TY - JOUR
T1 - Harmonization of Next-Generation Sequencing Procedure in Italian Laboratories
T2 - A Multi-Institutional Evaluation of the SiRe® Panel
AU - Malapelle, Umberto
AU - Pepe, Francesco
AU - Pisapia, Pasquale
AU - Sgariglia, Roberta
AU - Nacchio, Mariantonia
AU - De Luca, Caterina
AU - Lacalamita, Rosanna
AU - Tommasi, Stefania
AU - Pinto, Rosamaria
AU - Palomba, Grazia
AU - Palmieri, Giuseppe
AU - Vacirca, Davide
AU - Barberis, Massimo
AU - Bottillo, Irene
AU - Grammatico, Paola
AU - Grillo, Lucia Rosalba
AU - Costa, Valerio
AU - Smeraglio, Riccardo
AU - Bruzzese, Dario
AU - Troncone, Giancarlo
N1 - Funding Information:
This study was funded by the Department of Public Health, University of Naples Federico II.
Publisher Copyright:
© Copyright © 2020 Malapelle, Pepe, Pisapia, Sgariglia, Nacchio, De Luca, Lacalamita, Tommasi, Pinto, Palomba, Palmieri, Vacirca, Barberis, Bottillo, Grammatico, Grillo, Costa, Smeraglio, Bruzzese and Troncone.
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020/3/11
Y1 - 2020/3/11
N2 - Background: Next-generation sequencing (NGS) needs to be validated and standardized to ensure that cancer patients are reliably selected for target treatments. In Italy, NGS is performed in several institutions and harmonization of wet and dry procedures is needed. To this end, a consortium of five different laboratories, covering the most part of the Italian peninsula, was constituted. A narrow gene panel (SiRe®) covering 568 clinically relevant mutations in six different genes (EGFR, KRAS, NRAS, BRAF, cKIT, and PDGFRα) with a predictive role for therapy selection in non-small cell lung cancer (NSCLC), gastrointestinal stromal tumor, colorectal carcinoma (CRC), and melanoma was evaluated in each participating laboratory. Methods: To assess the NGS inter-laboratory concordance, the SiRe® panel, with a related kit and protocol for library preparation, was used in each center to analyze a common set of 20 NSCLC and CRC routine samples. Concordance rate, in terms of mutation detected and relative allelic frequencies, was assessed. Then, each institution prospectively analyzed an additional set of 40 routine samples (for a total of 160 specimens) to assess the reproducibility of the NGS run parameters in each institution. Results: An inter-laboratory agreement of 100% was reached in analyzing the data obtained from the 20 common sample sets; the concordance rate of allelic frequencies distribution was 0.989. The prospective analysis of the run metric parameters obtained by each center locally showed that the analytical performance of the SiRe® panel in the different institutions was highly reproducible. Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.
AB - Background: Next-generation sequencing (NGS) needs to be validated and standardized to ensure that cancer patients are reliably selected for target treatments. In Italy, NGS is performed in several institutions and harmonization of wet and dry procedures is needed. To this end, a consortium of five different laboratories, covering the most part of the Italian peninsula, was constituted. A narrow gene panel (SiRe®) covering 568 clinically relevant mutations in six different genes (EGFR, KRAS, NRAS, BRAF, cKIT, and PDGFRα) with a predictive role for therapy selection in non-small cell lung cancer (NSCLC), gastrointestinal stromal tumor, colorectal carcinoma (CRC), and melanoma was evaluated in each participating laboratory. Methods: To assess the NGS inter-laboratory concordance, the SiRe® panel, with a related kit and protocol for library preparation, was used in each center to analyze a common set of 20 NSCLC and CRC routine samples. Concordance rate, in terms of mutation detected and relative allelic frequencies, was assessed. Then, each institution prospectively analyzed an additional set of 40 routine samples (for a total of 160 specimens) to assess the reproducibility of the NGS run parameters in each institution. Results: An inter-laboratory agreement of 100% was reached in analyzing the data obtained from the 20 common sample sets; the concordance rate of allelic frequencies distribution was 0.989. The prospective analysis of the run metric parameters obtained by each center locally showed that the analytical performance of the SiRe® panel in the different institutions was highly reproducible. Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.
KW - biomarkers
KW - colon cancer
KW - lung cancer
KW - next-generation sequencing
KW - predictive molecular pathology
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U2 - 10.3389/fonc.2020.00236
DO - 10.3389/fonc.2020.00236
M3 - Article
AN - SCOPUS:85082678222
VL - 10
JO - Frontiers in Oncology
JF - Frontiers in Oncology
SN - 2234-943X
M1 - 236
ER -