{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T21:34:27Z","timestamp":1793741667487,"version":"4.6.1"},"reference-count":19,"publisher":"SAGE Publications","issue":"3","license":[{"start":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T00:00:00Z","timestamp":1581379200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"DOI":"10.13039\/501100000761","name":"imperial college london","doi-asserted-by":"publisher","award":["Imperial College London Tissue Bank"],"award-info":[{"award-number":["Imperial College London Tissue Bank"]}],"id":[{"id":"10.13039\/501100000761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011965","name":"integrated biobank of luxembourg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011965","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["J Histochem Cytochem."],"published-print":{"date-parts":[[2020,3]]},"abstract":"<jats:p>\n                    DNA extracted from formalin-fixed, paraffin-embedded tissue sections is often inadequate for sequencing, due to poor yield or degradation. We optimized the proteinase K digest by testing increased volume of enzyme and increased digest length from the manufacturer\u2019s protocol using 54 biospecimens, performing the digest in centrifuge tubes. Doubling the quantity of proteinase K resulted in a median increase in yield of 96%. Applying the optimized proteinase K protocol to sections deparaffinized on microscope slides generated a further increase in yield of 41%, but only at &gt;50,000 epithelial tumor cells\/section. DNA yield now correlated with (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 0.84) and could be predicted from the epithelial tumor cell number. DNA integrity was assayed using end point multiplex PCR (amplicons of 100\u2013400 bp visualized on a gel), quantitative PCR (qPCR; Illumina FFPE QC Assay), and nanoelectrophoresis (DNA Integrity Numbers [DINs]). Generally, increases in yield were accompanied by increases in integrity, but sometimes qPCR and DIN results were conflicting. Amplicons of 400 bp were almost universally obtained. The process of optimization enabled us to reduce the percentage of samples that failed published quality control thresholds for determining amenability to whole genome sequencing from 33% to 7%.\n                  <\/jats:p>","DOI":"10.1369\/0022155420906234","type":"journal-article","created":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T11:09:53Z","timestamp":1581419393000},"page":"171-184","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":22,"title":["Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue"],"prefix":"10.1369","volume":"68","author":[{"given":"Zoe","family":"Frazer","sequence":"first","affiliation":[{"name":"Department of Surgery and Cancer, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changyoung","family":"Yoo","sequence":"additional","affiliation":[{"name":"Department of Surgery and Cancer, Imperial College London, London, UK"},{"name":"Department of Pathology, The Catholic University of Korea, St. Vincent\u2019s Hospital, Seoul, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manveer","family":"Sroya","sequence":"additional","affiliation":[{"name":"Department of Surgery and Cancer, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Bellora","sequence":"additional","affiliation":[{"name":"Integrated Biobank of Luxembourg, Dudelange, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian L.","family":"DeWitt","sequence":"additional","affiliation":[{"name":"Integrated Biobank of Luxembourg, Dudelange, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio","family":"Sanchez","sequence":"additional","affiliation":[{"name":"Integrated Biobank of Luxembourg, Dudelange, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geraldine A.","family":"Thomas","sequence":"additional","affiliation":[{"name":"Department of Surgery and Cancer, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Mathieson","sequence":"additional","affiliation":[{"name":"Integrated Biobank of Luxembourg, Dudelange, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2020,2,11]]},"reference":[{"key":"bibr1-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1982-6"},{"key":"bibr2-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-016-2720-4"},{"key":"bibr3-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0195471"},{"key":"bibr4-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0098187"},{"key":"bibr5-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0144162"},{"key":"bibr6-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2017.241"},{"key":"bibr7-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexmp.2017.02.002"},{"key":"bibr8-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1093\/ajcp\/aqw023"},{"key":"bibr9-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1089\/bio.2015.0008"},{"key":"bibr10-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bjc.6602889"},{"key":"bibr11-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1016\/j.cancergen.2015.05.001"},{"key":"bibr12-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1007\/s40139-019-00194-6"},{"key":"bibr13-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2013.05.004"},{"key":"bibr14-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1016\/j.jss.2017.06.077"},{"key":"bibr15-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005548"},{"key":"bibr16-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3.6.S113"},{"key":"bibr17-0022155420906234","doi-asserted-by":"publisher","DOI":"10.7150\/ijms.8842"},{"key":"bibr18-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1016\/j.ab.2015.01.019"},{"key":"bibr19-0022155420906234","doi-asserted-by":"publisher","DOI":"10.1089\/bio.2018.0009."}],"container-title":["Journal of Histochemistry &amp; 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