{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,21]],"date-time":"2026-06-21T04:29:45Z","timestamp":1782016185265,"version":"3.54.5"},"reference-count":21,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T00:00:00Z","timestamp":1703030400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Diagnostic Cytopathology"],"published-print":{"date-parts":[[2024,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Genomic profiling using next\u2010generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin\u2010fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non\u2010FFPE may represent an alternative. However, studies comparing the NGS performance of non\u2010FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non\u2010FFPE preparations the nucleic acid yield and NGS performance on both a capture\u2010based and an amplicon\u2010based NGS platform. NGS quality metrics obtained from non\u2010FFPE preparations were compared to FFPE.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We analyzed the cellularity and nucleic acid yield in 111 tumors from non\u2010FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non\u2010FFPE and FFPE samples. A paired comparison between non\u2010FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The mean target coverage from DNA libraries was 2\u00d7 higher in non\u2010FFPE samples than in FFPE. The detection of exogenous DNA was 2.5\u00d7 higher in non\u2010FFPE than in FFPE. Conversely, a lower performance was observed in non\u2010FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non\u2010FFPE was found to be comparable to that of FFPE tumor samples in matched samples.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Non\u2010FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.<\/jats:p><\/jats:sec>","DOI":"10.1002\/dc.25267","type":"journal-article","created":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T05:34:09Z","timestamp":1703136849000},"page":"171-182","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Performance of non\u2010formalin fixed paraffin embedded samples in hybrid capture and amplicon next\u2010generation sequencing panels"],"prefix":"10.1002","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3143-2305","authenticated-orcid":false,"given":"Sibele In\u00e1cio","family":"Meireles","sequence":"first","affiliation":[{"name":"Departamento de Anatomia Patol\u00f3gica e Molecular Hospital S\u00edrio Liban\u00eas  S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana Vargas","family":"Cruz","sequence":"additional","affiliation":[{"name":"Departamento de Anatomia Patol\u00f3gica e Molecular Hospital S\u00edrio Liban\u00eas  S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla Daniele","family":"de Godoy","sequence":"additional","affiliation":[{"name":"Departamento de Anatomia Patol\u00f3gica e Molecular Hospital S\u00edrio Liban\u00eas  S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo","family":"de Testagrossa","sequence":"additional","affiliation":[{"name":"Departamento de Anatomia Patol\u00f3gica e Molecular Hospital S\u00edrio Liban\u00eas  S\u00e3o Paulo 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generation sequencing in cytopathology: focus on non\u2010small cell lung cancer","volume":"8","author":"Pisapia P","year":"2021","journal-title":"Front Med"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/cyt.12974"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.3390\/cancers14102457"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2015.11.006"},{"key":"e_1_2_10_18_1","volume-title":"R: A Language and Environment for Statistical Computing","author":"RCoreTeam","year":"2022"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21699"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1097\/JTO.0b013e318290868f"},{"key":"e_1_2_10_21_1","first-page":"373","article-title":"Evaluating diff\u2010Quik cytology smears for large\u2010panel mutation testing in lung cancer\u2014predicting DNA content and success with low\u2010malignant\u2010cellularity samples","volume":"2023","author":"Fielding DI","year":"2022","journal-title":"Cancer Cytopathol"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes12101472"}],"container-title":["Diagnostic Cytopathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/dc.25267","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,7]],"date-time":"2024-02-07T07:26:22Z","timestamp":1707290782000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/dc.25267"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,20]]},"references-count":21,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3]]}},"alternative-id":["10.1002\/dc.25267"],"URL":"https:\/\/doi.org\/10.1002\/dc.25267","archive":["Portico"],"relation":{},"ISSN":["8755-1039","1097-0339"],"issn-type":[{"value":"8755-1039","type":"print"},{"value":"1097-0339","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,20]]},"assertion":[{"value":"2023-09-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication 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