Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice

PloS One
Leah M PrenticeBrandon S Sheffield


Genomic analysis of cancer tissues is an essential aspect of personalized oncology treatment. Though it has been suggested that formalin fixation of patient tissues may be suboptimal for molecular studies, this tissue processing approach remains the industry standard. Therefore clinical molecular laboratories must be able to work with formalin fixed, paraffin embedded (FFPE) material. This study examines the effects of pre-analytic variables introduced by routine pathology processing on specimens used for clinical reports produced by next-generation sequencing technology. Tissue resected from three colorectal cancer patients was subjected to 2, 15, 24, and 48 hour fixation times in neutral buffered formalin. DNA was extracted from all tissues twice, once with uracil-N-glycosylase (UNG) treatment to counter deamination effects, and once without. Of note, deamination events at methylated cytosine, as found at CpG sites, remains unaffected by UNG. After extraction a two-step PCR targeted sequencing method was performed using the Illumina MiSeq and the data was analyzed via a custom-built bioinformatics pipeline, including filtration of reads with mapping quality <30. A larger baseline group of samples (n = 20) was examined to esta...Continue Reading


Nov 7, 1999·The American Journal of Pathology·C WilliamsJ Lundeberg
Dec 6, 2002·The American Journal of Pathology·Mythily SrinivasanScott Jewell
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jan 28, 2010·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Stephan E BaldusHelmut E Gabbert
Apr 26, 2011·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Aude LamyJean-Christophe Sabourin
Jul 3, 2013·The Journal of Molecular Diagnostics : JMD·David H SpencerEric J Duncavage
Oct 9, 2013·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Antonio C WolffCollege of American Pathologists
Aug 6, 2014·Molecular Diagnosis & Therapy·Guoli ChenJames R Eshleman
Nov 26, 2014·Clinical Chemistry·Hongdo Do, Alexander Dobrovic
Feb 20, 2015·American Journal of Clinical Pathology·Rachel M RothWendy L Frankel


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Nov 13, 2019·The American Journal of Surgical Pathology·Jennifer PorsLynn N Hoang
Jul 23, 2020·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·William Mathieson, Geraldine A Thomas
Apr 3, 2020·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Emily ThompsonLynn N Hoang
Aug 15, 2020·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Basile Tessier-CloutierLynn N Hoang
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Nov 19, 2020·The British Journal of Dermatology·M NakamuraA Morita

Related Concepts

False Positive Reactions
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