Comparison of Next-generation Sequencing and Cobas EGFR Mutation Test V2 in Detecting EGFR Mutations

Background: As the number of genetic mutations that must be tested increases, the Oncomine Dx Target test (ODxTT), which can simultaneously detect multiple cancer-related genes is becoming the main test used in preference to single-molecule testing. In this study, we evaluated the performance of ODxTT and cobas EGFR mutation test v2 (cobas EGFR), one of the single-molecule tests, in detecting EGFR mutations.

Methods: Samples from 211 patients diagnosed with NS-NSCLC were tested simultaneously or sequentially with the cobas EGFR mutation test and ODxTT. We compared the success and detection rates of both tests and evaluated their equivalence by determining the concordance rate and k-coefficient of both tests.

Results: The success rate in detecting EGFR mutations was 95.7% for ODxTT and 100% for cobas EGFR. EGFR mutations were detected in 26.5% of samples with ODxTT and in 28.0% with cobas EGFR. For the 200 samples successfully analyzed with both tests, the concordance rate and k-coefficient were 97.5% and 0.938, respectively. ODxTT failed to detect two exon 19 deletion mutations (p.E746_P753delinsVS and p.E746_P753delinsLS), and cobas EGFR failed to detect three instances of an exon 19 deletion (p.L747_P753delinsS), L861R, and an exon 20 insertion.

Discussion: The success rate of ODxTT is slightly inferior to that of cobas EGFR. ODxTT shared a high concordance rate and k-coefficient with cobas EGFR in detecting EGFR mutations, but discordant results between the two tests were observed in a few cases, mainly due to the difference of detectable EGFR variants.