Skip to main content

Table 1 Average genotyping score, assigned score criteria and error rates for every case analysed by the pilot scheme participants

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

Sample A B C D E F G H I J A-J
Variant status 5% KRAS c.35G>C; p.(G12A) 1% KRAS c.35G>C; p.(G12A) 5% NRAS c.182A>G; p.(Q61R) 1% NRAS c.182A>G; p.(Q61R) KRAS/NRAS Wild-type 5% EGFR c.2235_2249del15; p.E746_A750del 1% EGFR c.2235_2249del15; p.E746_A750del 5% EGFR c.2573T>G; p.(L858R) and c.2369C>T; p.(T790M) 1% EGFR c.2573T>G; p.(L858R) and c.2369C>T; p.(T790M) EGFR Wild-type Overall
Average score per sample on 2 points 1.5 1.3 1.7 1.5 2.0 1.7 1.7 1.9 1.6 1.9 1.7
Score criteria # obtained scores (%)
 Correct (2 points) 11 (35.5%) 7 (22.6%) 12 (38.7%) 8 (25.8%) 23 (74.2%) 5 (16.1%) 4 (12.9%) 29 (93.5%) 18 (58.1%) 30 (96.8%) 147 (47.4%)
 Correct but unspecified (2 points) 5 (16.1%) 3 (9.7%) 4 (12.9%) 2 (6.5%) 0 (0.0%) 16 (51.6%) 16 (51.6%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 46 (14.8%)
 False-negative ≤ LOD (2 points)a 0 (0.0%) 5 (16.1%) 0 (0.0%) 4 (12.9%) 0 (0.0%) 0 (0.0%) 2 (6.5%) 0 (0.0%) 6 (19.4%) 0 (0.0%) 17 (5.5%)
 False-negative but variant not tested for (2 points)a 0 (0.0%) 0 (0.0%) 3 (9.7%) 3 (9.7%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 6 (1.9%)
 False-negative >/unknown LOD (0 points)a 1 (3.2%) 5 (16.1%) 3 (9.7%) 4 (12.9%) 0 (0.0%) 0 (0.0%) 1 (3.2%) 0 (0.0%) 3 (9.7%) 0 (0.0%) 17 (5.5%)
 False-positive (0 points)a 2 (6.5%) 2 (6.5%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (3.2%) 0 (0.0%) 0 (0.0%) 1 (3.2%) 6 (1.9%)
 Incorrect mutation detected with therapeutic implications (0 points)a 0 (0.0%) 0 (0.0%) 1 (3.2%) 1 (3.2%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 2 (0.6%)
 Incorrect mutation detected without therapeutic implications (2 points) 3 (9.7%) 1 (3.2%) 0 (0.0%) 1 (3.2%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 5 (1.6%)
 One variant missed in double mutation sample (0 points)a N/A N/A N/A N/A N/A N/A N/A 2 (6.5%) 4 (12.9%) N/A 6 (1.9%)
 Mutation described incorrectly (1 point) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 10 (32.3%) 6 (19.4%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 16 (5.2%)
 Technical failure (not scored) 1 (3.2%) 0 (0.0%) 0 (0.0%)° 0 (0.0%)° 0 (0.0%) 0 (0.0%) 1 (3.2%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 2 (0.6%)
 Not tested (not scored) 8 (25.8%) 8 (25.8%) 8 (25.8%) 8 (25.8%) 8 (25.8%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 40 (12.9%)
 Total scored (n = 31) 22 (71.0%) 23 (74.2%) 23 (74.2%) 23 (74.2%) 23 (74.2%) 31 (100.0%) 30 (96.8%) 31 (100.0%) 31 (100.0%) 31 (100.0%) 268 (86.5%)
Error rate # obtained scores (%)
 Total with implication on therapy decisiona 3 (13.6%) 12 (52.2%) 7 (30.4%) 12 (52.2%) 0 (0.0%) 0 (0.0%) 4 (13.3%) 2 (6.5%) 13 (41.9%) 1 (3.2%) 54 (20.1%)
Gene not tested/No method info given 0 0 3 3 0 0 0 0 0 0 6
NGS 2 7 3 7 0 0 1 1 7 1 29
Commercial Kit 0 3 1 1 0 0 0 0 1 0 6
LDT 1 1 0 0 0 0 1 0 1 0 4
BEAMing 0 0 0 0 0 0 0 0 0 0 0
ddPCR 0 1 0 1 0 0 2 1 4 0 9
  1. N/A Not applicable
  2. aValues were used to calculate the error rates. °One partial technical failure for NRAS, only correct KRAS WT status was assessed on these cases. 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. Methods are ranked from least to more sensitive techniques as reported in literature: NGS 1–3%, commercial kit 0.1%, BEAMing 0.01%, ddPCR 0.001% [28]. For the LDT, a LOD of 0.1% was reported by the laboratory. Abbreviations: BEAMing Beads, emulsification, amplification, and magnetics, ddPCR Droplet digital polymerase chain reaction, LDT Laboratory-developed test, NGS Next-generation sequencing