Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization

Clinical Chemistry
Hongdo Do, Alexander Dobrovic

Abstract

Precision medicine is dependent on identifying actionable mutations in tumors. Accurate detection of mutations is often problematic in formalin-fixed paraffin-embedded (FFPE) tissues. DNA extracted from formalin-fixed tissues is fragmented and also contains DNA lesions that are the sources of sequence artifacts. Sequence artifacts can be difficult to distinguish from true mutations, especially in the context of tumor heterogeneity, and are an increasing interpretive problem in this era of massively parallel sequencing. Understanding of the sources of sequence artifacts in FFPE tissues and implementation of preventative strategies are critical to improve the accurate detection of actionable mutations. This mini-review focuses on DNA template lesions in FFPE tissues as the source of sequence artifacts in molecular analysis. In particular, fragmentation, base modification (including uracil and thymine deriving from cytosine deamination), and abasic sites are discussed as indirect or direct sources of sequence artifacts. We discuss strategies that can be implemented to minimize sequence artifacts and to distinguish true mutations from sequence artifacts. These strategies are applicable for the detection of actionable mutations in b...Continue Reading

References

Oct 1, 1979·European Journal of Biochemistry·Y OhbaA Watarai
May 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·G VesnaverK J Breslauer
Jan 1, 1973·Progress in Nucleic Acid Research and Molecular Biology·M Y Feldman
Sep 12, 1972·Biochemistry·T Lindahl, B Nyberg
Oct 9, 1980·Nature·B K Duncan, J H Miller
Mar 25, 1994·Nucleic Acids Research·J C ShenP A Jones
Nov 11, 1998·Cancer Genetics and Cytogenetics·C WongM S Piver
Aug 4, 1999·Proceedings of the National Academy of Sciences of the United States of America·M A GreaggL H Pearl
Nov 7, 1999·The American Journal of Pathology·C WilliamsJ Lundeberg
Jan 10, 2002·Proceedings of the National Academy of Sciences of the United States of America·Holly H HogrefeKirk B Nielson
Jul 23, 2002·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·Shan-Rong ShiClive R Taylor
Oct 10, 2002·Applied Immunohistochemistry & Molecular Morphology : AIMM·Lin WuBuena Chui
Feb 1, 2005·The Journal of Molecular Diagnostics : JMD·Mansour AkbariHans E Krokan
Feb 25, 2005·The New England Journal of Medicine·Susumu KobayashiBalázs Halmos
Jul 15, 2005·The New England Journal of Medicine·Ming-Sound TsaoFrances A Shepherd
Feb 3, 2006·The New England Journal of Medicine·Antonio MarchettiFiamma Buttitta
Jan 27, 2007·Journal of the American Chemical Society·Sanjay DuttaKent S Gates
Feb 17, 2007·Biochemical and Biophysical Research Communications·Jan A SikorskyJames Denvir
Aug 2, 2008·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Samuel MurrayParis Kosmidis
Aug 1, 1948·Journal of the American Chemical Society·H FRAENKEL-CONRAT, H S OLCOTT
Oct 24, 2008·The New England Journal of Medicine·Christos S KarapetisJohn R Zalcberg
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jun 17, 2010·Nature Reviews. Clinical Oncology·Charles FertéJean-Charles Soria
Apr 26, 2011·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Aude LamyJean-Christophe Sabourin
May 17, 2011·PloS One·Silvia QueringsRoman K Thomas
May 19, 2011·Proceedings of the National Academy of Sciences of the United States of America·Isaac KindeBert Vogelstein
Jan 25, 2012·Virchows Archiv : an International Journal of Pathology·Natalie LudygaMichaela Aubele
May 25, 2012·Genome Biology·Mingkun Li, Mark Stoneking
Aug 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael W SchmittLawrence A Loeb
Nov 24, 2012·Cancer Letters·Jiekun XuanLeming Shi
Aug 16, 2013·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Xin YeQunsheng Ji
Sep 3, 2013·Nature Methods·Christopher M HindsonMuneesh Tewari
Dec 11, 2013·Nature Reviews. Genetics·Kimberly RobaskyGeorge M Church
May 20, 2014·American Journal of Clinical Pathology·Ming-Tseh LinJames R Eshleman
May 23, 2014·Analytical Chemistry·Julia Kennedy-Darling, Lloyd M Smith
Aug 6, 2014·Molecular Diagnosis & Therapy·Guoli ChenJames R Eshleman

