{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T21:21:51Z","timestamp":1791148911750,"version":"4.1.0"},"reference-count":39,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Over the years, increasing information has been asked of the pathologist: we have moved from a purely morphological diagnosis to biomolecular and genetic studies, which have made it possible to implement the use of molecular targeted therapies, such as anti-epidermal growth factor receptor (EGFR) molecules in EGFR-mutated lung cancer, for example. Today, next generation sequencing (NGS) has changed the approach to neoplasms, to the extent that, in a short time, it has gained a place of absolute importance and diagnostic, prognostic and therapeutic utility. In this scenario, formaldehyde-fixed and paraffin-embedded (FFPE) biological tissue samples are a source of clinical and molecular information. However, problems can arise in the genetic material (DNA and RNA) for use in NGS due to fixation, and work is being devoted to possible strategies to reduce its effects. In this paper, we discuss the applications of FFPE tissue samples in the execution of NGS, we focus on the problems arising with the use of this type of material for nucleic acid extraction and, finally, we consider the most useful strategies to prevent and reduce single nucleotide polymorphisms (SNV) and other fixation artifacts.<\/jats:p>","DOI":"10.3390\/genes12101472","type":"journal-article","created":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T09:59:15Z","timestamp":1632391155000},"page":"1472","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0325-4316","authenticated-orcid":false,"given":"Gerardo","family":"Cazzato","sequence":"first","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency 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Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4676-0761","authenticated-orcid":false,"given":"Anna","family":"Colagrande","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4006-6421","authenticated-orcid":false,"given":"Vera","family":"Loizzi","sequence":"additional","affiliation":[{"name":"Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5745-372X","authenticated-orcid":false,"given":"Gennaro","family":"Cormio","sequence":"additional","affiliation":[{"name":"Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0860-3044","authenticated-orcid":false,"given":"Teresa","family":"Lettini","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0472-5338","authenticated-orcid":false,"given":"Eugenio","family":"Maiorano","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincenza","family":"Scarcella","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Tarantino","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1058-7269","authenticated-orcid":false,"given":"Maricla","family":"Marrone","sequence":"additional","affiliation":[{"name":"Section of Legal Medicine, Interdisciplinary Department of Medicine, Bari Policlinico Hospital, University of Bari \u201cAldo Moro\u201d, Piazza Giulio Cesare 11, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7397-0097","authenticated-orcid":false,"given":"Alessandra","family":"Stellacci","sequence":"additional","affiliation":[{"name":"Section of Legal Medicine, Interdisciplinary Department of Medicine, Bari Policlinico Hospital, University of Bari \u201cAldo Moro\u201d, Piazza Giulio Cesare 11, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0591-6723","authenticated-orcid":false,"given":"Paola","family":"Parente","sequence":"additional","affiliation":[{"name":"UOC di Anatomia Patologica, Fondazione IRCCS Casa Sollievo Della Sofferenza, 71013 San Giovanni Rotondo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Romita","sequence":"additional","affiliation":[{"name":"Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari \u201cAldo Moro\u201d, Piazza Giulio Cesare 11, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aurora","family":"De Marco","sequence":"additional","affiliation":[{"name":"Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari \u201cAldo Moro\u201d, Piazza Giulio Cesare 11, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincenzo","family":"Venerito","sequence":"additional","affiliation":[{"name":"Section of Reumathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caterina","family":"Foti","sequence":"additional","affiliation":[{"name":"Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari \u201cAldo Moro\u201d, Piazza Giulio Cesare 11, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4792-3545","authenticated-orcid":false,"given":"Giuseppe","family":"Ingravallo","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Rossi","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4335-4776","authenticated-orcid":false,"given":"Leonardo","family":"Resta","sequence":"additional","affiliation":[{"name":"Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari \u201cAldo Moro\u201d, 70124 Bari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"260","DOI":"10.5114\/amsik.2015.61029","article-title":"Next generation sequencing (NGS): A golden tool in forensic toolkit","volume":"4","author":"Aly","year":"2015","journal-title":"Arch. 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