Supplementary Material for: EGFR T790M Mutation in TKI-Naïve Clinical Samples: Frequency, Tissue Mosaicism, Predictive Value and Awareness on Artifacts

E.D., Lavdovskaia; A.G., Iyevleva; A.P., Sokolenko; N.V., Mitiushkina; E.V., Preobrazhenskaya; V.I., Tiurin; A.O., Ivantsov; I.V., Bizin; L.V., Stelmakh; F.V., Moiseyenko; N.A., Karaseva; S.V., Orlov; V.M., Moiseyenko; M.A., Korzhenevskaya; I.A., Zaitsev; A.R., Kozak; I.V., Chistyakov; A.L., Akopov; N.M., Volkov; A.V., Togo; E.N., Imyanitov

doi:10.6084/m9.figshare.7007450.v1

ORT491441_sm_suppl.mat.pdf (1.63 MB)

Supplementary Material for: EGFR T790M Mutation in TKI-Naïve Clinical Samples: Frequency, Tissue Mosaicism, Predictive Value and Awareness on Artifacts

journal contribution

posted on 2018-08-24, 09:16 authored by Lavdovskaia E.D., Iyevleva A.G., Sokolenko A.P., Mitiushkina N.V., Preobrazhenskaya E.V., Tiurin V.I., Ivantsov A.O., Bizin I.V., Stelmakh L.V., Moiseyenko F.V., Karaseva N.A., Orlov S.V., Moiseyenko V.M., Korzhenevskaya M.A., Zaitsev I.A., Kozak A.R., Chistyakov I.V., Akopov A.L., Volkov N.M., Togo A.V., Imyanitov E.N.

Background: This study evaluated the distribution of epidermal growth factor receptor (EGFR) T790M mutations in treatment-naïve tumor and normal samples obtained from cancer patients. Methods: We utilized allele-specific PCR (AS-PCR), digital droplet PCR (ddPCR) and next generation sequencing (NGS) to detect EGFR T790M allele in several collections of tumor and normal human tissues. Results: AS-PCR analysis of treatment-naïve tumor samples revealed somatic T790M mutation in 3/394 (1%) non-small cell lung carcinomas (NSCLC) carrying the tyrosine kinase inhibitor (TKI)-sensitizing EGFR mutation, but in none of 334 NSCLC lacking EGFR exon 19 deletions (ex19del) or L858R substitutions and in none of 235 non-lung tumors. Use of highly sensitive and quantitative assays, such as ddPCR and NGS, produced a high number of T790M-specific signals even in presumably T790M-negative DNA specimens. This background noise was evidently higher in degraded DNA isolated from formalin-fixed paraffin-embedded tissues as compared to high molecular weight DNA. A combination of AS-PCR, ddPCR and NGS revealed mosaic EGFR T790M allele in 2/68 (3%) NSCLC treated with the first-generation TKI. Both these tumors produced evident and durable response to gefitinib. Conclusion: Detection of mosaic EGFR T790M mutation in treatment-naïve samples may be compromised by yet unresolved technical issues and may have limited clinical value.