Citations

Dec 19, 2015·Expert Review of Molecular Diagnostics·Leomar Y BallesterRajesh R Singh
Feb 3, 2016·Journal of the National Cancer Institute·Michael S AnglesioDavid G Huntsman
Feb 11, 2015·Clinica Chimica Acta; International Journal of Clinical Chemistry·Marc G DenisSandrine Théoleyre
Jan 23, 2016·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Jerzy LasotaMarkku Miettinen
Feb 28, 2016·The Journal of Molecular Diagnostics : JMD·Maja H OktaySumanta Goswami
Jul 30, 2015·Genome Medicine·Jeffrey Gagan, Eliezer M Van Allen
Aug 16, 2016·The Breast : Official Journal of the European Society of Mastology·Michael J DuffyJohn Crown
Sep 7, 2016·Cancer Cytopathology·Andrew H Fischer, Lloyd M Hutchinson
Nov 30, 2016·Expert Review of Molecular Diagnostics·Michelangelo FiorentinoRodolfo Montironi
Jun 20, 2017·Molecular and Cellular Probes·Wendy Pérez-BáezLucía Taja-Chayeb
Jul 21, 2017·Cancer Cytopathology·David H HwangLynette M Sholl
Mar 27, 2018·Nature Reviews. Genetics·Jesse J SalkLawrence A Loeb
Mar 27, 2018·Cytopathology : Official Journal of the British Society for Clinical Cytology·Gilda da Cunha SantosP Zeppa
Jan 26, 2018·Neuropathology and Applied Neurobiology·M Leija-SalazarC Proukakis
Mar 13, 2018·Epigenetics : Official Journal of the DNA Methylation Society·Liesbeth Van WesenbeeckLieven Stuyver
Apr 21, 2018·International Journal of Molecular Sciences·Yann GuillerminSarah Huet
Nov 17, 2017·Current Treatment Options in Oncology·Xiaomin NiuHeather A Wakelee
Dec 12, 2017·Critical Reviews in Clinical Laboratory Sciences·José Luis García-GiménezFederico V Pallardó
May 5, 2018·Advances in Anatomic Pathology·Ruta GuptaSandra O'Toole
Aug 17, 2018·Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission·E F GaffneyP H Watson
Aug 18, 2018·Annals of Clinical Biochemistry·Michael J Duffy
Sep 21, 2018·Biopreservation and Biobanking·Wim AmmerlaanFay Betsou
Jul 30, 2015·PloS One·Danielle Mercatante CarrickSheri D Schully
Nov 3, 2018·PLoS Genetics·Yang LiuWei Sun
Oct 20, 2018·Cancer Science·Masayuki NagahashiToshifumi Wakai
Feb 2, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Pauline Robbe100,000 Genomes Project
Mar 5, 2019·American Journal of Hematology·Francesco MauraPaolo Corradini
Nov 15, 2017·Endocrine Connections·Tiemo S GerberThomas J Musholt
Apr 12, 2019·PloS One·Samantha J McDonoughJulie M Cunningham
Aug 8, 2017·Laboratory Investigation; a Journal of Technical Methods and Pathology·Nenggang JiangWing C Chan
Jun 5, 2019·Molecular Genetics & Genomic Medicine·Peter GeorgesonDaniel D Buchanan
Mar 31, 2018·Journal of the Endocrine Society·Cora BallmannUte I Scholl
Oct 2, 2019·The Journal of Pathology. Clinical Research·Mark SouthwoodSTRATfix Consortium
Jan 25, 2020·Annual Review of Pathology·Noah A Brown, Kojo S J Elenitoba-Johnson
Jan 31, 2020·PloS One·Christian A TotoiuGregory A Weiss
Apr 5, 2015·Clinical Chemistry·Alexander Dobrovic
Aug 11, 2017·The American Journal of Surgical Pathology·Isaac H SolomonDanny A Milner
Dec 19, 2017·Current Opinion in Oncology·Felicitas Oberndorfer, Leonhard Müllauer
Jul 12, 2018·Gut·Ann-Marie BakerTrevor A Graham
Oct 11, 2017·Clinical Obstetrics and Gynecology·Michael S Anglesio, Paul J Yong
Jul 23, 2020·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·William Mathieson, Geraldine A Thomas
