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Table 2 Overview of error rates per case for different methods for cfDNA extraction and variant analysis during validation

From: International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA

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%)
  1. /, Sample not tested because gene not included in validated methodology. °Reference laboratory n°3 did not test NRAS status. Reference sequence at time of scoring: EGFR: NM_005228.4 or LRG_304t1; KRAS: NM_033360.3 or NM_004985.4; NRAS: NM_002524.4 or LRG_92t1