228T | 21 | 0.02 | 1 | 9 | 993 | Positive | |||
| PP-7 | KDM6A c.3293delT | 27 | 0 | 0 | 0 | 630 | Negative | Negative | 1740 |
| TERT C228T | 14 | 0.05 | 0 | 0 | 1110 | Negative | |||
| KDM6A c.3293delT | 0 | 0 | 947 | Negative | Negative | 2418 | |||
| TERT C228T | 0 | 0 | 1471 | Negative | |||||
| KDM6A c.3293delT | 0.4 | 3 | 822 | Positive | Positive | 2103 | |||
| TERT C228T | 0.3 | 4 | 1274 | Positive | |||||
| PP-9 | ELF3 c.740G > A | 19 | 0.02 | 0 | 0 | 3931 | Negative | Positive | 7943 |
| KMT2D c.11024delG | 12 | 0.05 | 0.2 | 8 | 4004 | Positive | |||
VAF variant allele frequency; wt wild type