1. TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: An international performance evaluation study
- Author
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Giancarlo Troncone, Carlos E. de Andrea, Francesco Pepe, Giovanni Tallini, Maria D. Lozano, Paul Hofman, Verena Tischler, Natalie Pelusi, Roberta Sgariglia, Sabine Merkelbach-Bruse, Pasquale Pisapia, Sara Vander Borght, Janna Siemanowski, Daniela Cabibi, Marta Castiglia, Javier Freire, Dario de Biase, Spasenija Savic, Gabriella Fontanini, Antonio Russo, Reinhard Büttner, Lukas Bubendorf, Birgit Weynand, Catherine I. Dumur, Marius Ilie, Umberto Malapelle, Tom Xu, Roberto Pappesch, Michel Bilh, Valerio Gristina, Gianluca Roma, Massimo Barberis, Mariantonia Nacchio, Malapelle U., Pepe F., Pisapia P., Sgariglia R., Nacchio M., Barberis M., Bilh M., Bubendorf L., Buttner R., Cabibi D., Castiglia M., De Andrea C.E., De Biase D., Dumur C.I., Fontanini G., Freire J., Gristina V., Hofman P., Ilie M., Lozano M.D., Merkelbach-Bruse S., Pappesch R., Pelusi N., Roma G., Russo A., Savic S., Siemanowski J., Tallini G., Tischler V., Vander Borght S., Weynand B., Xu T., Troncone G., Malapelle, Umberto, Pepe, Francesco, Pisapia, Pasquale, Sgariglia, Roberta, Nacchio, Mariantonia, Barberis, Massimo, Bilh, Michel, Bubendorf, Luka, Büttner, Reinhard, Cabibi, Daniela, Castiglia, Marta, De Andrea, Carlos E, de Biase, Dario, Dumur, Catherine I, Fontanini, Gabriella, Freire, Javier, Gristina, Valerio, Hofman, Paul, Ilie, Mariu, Lozano, Maria Dolore, Merkelbach-Bruse, Sabine, Pappesch, Roberto, Pelusi, Natalie, Roma, Gianluca, Russo, Antonio, Savic, Spasenija, Siemanowski, Janna, Tallini, Giovanni, Tischler, Verena, Vander Borght, Sara, Weynand, Birgit, Xu, Tom, and Troncone, Giancarlo
- Subjects
0301 basic medicine ,Library ,Computer science ,Genomics ,Computational biology ,lung neoplasms ,DNA sequencing ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Humans ,molecular biology ,molecular ,biomarkers ,pathology ,tumour ,Gene Library ,Paraffin Embedding ,Sire ,Clinical performance ,High-Throughput Nucleotide Sequencing ,General Medicine ,DNA extraction ,Paraffin embedded ,lung neoplasm ,030104 developmental biology ,Workflow ,030220 oncology & carcinogenesis ,Mutation ,biomarker - Abstract
AimNext generation sequencing (NGS) represents a key diagnostic tool to identify clinically relevant gene alterations for treatment-decision making in cancer care. However, the complex manual workflow required for NGS has limited its implementation in routine clinical practice. In this worldwide study, we validated the clinical performance of the TargetPlex FFPE-Direct DNA Library Preparation Kit for NGS analysis. Impressively, this new assay obviates the need for separate, labour intensive and time-consuming pre-analytical steps of DNA extraction, purification and isolation from formalin-fixed paraffin embedded (FFPE) specimens in the NGS workflow.MethodsThe TargetPlex FFPE-Direct DNA Library Preparation Kit, which enables NGS analysis directly from FFPE, was specifically developed for this study by TargetPlex Genomics Pleasanton, California. Eleven institutions agreed to take part in the study coordinated by the Molecular Cytopathology Meeting Group (University of Naples Federico II, Naples, Italy). All participating institutions received a specific Library Preparation Kit to test eight FFPE samples previously assessed with standard protocols. The analytical parameters and mutations detected in each sample were then compared with those previously obtained with standard protocols.ResultsOverall, 92.8% of the samples were successfully analysed with the TargetPlex FFPE-Direct DNA Library Preparation Kit on Thermo Fisher Scientific and Illumina platforms. Altogether, in comparison with the standard workflow, the TargetPlex FFPE-Direct DNA Library Preparation Kit was able to detect 90.5% of the variants.ConclusionThe TargetPlex FFPE-Direct DNA Library Preparation Kit combined with the SiRe panel constitutes a convenient, practical and robust cost-saving solution for FFPE NGS analysis in routine practice.
- Published
- 2021