Table 1 Summary of extraction and sequence QC results.
From: Analytical evaluation of circulating tumor DNA sequencing assays
Assay | cfDNA extraction (min/avg/max) | Sequence QC (min/avg/max) | |||||
|---|---|---|---|---|---|---|---|
< 20 ng | 20–50 ng | > 50 ng | Plasma 150 ng | Mapping percentage | Mean sequence depth | On-target rate | |
A | 7.3/10.4/12.0 | 23.3/30.7/40.0 | 52.2/58.4/63.5 | 107.0/108.7/110.0 | 0.990/0.998/0.999 | 7684/13729/31483 | 0.65/0.70/0.73 |
B | 5.0/9.0/15.0 | 29.0/36.4/52.0 | 47.0/53.0/58.0 | 146.0/150.7/159.0 | 0.999/0.999/1 | 1644/6047/10468 | 0.63/0.68/0.71 |
C | 7.9/12.9/20.4 | 34.8/40.9/48.0 | 60.3/65.4/69.3 | 91.2/104.0/120.0 | 0.856/0.887/0.908 | 3256/7555/10551 | 0.64/0.74/0.78 |
D (big) | 6.1/9.2/12.0 | 36.1/56.1/107.0 | 145.0/163.7/187.1 | 32.4/129.9/223.6 | 0.995/0.995/0.995 | 1111/4036/7688 | 0.59/0.65/0.71 |
E (big) | 11.0/12.9/15.4 | 28.1/39.6/47.5 | 39.8/50.1/61.2 | 145.6/160.5/175.8 | 0.999/0.999/0.999 | 1895/2624/3456 | 0.72/0.72/0.73 |
F | 7.2/10.4/19.6 | 32.9/36.8/42.4 | 45.6/52.1/58.0 | 14.7/24.9/30.5 | 0.998/0.999/0.999 | 1515/3417/5022 | 0.51/0.58/0.64 |
G | 7.5/10.4/14.1 | 28.4/35.0/50.6 | 69.1/77.1/90.6 | 124.3/127.4/131.0 | 0.993/0.995/0.997 | 7110/14898/36100 | 0.54/0.77/0.87 |
H | 5.9/5.8/11.8 | 23.8/28.1/34.8 | 41.8/53.5/66.6 | 108.3/121.9/133.8 | 0.998/0.999/0.999 | 2056/4946/7026 | 0.69/0.71/0.72 |
I (big) | 5.4/6.7/7.6 | 17.6/18.9/20.3 | 29.3/32.2/35.0 | 77.3/83.0/90.2 | NA | NA | NA |
Assay | Panel sensitivity | Specificity (# FP; Definition 2) | Expected vs. Observed VAF correlation | ||||
|---|---|---|---|---|---|---|---|
0.1% | 0.2% | 0.5% | 1.0% | 2.5% | 0.0% | < 20 ng/20–50 ng/> 50 ng | |
A | 0.28 | 0.38 | 0.76 | 0.82 | 0.84 | 0 | 0.86/0.81/0.93 |
B | 0.64 | 0.95 | 0.90 | 0.95 | 0.95 | 0 | 0.91/0.96/0.94 |
C | 0.33 | 0.55 | 0.68 | 0.75 | 0.77 | 0 | 0.82/0.88/0.86 |
D (big) | 0.47 | 0.91 | 0.96 | 0.96 | 0.98 | 0 | 0.7/0.91/0.9 |
E (big) | 0.18 | 0.41 | 0.68 | 0.80 | 0.89 | 0 | 0.82/0.81/0.81 |
F | 0.17 | 0.56 | 0.73 | 0.72 | 0.81 | 1 | 0.77/0.82/0.86 |
G | 0.68 | 0.98 | 0.94 | 0.98 | 0.98 | 0 | 0.83/0.88/0.87 |
H | 0.30 | 0.60 | 0.81 | 0.85 | 0.95 | 0 | 0.86/0.91/0.92 |
I (big) | 0.18 | 0.79 | 0.55 | 0.78 | 0.92 | 0 | 0.53/0.87/0.89 |
