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A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies

DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exp...

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Autores principales: Crary-Dooley, Florence K., Tam, Mitchell E., Dunaway, Keith W., Hertz-Picciotto, Irva, Schmidt, Rebecca J., LaSalle, Janine M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406214/
https://www.ncbi.nlm.nih.gov/pubmed/28055307
http://dx.doi.org/10.1080/15592294.2016.1276680
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author Crary-Dooley, Florence K.
Tam, Mitchell E.
Dunaway, Keith W.
Hertz-Picciotto, Irva
Schmidt, Rebecca J.
LaSalle, Janine M.
author_facet Crary-Dooley, Florence K.
Tam, Mitchell E.
Dunaway, Keith W.
Hertz-Picciotto, Irva
Schmidt, Rebecca J.
LaSalle, Janine M.
author_sort Crary-Dooley, Florence K.
collection PubMed
description DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies.
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spelling pubmed-54062142017-05-05 A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies Crary-Dooley, Florence K. Tam, Mitchell E. Dunaway, Keith W. Hertz-Picciotto, Irva Schmidt, Rebecca J. LaSalle, Janine M. Epigenetics Research Paper DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies. Taylor & Francis 2017-01-05 /pmc/articles/PMC5406214/ /pubmed/28055307 http://dx.doi.org/10.1080/15592294.2016.1276680 Text en © 2017 The Author(s). Published with license by Taylor & Francis Group, LLC http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.
spellingShingle Research Paper
Crary-Dooley, Florence K.
Tam, Mitchell E.
Dunaway, Keith W.
Hertz-Picciotto, Irva
Schmidt, Rebecca J.
LaSalle, Janine M.
A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title_full A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title_fullStr A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title_full_unstemmed A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title_short A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
title_sort comparison of existing global dna methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406214/
https://www.ncbi.nlm.nih.gov/pubmed/28055307
http://dx.doi.org/10.1080/15592294.2016.1276680
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