Table 2 Overview of error rates per case for different methods for cfDNA extraction and variant analysis during validation
cfDNA extraction method | Cobas cfDNA sample preparation kit (Roche) | QIAamp Circulating Nucleic Acid Kit (Qiagen) | |||||
|---|---|---|---|---|---|---|---|
Variant analysis method | Cobas® EGFR Mutation Test v2 (Roche) | Capture SureSelect (Agilent), MiSeq (Illumina) | QX200 Droplet Digital PCR System (Bio-rad) | Ampliseq 50 gene hotspot panel, Ion Proton (LifeTechnologies) | Therascreen® EGFR Plasma RGQ PCR Kit (Qiagen) | OncoBEAM® RAS CRC IVD KIT (Sysmex-Inostics) | |
Reference laboratory code | 1, 2 | 2 | 3°, 4 | 4 | 5 | 5 | 1–5 |
Sample | # errors/# genotypes analyzed (error rate in %) | ||||||
A | / | 1/1 (100.0%) | 0/2 (0.0%) | 0/1 (0.0%) | / | 0/1 (0.0%) | 1/5 (20.0%) |
B | / | 1/1 (100.0%) | 0/2 (0.0%) | 1/1 (100.0%) | / | 0/1 (0.0%) | 2/5 (40.0%) |
C | / | 1/1 (100.0%) | 0/1 (0.0%) | 0/1 (0.0%) | / | 0/1 (0.0%) | 1/4 (25.0%) |
D | / | 1/1 (100.0%) | 1/1 (100.0%) | 1/1 (100.0%) | / | 0/1 (0.0%) | 3/4 (75.0%) |
E | / | 0/1 (0.0%) | 0/2 (0.0%) | 0/1 (0.0%) | / | 0/1 (0.0%) | 0/5 (0.0%) |
F | 0/2 (0.0%) | 1/1 (100.0%) | 0/2 (0.0%) | 0/1 (0.0%) | 0/1 (0.0%) | / | 1/7 (14.3%) |
G | 0/2 (0.0%) | 1/1 (100.0%) | 0/2 (0.0%) | 0/1 (0.0%) | 0/1 (0.0%) | / | 1/7 (14.3%) |
H | 0/2 (0.0%) | 1/1 (100.0%) | 0/2 (0.0%) | 1/1 (100.0%) | 0/1 (0.0%) | / | 2/7 (28.6%) |
I | 1/2 (50.0%) | 1/1 (100.0%) | 1/2 (50.0%) | 1/1 (100.0%) | 0/1 (0.0%) | / | 4/7 (57.1%) |
J | 0/2 (0.0%) | 0/1 (0.0%) | 0/2 (0.0%) | 0/1 (0.0%) | 0/1 (0.0%) | / | 0/7 (0.0%) |
A-J | 1/10 (10.0%) | 8/10 (80.0%) | 2/18 (11.1%) | 4/10 (40.0%) | 0/5 (0.0%) | 0/5 (0.0%) | 15/58 (25.9%) |