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Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens

Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens

Authors :
Malapelle, Umberto
Mayo de Las Casas, Clara
Molina Vila, Miguel A
Rosell, Rafael
Savic, Spasenija
Bihl, Michel
Bubendorf, Lukas
Salto Tellez, Manuel
de Biase, Dario
Tallini, Giovanni
Hwang, David H
Sholl, Lynette M
Luthra, Rajyalakshmi
Weynand, Birgit
Vander Borght, Sara
Missiaglia, Edoardo
Bongiovanni, Massimo
Stieber, Daniel
Vielh, Philippe
Schmitt, Fernando
Rappa, Alessandra
Barberis, Massimo
Pepe, Francesco
Pisapia, Pasquale
Serra, Nicola
Vigliar, Elena
Bellevicine, Claudio
Fassan, Matteo
Rugge, Massimo
de Andrea, Carlos E
Lozano, Maria D
Basolo, Fulvio
Fontanini, Gabriella
Nikiforov, Yuri E
Kamel Reid, Suzanne
da Cunha Santos, Gilda
Nikiforova, Marina N
Roy Chowdhuri, Sinchita
Troncone, Giancarlo
Malapelle, Umberto
Mayo de Las Casas, Clara
Molina Vila, Miguel A.
Rosell, Rafael
Savic, Spasenija
Bihl, Michel
Bubendorf, Luka
Salto Tellez, Manuel
DE BIASE, Dario
Tallini, Giovanni
Hwang, David H.
Sholl, Lynette M.
Luthra, Rajyalakshmi
Weynand, Birgit
Vander Borght, Sara
Missiaglia, Edoardo
Bongiovanni, Massimo
Stieber, Daniel
Vielh, Philippe
Schmitt, Fernando
Rappa, Alessandra
Barberis, Massimo
Pepe, Francesco
Pisapia, Pasquale
Serra, Nicola
Vigliar, Elena
Bellevicine, Claudio
Fassan, Matteo
Rugge, Massimo
de Andrea, Carlos E.
Lozano, Maria D.
Basolo, Fulvio
Fontanini, Gabriella
Nikiforov, Yuri E.
Kamel Reid, Suzanne
da Cunha Santos, Gilda
Nikiforova, Marina N.
Roy Chowdhuri, Sinchita
Troncone, Giancarlo
Malapelle, U
Mayo-de-Las-Casas, C
Molina-Vila, Ma
Rosell, R
Savic, S
Bihl, M
Bubendorf, L
Salto-Tellez, M
de Biase, D
Tallini, G
Hwang, Dh
Sholl, Lm
Luthra, R
Weynand, B
Vander Borght, S
Missiaglia, E
Bongiovanni, M
Stieber, D
Vielh, P
Schmitt, F
Rappa, A
Barberis, M
Pepe, F
Pisapia, P
Serra, N
Vigliar, E
Bellevicine, C
Fassan, M
Rugge, M
de Andrea, Ce
Lozano, Md
Basolo, F
Fontanini, G
Nikiforov, Ye
Kamel-Reid, S
da Cunha Santos, G
Nikiforova, Mn
Roy-Chowdhuri, S
Troncone, G
Publication Year :
2017

Abstract

Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences.Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology.All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification.Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.pmid.dedup....809b1350f923652b496d5a51fdd4e3c6