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EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies

DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a co...

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Autores principales: Krainer, Julie, Weinhäusel, Andreas, Hanak, Karel, Pulverer, Walter, Özen, Seza, Vierlinger, Klemens, Pabinger, Stephan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602470/
https://www.ncbi.nlm.nih.gov/pubmed/31106358
http://dx.doi.org/10.1093/nar/gkz398
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author Krainer, Julie
Weinhäusel, Andreas
Hanak, Karel
Pulverer, Walter
Özen, Seza
Vierlinger, Klemens
Pabinger, Stephan
author_facet Krainer, Julie
Weinhäusel, Andreas
Hanak, Karel
Pulverer, Walter
Özen, Seza
Vierlinger, Klemens
Pabinger, Stephan
author_sort Krainer, Julie
collection PubMed
description DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/.
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spelling pubmed-66024702019-07-05 EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies Krainer, Julie Weinhäusel, Andreas Hanak, Karel Pulverer, Walter Özen, Seza Vierlinger, Klemens Pabinger, Stephan Nucleic Acids Res Web Server Issue DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application for the analysis of targeted sequencing data that additionally allows the integration of array-based methylation results. The tool can handle multiple targets as well as multiple sequencing files in parallel and covers the complete data analysis workflow from calculation of quality metrics to methylation calling and interactive result presentation. The graphical user interface offers an unprecedented way to interpret TBS data alone or in combination with array-based methylation studies. Together with the computation of target-specific epialleles it is useful in validation, research, and routine diagnostic environments. EPIC-TABSAT is freely accessible to all users at https://tabsat.ait.ac.at/. Oxford University Press 2019-07-02 2019-05-20 /pmc/articles/PMC6602470/ /pubmed/31106358 http://dx.doi.org/10.1093/nar/gkz398 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Krainer, Julie
Weinhäusel, Andreas
Hanak, Karel
Pulverer, Walter
Özen, Seza
Vierlinger, Klemens
Pabinger, Stephan
EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title_full EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title_fullStr EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title_full_unstemmed EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title_short EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
title_sort epic-tabsat: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602470/
https://www.ncbi.nlm.nih.gov/pubmed/31106358
http://dx.doi.org/10.1093/nar/gkz398
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