Satu Mäki-Nevala, Aija Knuuttila, Sakari Knuutila and Virinder Kaur Sarhadi
Nowaday screening of non-small cell lung cancer (NSCLC) patients for epidermal growth factor receptor (EGFR) activating mutations is carried out in routine diagnostics to select patients who could benefit from EGFR inhibitor therapies. We aimed to compare EGFR mutation testing by Ion Torrent PGM technology, using AmpliSeq Colon and Lung Cancer panel, with real-time PCR in order to evaluate the accuracy of next generation sequencing (NGS) in detecting clinically relevant EGFR mutations in NSCLC. In total, 368 NSCLC patient samples were tested for EGFR by PCR and were also sequenced by Ion Torrent PGM by using AmpliSeq Colon and Lung panel. Samples were formalin-fixed, paraffin-embedded tumor specimens of Finnish NSCLC patients. The mutations studied for comparison were G719X, S768I, T790M, L858R, L861Q, deletions in exon 19 and insertions in exon 20. Comparison of EGFR mutations detectable by both PCR kit and NGS panel, showed a high degree of concordance between the two methods. Out of 368 samples, 31 out of 32 positive by PCR were also positive by NGS, and 336 out of 336 negative by PCR for these mutations were also negative by NGS giving a concordance of 99.7%. Two negative samples by PCR showed insertions in exon 20, which were not detectable by PCR. In one sample NGS failed to detect G719X mutation that had a very weak signal in PCR. Our study shows that the Ion Torrent PGM technology gives highly comparable results with the golden standard PCR. Thus, this NGS methodology is sensitive and reliable while testing clinically and diagnostically significant EGFR mutations in FFPE samples.
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