{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T00:50:58Z","timestamp":1760316658333,"version":"build-2065373602"},"reference-count":53,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2019,11,11]],"date-time":"2019-11-11T00:00:00Z","timestamp":1573430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006041","name":"Innovate UK","doi-asserted-by":"publisher","award":["38618\u2010281179"],"award-info":[{"award-number":["38618\u2010281179"]}],"id":[{"id":"10.13039\/501100006041","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["pathsocjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Journal of Pathology CR"],"published-print":{"date-parts":[[2020,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Whilst adequate for most existing pathological tests, formalin is generally considered a poor DNA preservative and use of alternative fixatives may prove advantageous for molecular testing of tumour material; an increasingly common approach to identify targetable driver mutations in lung cancer patients. We collected paired PAXgene\u00ae tissue\u2010fixed and formalin\u2010fixed samples of block\u2010sized tumour and lung parenchyma, Temno\u2010needle core tumour biopsies and fine needle tumour aspirates (FNAs) from non\u2010small cell lung cancer resection specimens. Traditionally processed formalin fixed paraffin wax embedded (FFPE) samples were compared to paired PAXgene\u00ae tissue fixed paraffin\u2010embedded (PFPE) samples. We evaluated suitability for common laboratory tests (H&amp;E staining and immunohistochemistry) and performance for downstream molecular investigations relevant to lung cancer, including RT\u2010PCR and next generation DNA sequencing (NGS). Adequate and comparable H&amp;E staining was seen in all sample types and nuclear staining was preferable in PAXgene\u00ae fixed Temno tumour biopsies and tumour FNA samples. Immunohistochemical staining was broadly comparable. PFPE samples enabled greater yields of less\u2010fragmented DNA than FFPE comparators. PFPE samples were also superior for PCR and NGS performance, both in terms of quality control metrics and for variant calling. Critically we identified a greater number of genetic variants in the epidermal growth factor receptor gene when using PFPE samples and the Ingenuity\u00ae Variant Analysis pipeline. In summary, PFPE samples are adequate for histopathological diagnosis and suitable for the majority of existing laboratory tests. PAXgene\u00ae fixation is superior for DNA and RNA integrity, particularly in low\u2010yield samples and facilitates improved NGS performance, including the detection of actionable lung cancer mutations for precision medicine in lung cancer samples.<\/jats:p>","DOI":"10.1002\/cjp2.145","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T02:22:46Z","timestamp":1569896566000},"page":"40-54","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Systematic evaluation of PAXgene\u00ae tissue fixation for the histopathological and molecular study of lung cancer"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3493-9599","authenticated-orcid":false,"given":"Mark","family":"Southwood","sequence":"first","affiliation":[{"name":"Pathology Research Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine  Cambridge UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Krenz","sequence":"additional","affiliation":[{"name":"Sample Technologies Department QIAGEN GmbH  Hilden Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natasha","family":"Cant","sequence":"additional","affiliation":[{"name":"Sample Technologies Department QIAGEN Ltd.  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