Malapelle, Umberto, Pepe, Francesco, Pisapia, Pasquale, Sgariglia, Roberta, Nacchio, Mariantonia, Barberis, Massimo, Bilh, Michel, Bubendorf, Lukas, Buettner, Reinhard, Cabibi, Daniela, Castiglia, Marta, De Andrea, Carlos E., de Biase, Dario ORCID: 0000-0002-0609-8817, Dumur, Catherine, I, Fontanini, Gabriella, Freire, Javier, Gristina, Valerio, Hofman, Paul, Ilie, Marius, Lozano, Maria Dolores, Merkelbach-Bruse, Sabine, Pappesch, Roberto, Pelusi, Natalie, Roma, Gianluca, Russo, Antonio, Savic, Spasenija, Siemanowski, Janna, Tallini, Giovanni ORCID: 0000-0003-0113-6682, Tischler, Verena, Vander Borght, Sara, Weynand, Birgit, Xu, Tom and Troncone, Giancarlo . TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: an international performance evaluation study. J. Clin. Pathol.. LONDON: BMJ PUBLISHING GROUP. ISSN 1472-4146

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Abstract

Aim Next 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. Methods The 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. Results Overall, 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. Conclusion The 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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Malapelle, UmbertoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pepe, FrancescoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pisapia, PasqualeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sgariglia, RobertaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nacchio, MariantoniaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Barberis, MassimoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bilh, MichelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bubendorf, LukasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buettner, ReinhardUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cabibi, DanielaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Castiglia, MartaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
De Andrea, Carlos E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
de Biase, DarioUNSPECIFIEDorcid.org/0000-0002-0609-8817UNSPECIFIED
Dumur, Catherine, IUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fontanini, GabriellaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Freire, JavierUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gristina, ValerioUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hofman, PaulUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ilie, MariusUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lozano, Maria DoloresUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Merkelbach-Bruse, SabineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pappesch, RobertoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pelusi, NatalieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roma, GianlucaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Russo, AntonioUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Savic, SpasenijaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Siemanowski, JannaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tallini, GiovanniUNSPECIFIEDorcid.org/0000-0003-0113-6682UNSPECIFIED
Tischler, VerenaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vander Borght, SaraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Weynand, BirgitUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xu, TomUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Troncone, GiancarloUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-603069
DOI: 10.1136/jclinpath-2021-207450
Journal or Publication Title: J. Clin. Pathol.
Publisher: BMJ PUBLISHING GROUP
Place of Publication: LONDON
ISSN: 1472-4146
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
METASTATIC COLORECTAL-CANCER; MOLECULAR TESTING GUIDELINE; WORLDWIDE RING TRIAL; CELL LUNG-CANCER; 1ST-LINE TREATMENT; REPRODUCIBILITY; ASSOCIATION; CONSISTENCY; MUTATIONS; SELECTIONMultiple languages
PathologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/60306

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