Table 2.
Extraction and Quantitation Methods and DNA Yields for the Reference Material Samples
| Laboratory | Extraction kit | Elution buffer | Quantitation method | DNA yield per VAF, ng/mL |
|||
|---|---|---|---|---|---|---|---|
| 0% | 0.125% | 0.50% | 2% | ||||
| A | Nucleosnap DNA Plasma Kit | 5 mmol/L Tris, pH 8.5 | Qubit HS kit | 31.33 ± 0.12 | 23.73 ± 1.03 | 30.80 ± 2.96 | 24.07 ± 1.47 |
| B | QIAamp CNA Kit | Kit supplied buffer∗ | Qubit HS kit | 30.96 ± 4.15 | 14.60 ± 6.03 | 27.79 ± 8.21 | 21.17 ± 7.11 |
| C | Maxwell RSC LV ccfDNA Kit (automated) | 10 mmol/L Tris, pH 8.0 | Qubit HS kit | 15.24 ± 2.27 | 12.01 ± 1.72 | 16.25 ± 2.18 | 9.18 ± 5.32 |
| D | QIAsymphony DSP Circulating DNA Kit (automated) | Kit supplied buffer | Qubit HS kit | 18.20 ± 0.47 | 18.27 ± 5.85 | 17.53 ± 4.24 | 15.93 ± 0.28 |
| E | QIAamp CNA Kit | 10 mmol/L Tris, pH8.0 | Qubit HS kit | 17.51± 5.19 | 11.45 ± 1.85 | 16.64 ± 1.66 | 11.75 ± 1.27 |
| F | QIAamp CNA Kit | Kit supplied buffer∗ | Qubit BR kit | 30.71 ± 4.32 | 26.78 ± 1.75 | 30.09 ± 4.21 | 27.31 ± 5.00 |
| G | Zymo Quick-cfDNA Serum and Plasma kit | Water | Qubit HS kit | 4.34 ± 0.44 | 3.16 ±.94 | 4.32 ± 2.75 | 4.05 ± 0.34 |
Data are expressed as means ± SD. Samples were prepared in triplicate for the laboratories with the exception of laboratory G, where four samples were measured.
BR, broad range; ccfDNA, circulating cell-free DNA; cfDNA, cell-free DNA; CNA, circulating nucleic acid; DSP, digital spatial profiling; HS, high sensitivity.
∗
Carrier RNA was added in the lysis step.