Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)
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RESEARCH
Open Access
Quality assessment of a clinical nextgeneration sequencing melanoma panel within the Italian Melanoma Intergroup (IMI) Irene Vanni1,2†, Milena Casula3†, Lorenza Pastorino1,2†, Antonella Manca3, Bruna Dalmasso1,2, Virginia Andreotti1,2, Marina Pisano3, Maria Colombino3, Italian Association for Cancer Research (AIRC) Study Group, Ulrich Pfeffer4, Enrica Teresa Tanda5, Carla Rozzo3, Panagiotis Paliogiannis6, Antonio Cossu3, Paola Ghiorzo1,2*, Giuseppe Palmieri3 for the Italian Melanoma Intergroup (IMI)
Abstract Background: Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. Methods: We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. Results: The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. Conclusion: This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results. Keywords: Melanoma, Gene panel testing, Next generation sequencing (NGS), Somatic mutations, Quality controls, BRAF, Target therapy
* Correspondence: [email protected] † Irene Vanni, Milena Casula and Lorenza Pastorino contributed equally to this work. 1 Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132 Genoa, Italy 2 Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permi
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