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Table 2 Validated results for EQA samples

From: Results of a worldwide external quality assessment of cfDNA testing in lung Cancer

 

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)

Oncomineâ„¢ 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)

GeneReadâ„¢ 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)

  1. 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
  2. Nomenclature according to EGFR gene reference sequence LRG_304t1
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BMC Cancer

ISSN: 1471-2407

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