10.3389/fonc.2020.00236.s003
Umberto Malapelle
Umberto
Malapelle
Francesco Pepe
Francesco
Pepe
Pasquale Pisapia
Pasquale
Pisapia
Roberta Sgariglia
Roberta
Sgariglia
Mariantonia Nacchio
Mariantonia
Nacchio
Caterina De Luca
Caterina
De Luca
Rosanna Lacalamita
Rosanna
Lacalamita
Stefania Tommasi
Stefania
Tommasi
Rosamaria Pinto
Rosamaria
Pinto
Grazia Palomba
Grazia
Palomba
Giuseppe Palmieri
Giuseppe
Palmieri
Davide Vacirca
Davide
Vacirca
Massimo Barberis
Massimo
Barberis
Irene Bottillo
Irene
Bottillo
Paola Grammatico
Paola
Grammatico
Lucia Rosalba Grillo
Lucia Rosalba
Grillo
Valerio Costa
Valerio
Costa
Riccardo Smeraglio
Riccardo
Smeraglio
Dario Bruzzese
Dario
Bruzzese
Giancarlo Troncone
Giancarlo
Troncone
Table_2_Harmonization of Next-Generation Sequencing Procedure in Italian Laboratories: A Multi-Institutional Evaluation of the SiRe® Panel.docx
Frontiers
2020
colon cancer
lung cancer
predictive molecular pathology
next-generation sequencing
biomarkers
2020-03-11 04:26:55
Dataset
https://frontiersin.figshare.com/articles/dataset/Table_2_Harmonization_of_Next-Generation_Sequencing_Procedure_in_Italian_Laboratories_A_Multi-Institutional_Evaluation_of_the_SiRe_Panel_docx/11966673
<p>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.</p><p>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.</p><p>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.</p><p>Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.</p>