{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Frazer Z"],"funding":["imperial college london","integrated biobank of luxembourg"],"pagination":["171-184"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7045302"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["68(3)"],"pubmed_abstract":["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's 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 >50,000 epithelial tumor cells/section. DNA yield now correlated with (χ<sup>2</sup> = 0.84) and could be predicted from the epithelial tumor cell number. DNA integrity was assayed using end point multiplex PCR (amplicons o"],"journal":["The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society"],"pubmed_title":["Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue."],"pmcid":["PMC7045302"],"funding_grant_id":["Imperial College London Tissue Bank"],"pubmed_authors":["DeWitt BL","Yoo C","Sroya M","Bellora C","Thomas GA","Frazer Z","Sanchez I","Mathieson W"],"additional_accession":[]},"is_claimable":false,"name":"Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue.","description":"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's 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 >50,000 epithelial tumor cells/section. DNA yield now correlated with (χ<sup>2</sup> = 0.84) and could be predicted from the epithelial tumor cell number. DNA integrity was assayed using end point multiplex PCR (amplicons o","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Mar","modification":"2025-04-19T02:21:04.316Z","creation":"2021-03-03T08:08:48Z"},"accession":"S-EPMC7045302","cross_references":{"pubmed":["32043912"],"doi":["10.1369/0022155420906234"]}}