Table 2.
Next-generation sequencing results for cfDNA reference material with defined mutations extracted using the ATPS-based process. DNA-free plasma was spiked at 5% variant allele frequency (VAF). Detected variants, total sequencing depth, and measured VAF are reported for extracts obtained using a single ATPS step (ATPS 1) or two consecutive ATPS steps (ATPS 2). Data is reported for a representative experiment.
| Variant | ATPS 1 | ATPS 2 | ||||
|---|---|---|---|---|---|---|
| Gene | cDNA | Protein | Depth | VAF | Depth | VAF |
| AKT1 | c.49G>A | p.E17K | 4702 | 0.070 | 6789 | 0.068 |
| BRAF | c.1799T>A | p.V600E | 3431 | 0.055 | 4851 | 0.059 |
| ERBB2 | c.2313_2324dup | p.Y772_A775dup | 7473 | 0.059 | 10915 | 0.060 |
| KRAS | c.35G>A | p.G12D | 4433 | 0.067 | 6471 | 0.075 |
| KRAS | c.181C>A | p.Q61K | 5151 | 0.086 | 7569 | 0.088 |
| KRAS | c.436G>A | p.A146T | 2964 | 0.054 | 4324 | 0.045 |
| PIK3CA | c.1633G>A | p.E545K | 2885 | 0.063 | 4169 | 0.052 |
| PIK3CA | c.3140A>G | p.H1047R | 4320 | 0.104 | 6488 | 0.102 |