Mar 2, 2018·Archives of Pathology & Laboratory Medicine·Gilda da Cunha Santos
Aug 29, 2020·Journal of the American Veterinary Medical Association·Alexandre B Le RouxTaryn A Donovan
Aug 15, 2018·Virchows Archiv : an International Journal of Pathology·Hannah L WilliamsZandra C Deans
Dec 7, 2018·Expert Review of Anticancer Therapy·Carlos Martínez-PérezJ Michael Dixon
Apr 22, 2019·European Journal of Cardio-thoracic Surgery : Official Journal of the European Association for Cardio-thoracic Surgery·Erin R LewisGabriele Di Luozzo
Mar 11, 2020·Frontiers in Oncology·Sidney P WalkerMarcus J Claesson
Jul 11, 2020·Scientific Reports·Carina HeydtSabine Merkelbach-Bruse
Sep 2, 2020·Virchows Archiv : an International Journal of Pathology·Yukiko MatsuoYukitoshi Satoh
Aug 28, 2020·Angewandte Chemie·Willem A VelemaEric T Kool
May 26, 2017·Journal of Pathology and Translational Medicine·Jihun KimMolecular Pathology Study Group of Korean Society of Pathologists
Mar 21, 2017·Journal of Cancer Research and Clinical Oncology·Richard OfnerJürgen C Becker
Aug 26, 2017·Neuropathology : Official Journal of the Japanese Society of Neuropathology·Koji YoshimotoKoji Iihara
May 12, 2018·Diagnostics·Francesc Castro-GinerNicola Aceto
Mar 13, 2019·Infectious Agents and Cancer·Kasper IngerslevJan Blaakaer
Nov 11, 2019·Scientific Reports·Chih-Yang WangHui-Ping Hsu
Apr 8, 2020·Pharmacogenomics and Personalized Medicine·Óscar Álvarez-MachancosesJuan Luis Fernández-Martínez
Mar 31, 2018·Nature Reviews. Clinical Oncology·Michael F Berger, Elaine R Mardis
Oct 5, 2018·Journal of the Endocrine Society·Wasita WarachitSarat Sunthornyothin
Mar 16, 2019·BMC Medical Genomics·Anna V KudryavtsevaAnastasiya V Snezhkina
Feb 23, 2019·Journal of the Endocrine Society·Jessica Costa-Guda
Aug 24, 2020·Microbiome·Yensi Flores BuesoMark Tangney
Jul 8, 2020·BMC Medical Genomics·Louise de Schaetzen van BrienenKathleen Marchal
Feb 20, 2020·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Beate M CrossleyKathy Toohey-Kurth
Nov 23, 2018·Cancers·Marcel NijlandAnke van den Berg
Dec 21, 2019·PloS One·Eirini PapadopoulouGeorge Nasioulas
Jun 21, 2018·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Simon Andreasen
Oct 6, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kelly E BlevinsAnne C Stone
Oct 6, 2020·PloS One·Emília DelarmelinaJenner Karlisson Pimenta Dos Reis
Oct 20, 2020·Biology Methods and Protocols·Yensi Flores BuesoMark Tangney
Nov 20, 2020·BMC Medical Genomics·Daniela NachmansonOlivier Harismendy
Dec 1, 2020·Journal of Medical Microbiology·Joseph JillwinArunaloke Chakrabarti
Dec 17, 2020·International Journal of Molecular Sciences·Marta Tellez-GabrielMaria Perander
Oct 2, 2019·Molecular Cancer Research : MCR·Kate MegquierKerstin Lindblad-Toh
Aug 2, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Pauline KrämerMichael S Anglesio
Jan 13, 2021·Journal of the American Heart Association·Lauren E Parker, Andrew P Landstrom

Related Concepts

DNA, Double-Stranded
Genotoxic Stress
False Negative Reactions
False Positive Reactions
Formalin
Malignant Neoplasms
Genetic Template
Reproducibility of Results
Morphologic Artifacts
Paraffin Embedding

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