Table 2.
Validated results for EQA samples
| Sample / Case | Testing method | |||||
|---|---|---|---|---|---|---|
| A / 1 | B / 2 | C / 3 | D / 4 | E / 5 | ||
| Expected results (manufacturer’s data using ddPCR) | c.2236_2250del p.(Glu746_Ala750del) (1.3% VAF) |
WT | c.2369C > T p.(Thr790Met) (5.1% VAF) and c.2573 T > G p.(Leu858Arg) (4.7% va) |
c.2236_2250del p.(Glu746_Ala750del) (6.2% VAF) |
c.2369C > T p.(Thr790Met) (0.81% VAF) and c.2573 T > G p.(Leu858Arg) (0.49% VAF) |
|
| Laboratory 1 | Deletion in exon 19 (uncharacterised) | WT |
c.2369C > T p.(Thr790Met) c.2573 T > G; p.(Leu858Arg) |
Deletion in exon 19 (uncharacterised) | c.2573 T > G p.(Leu858Arg) | therascreen® EGFR Plasma RGQ PCR Kit (Qiagen) |
|
c.2236_2250del p.(Glu746_Ala750del) (1.11% VAF) |
WT |
c.2369C > T p.(Thr790Met) (4.46% VAF) c.2573 T > G p.(Leu858Arg) (5.10% VAF) |
c.2236_2250del p.(Glu746_Ala750del) (6.26% VAF) |
c.2369C > T p.(Thr790Met) (0.66% VAF) c.2573 T > G p.(Leu858Arg) (0.33% VAF) |
Oncomine™ Lung cfDNA Assay (Life Technologies) on S5XL System (Life Technologies) | |
|
c.2236_2250del p.(Glu746_Ala750del) (1.17% VAF) |
WT |
c.2369C > T p.(Thr790Met) (4.56% VAF) c.2573 T > G p.(Leu858Arg) (3.72% VAF) |
c.2236_2250del p.(Glu746_Ala750del) (2.62% VAF) |
c.2573 T > G p.(Leu858Arg) (1.35% VAF) | GeneRead™ QIAact Lung UMI Panel (Qiagen) on GeneReader NGS System (Qiagen) | |
| Laboratory 2 | Deletion in exon 19 (uncharacterised) | WT |
c.2369C > T p.(Thr790Met) c.2573 T > G p.(Leu858Arg) |
Deletion in exon 19 (uncharacterised) | c.2573 T > G; p.(Leu858Arg) | Stilla ddPCR Technologies |
| Laboratory 3 | Deletion in exon 19 (uncharacterised) | WT |
c.2369C > T p.(Thr790Met) c.2573 T > G p.(Leu858Arg) |
Deletion in exon 19 (uncharacterised) | c.2369C > T p.(Thr790Met) | cobas® EGFR Mutation Test v2 (Roche) |
| Laboratory 4 | N/A | N/A |
c.2369C > T p.(Thr790Met) c.2573 T > G p.(Leu858Arg) |
N/A | c.2369C > T p.(Thr790Met) | cobas® EGFR Mutation Test v2 (Roche) |
| Deletion in exon 19 (uncharacterised) (2.7% VAF) | WT |
c.2369C > T p.(Thr790Met) (4.5% VAF) c.2573 T > G p.(Leu858Arg) (5.2% VAF) |
Deletion in exon 19 (uncharacterised) (5.6%) |
c.2369C > T p.(Thr790Met) (0.65% VAF) c.2573 T > G p.(Leu858Arg) (0.59% VAF) |
ddPCR (BioRad-assays) | |
| Laboratory5 | N/A | N/A |
c.2369C > T p.(Thr790Met) c.2573 T > G p.(Leu858Arg) |
N/A |
c.2369C > T p.(Thr790Met) |
cobas® EGFR Mutation Test v2 (Roche) |
N/A Not analysed; WT wild type (no mutation detected); ddPCR digital droplet PCR; Ex19del deletion in exon 19 of EGFR; VAF variant allele frequency
Nomenclature according to EGFR gene reference sequence LRG_304t1