Cytosine deamination is a major cause of baseline noise in next-generation sequencing

Molecular Diagnosis & Therapy
Guoli ChenJames R Eshleman

Abstract

As next-generation sequencing (NGS) becomes a major sequencing platform in clinical diagnostic laboratories, it is critical to identify artifacts that constitute baseline noise and may interfere with detection of low-level gene mutations. This is especially critical for applications requiring ultrasensitive detection, such as molecular relapse of solid tumors and early detection of cancer. We recently observed a ~10-fold higher frequency of C:G > T:A mutations than the background noise level in both wild-type peripheral blood and formalin-fixed paraffin-embedded samples. We hypothesized that these might represent cytosine deamination events, which have been seen using other platforms. To test this hypothesis, we pretreated samples with uracil N-glycosylase (UNG). Additionally, to test whether some of the cytosine deamination might be a laboratory artifact, we simulated the heat associated with polymerase chain reaction thermocycling by subjecting samples to thermocycling in the absence of polymerase. To test the safety of universal UNG pretreatment, we tested known positive samples treated with UNG. UNG pretreatment significantly reduced the frequencies of these mutations, consistent with a biologic source of cytosine deaminati...Continue Reading

References

Apr 1, 1986·Bioscience Reports·M EhrlichC W Gehrke
Oct 9, 1980·Nature·B K Duncan, Jeffrey H Miller
Nov 7, 1999·The American Journal of Pathology·C WilliamsJ Lundeberg
Apr 25, 2000·The Journal of Biological Chemistry·M Sandigursky, W A Franklin
Jun 18, 2002·The EMBO Journal·Alessandro A SartoriJosef Jiricny
Nov 26, 2003·Mutation Research·Svein Bjelland, Erling Seeberg
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Oct 26, 2005·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Michiel S van der HeijdenScott E Kern
Apr 5, 2008·The EMBO Journal·Nicholas C TurnerAlan Ashworth
Aug 2, 2008·Nature Medicine·Frank DiehlLuis A Diaz
Nov 7, 2008·Journal of Radiation Research·Shin-Ichiro YonekuraQiu-Mei Zhang-Akiyama
Dec 24, 2009·Nucleic Acids Research·Adrian W BriggsSvante Pääbo
Apr 8, 2010·Science Translational Medicine·Rebecca J LearyVictor E Velculescu
Jan 14, 2011·The Journal of Molecular Diagnostics : JMD·Ming-Tseh LinChristopher D Gocke
Jul 22, 2011·Science Translational Medicine·Jian WuBert Vogelstein
Jun 5, 2012·The Journal of Molecular Diagnostics : JMD·Colin C PritchardTom Walsh
Oct 30, 2012·Nature·Andrew V BiankinSean M Grimmond
Dec 1, 2012·Science Translational Medicine·Rebecca J LearyVictor E Velculescu
May 20, 2014·American Journal of Clinical Pathology·Ming-Tseh LinJames R Eshleman

Citations

Dec 8, 2014·Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association·James R EshlemanMichael G Goggins
Aug 2, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Barbara ArbeithuberIrene Tiemann-Boege
Jun 18, 2016·The Journal of Pathology·Hirofumi RokutanTatsuhiro Shibata
May 5, 2017·International Journal of Cancer. Journal International Du Cancer·Peter UlzMichael R Speicher
Mar 27, 2018·Nature Reviews. Genetics·Jesse J SalkLawrence A Loeb
Aug 8, 2017·Archives of Pathology & Laboratory Medicine·Sophia Yohe, Bharat Thyagarajan
Feb 23, 2018·Leukemia·J MalcikovaEuropean Research Initiative on Chronic Lymphocytic Leukemia (ERIC) — TP53 network
Apr 21, 2018·Expert Review of Molecular Diagnostics·Sara MarianiPaola Cassoni
Dec 5, 2017·Pancreas·Masaya SuenagaMichael G Goggins
Sep 20, 2015·American Journal of Clinical Pathology·Jamal CarterMing-Tseh Lin
Jul 4, 2018·Nature Reviews. Clinical Oncology·Christopher AbboshCharles Swanton
Jul 6, 2018·Molecular Diagnosis & Therapy·Marija DebeljakJames R Eshleman
May 5, 2018·The Journal of Clinical Endocrinology and Metabolism·Norman G NicolsonTobias Carling
Nov 10, 2018·Biopreservation and Biobanking·Bénedith ObenJean-Luc Rummens
Jan 16, 2019·Hepatology Research : the Official Journal of the Japan Society of Hepatology·Yuji EsoHiroshi Seno
Nov 26, 2014·Clinical Chemistry·Hongdo Do, Alexander Dobrovic
Dec 17, 2019·Genome Biology and Evolution·Kendra M MeerJoanna Masel
Apr 12, 2015·The Oncologist·Shidong JiaGary J Latham
Apr 26, 2020·Cancer Medicine·Erika F RodriguezMing-Tseh Li
Mar 21, 2017·Journal of Cancer Research and Clinical Oncology·Richard OfnerJürgen C Becker
Oct 12, 2019·Scientific Reports·Stéphane BuscaAlexandre Harlé
Jul 24, 2017·Genome Biology·Gahee ParkDonghyun Park
Mar 29, 2016·Nature Biotechnology·Aaron M NewmanAsh A Alizadeh
Mar 15, 2019·Genome Biology·Xiaotu MaJinghui Zhang
Oct 31, 2015·Oncotarget·Elaine I LinJames R Eshleman
Oct 20, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Ruben Van PaemelKatleen De Preter
Jan 6, 2018·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Masaya SuenagaMichael G Goggins
May 31, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Vincent P GrootJames R Eshleman

Related Concepts

Cytosine
DNA, Double-Stranded
Morphologic Artifacts
Sequence Determinations, DNA
Uracil-DNA glycosylase
High-Throughput Nucleotide Sequencing
Malignant Neoplasms
Cytosine
Laboratory
Polymerase Chain Reaction

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Computational Methods for Protein Structures

Computational methods employing machine learning algorithms are powerful tools that can be used to predict the effect of mutations on protein structure. This is important in neurodegenerative disorders, where some mutations can cause the formation of toxic protein aggregations. This feed follows the latests insights into the relationships between mutation and protein structure leading to better understanding of disease.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

Related Papers

Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology
Luisa BarzonGiorgio Palù
Investigative Ophthalmology & Visual Science
Kaoru FujinamiMichel Michaelides
Current Opinion in Obstetrics & Gynecology
Chee S KuDimitrios H Roukos
© 2021 Meta ULC. All rights reserved