Ann Lab Med.  2019 Sep;39(5):478-487. 10.3343/alm.2019.39.5.478.

Comparison of cobas EGFR Mutation Test v2 and PANAMutyper-R-EGFR for Detection and Semi-Quantification of Epidermal Growth Factor Receptor Mutations in Plasma and Pleural Effusion Supernatant

• Han AL
• Kim HR
• Choi KH
• Hwang KE
• Zhu M
• Huang Y
• Wu M
• Lee YJ
• Park MC
• Cho JH
• Park DS

• KMID: 2450971
• DOI: http://doi.org/10.3343/alm.2019.39.5.478

Abstract

BACKGROUND
Plasma epidermal growth factor receptor (EGFR) mutation tests are less invasive than tissue EGFR mutation tests. We determined which of two kits is more efficient: cobas EGFR Mutation test v2 (cobasv2; Roche Molecular Systems, Pleasanton, CA, USA) or PANAMutyper-R-EGFR (Mutyper; Panagene, Daejeon, Korea). We also evaluated whether pleural effusion supernatant (PE-SUP) samples are assayable, similar to plasma samples, using these two kits.
METHODS
We analyzed 156 plasma and PE-SUP samples (31 paired samples) from 116 individuals. We compared the kits in terms of accuracy, assessed genotype concordance (weighted κ with 95% confidence intervals), and calculated Spearman's rho between semi-quantitatively measured EGFR-mutant levels (SQIs) measured by each kit. We also compared sensitivity using 47 EGFR-mutant harboring samples divided into more-dilute and less-dilute samples (dilution ratio: ≥ or <1:1,000).
RESULTS
cobasv2 tended to have higher accuracy than Mutyper (73% vs 69%, P=0.53), and PE-SUP samples had significantly higher accuracy than plasma samples (97% vs 55-71%) for both kits. Genotype concordance was 98% (κ=0.92, 0.88-0.96). SQIs showed strong positive correlations (P<0.0001). In less-dilute samples, accuracy and sensitivity did not differ significantly between kits. In more-dilute samples, cobasv2 tended to have higher sensitivity than Mutyper (43% vs 20%, P=0.07).
CONCLUSIONS
The kits have similar performance in terms of EGFR mutation detection and semi-quantification in plasma and PE-SUP samples. cobasv2 tends to outperform Mutyper in detecting less-abundant EGFR-mutants. PE-SUP samples are assayable using either kit.

Keyword

Epidermal growth factor receptor; Mutation; Plasma; Pleural effusion supernatant; cobas EGFR Mutation test v2; PANAMutyper-R-EGFR

MeSH Terms

Epidermal Growth Factor*
Genotype
Plasma*
Pleural Effusion*
Receptor, Epidermal Growth Factor*
Epidermal Growth Factor
Receptor, Epidermal Growth Factor

Figure

• 

  Fig. 1 Mutation detection and semi-quantification using two plasma EGFR mutation assay kits with 47 serially diluted contrived samples. The numbers in the green-, yellow-, and blue-tinged boxes indicate the SQIs of the mutation-detected samples and the color tone indicates the SQI rank (light tones indicate lower SQIs and dark tones indicate higher SQIs). The en dash (–) in each white-colored box (except for the en dash indicating EGFR-mutant genotype) indicates that at least one of the EGFR mutations was detected in the corresponding sample using the corresponding plasma assay kits. NM (no mutation detected by cobasv2 analysis) or W (wild type by Mutyper analysis) written in blue in each white box indicates that no EGFR mutations were detected in the corresponding samples. The red-bordered boxes indicate the predicted limit of detection values of the two kits for the three major EGFR-mutant genotypes. The same upper-case or lower-case superscript letter in each dilution series box indicates the same batch analysis. The asterisk in each box indicates that the same mutant was observed following replicate analysis using the remaining aliquots of the extracted DNA samples. The correlation coefficients (ρ) between the dilution effect and SQI rank and P written in black were obtained using Spearman's rank correlation analysis. P or not significant (NS; P>0.05) written in white was obtained using Steiger's Z-test (St-Z), which served to calculate the difference between the two correlation coefficients (cobasv2-ρ vs Mutyper-ρ).Abbreviations: EGFR, epidermal growth factor receptor; E19del, an in-frame deletion in exon 19; L858R, p.Leu858Arg mutation; T790M, p.Thr790Met mutation; cobasv2, cobas EGFR Mutation test v2; Mutyper, PANAMutyper-R-EGFR; SQI, semi-quantitative index; St-Z, Steiger's Z-test; NS, not significant.

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