Formalin fixation in the '-omics' era: a primer for the surgeon-scientist

ANZ Journal of Surgery
Adam Frankel

Abstract

Formalin is the most commonly used tissue fixative worldwide. While it offers excellent morphological preservation for routine histology, it has detrimental effects on nucleic acids. Most studies of nucleic acids have therefore used fresh frozen tissue, the collection and storage of which is resource intensive. The ability to use modern genomic, transcriptomic and epigenomic methods with nucleic acids derived from formalin-fixed, paraffin-embedded (FFPE) tissues would allow enormous archives of routinely stored tissues (usually with well-annotated clinical data) to be used for translational research. This paper outlines the effects of formalin on nucleic acids, describes ways of minimizing nucleic acid degradation and optimizing extraction, and reviews recent studies that have used contemporary techniques to analyse FFPE-derived nucleic acids (with a focus on malignant tissue sources). Simple tips are also offered to ensure the utility of your institution's samples for future studies, and broadly applicable guidelines are listed for those contemplating their own study using FFPE-derived material.

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Jan 1, 1973·Progress in Nucleic Acid Research and Molecular Biology·M Y Feldman
Feb 1, 1995·Brain Research. Molecular Brain Research·A E KingsburyC D Marsden
Nov 7, 1999·The American Journal of Pathology·C WilliamsJ Lundeberg
Mar 4, 2000·Laboratory Investigation; a Journal of Technical Methods and Pathology·S KitazawaS Maeda
May 2, 2001·Nature Reviews. Genetics·M HofreiterS Pääbo
Oct 27, 2001·Science·M Lagos-QuintanaT Tuschl
Nov 5, 2002·The American Journal of Pathology·Atreya DashMark A Rubin
Oct 1, 1954·Biochimica Et Biophysica Acta·H FRAENKEL-CONRAT
Feb 1, 1961·Journal of Molecular Biology·L GROSSMANW S ALLISON
Dec 20, 2003·BioTechniques·Oliver SchoorStefan Stevanović
Apr 1, 2005·World Journal of Gastroenterology : WJG·Chang-Hee LeeIn-Chul Lee
Jun 10, 2005·Nature·Jun LuTodd R Golub
Jan 13, 2006·Laboratory Investigation; a Journal of Technical Methods and Pathology·Patrick MickeJohan Botling
Mar 1, 2006·Journal of Clinical Pathology·A A GhazaniS J Done
Jun 6, 2006·Laboratory Investigation; a Journal of Technical Methods and Pathology·Nicola A JohnsonMing-Qing Du
Oct 25, 2006·Nature Reviews. Cancer·George A Calin, Carlo M Croce
Feb 5, 2008·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Federico A MonzonRajiv Dhir
Feb 28, 2008·Diagnostic Molecular Pathology : the American Journal of Surgical Pathology, Part B·Maureen Lyons-WeilerFederico A Monzon
Feb 29, 2008·Laboratory Investigation; a Journal of Technical Methods and Pathology·Maria RavoAlessandro Weisz
Jul 30, 2008·Genes, Chromosomes & Cancer·Marianne TuefferdSophie Camilleri-Broët
Aug 6, 2008·Histochemistry and Cell Biology·Susan M FarragherD Paul Harkin
Aug 20, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Nadia HarbeckRalf Lesche
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder

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Citations

Jun 18, 2014·The American Journal of Gastroenterology·Paul LochheadShuji Ogino
Aug 4, 2012·ANZ Journal of Surgery·Adam FrankelAndrew Barbour
Nov 29, 2013·International Journal of Cancer. Journal International Du Cancer·Jie LuoGarth L Warnock
Nov 8, 2014·Journal of Applied Toxicology : JAT·Scott S AuerbachRaymond R Tice
Dec 6, 2014·Medical Oncology·Sousana AmptoulachNikolaos Tsavaris
Dec 23, 2014·Epigenomics·Christa NoehammerAndreas Weinhaeusel
Mar 29, 2014·Experimental Biology and Medicine·Samson S Y WongKwok-Yung Yuen
Jan 24, 2015·International Braz J Urol : Official Journal of the Brazilian Society of Urology·Szilveszter LukacsEvangelos Mazaris
Jan 9, 2014·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Anna GranatoFranco Mutinelli
Mar 15, 2018·International Journal of Molecular Sciences·Lukas ValihrachMikael Kubista
Oct 1, 2017·Experimental and Therapeutic Medicine·Mototsugu WatanabeShinichiro Miyoshi
Oct 21, 2020·Molecular Imaging and Biology : MIB : the Official Publication of the Academy of Molecular Imaging·Shrey KapoorNaoki Nishio
Jul 6, 2021·F&S Reports·Rachel S RudermanEve C Feinberg

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