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AmpliconDesign: an interactive web server for the design of high-throughput targeted DNA methylation assays

Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-through...

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Bibliographic Details
Main Authors: Schönung, Maximilian (Author) , Hess, Jana (Author) , Bawidamann, Pascal (Author) , Stäble, Sina (Author) , Hey, Joschka (Author) , Langstein, Jens (Author) , Assenov, Yassen (Author) , Weichenhan, Dieter (Author) , Lutsik, Pavlo (Author) , Lipka, Daniel (Author)
Format: Article (Journal)
Language:English
Published: 2021
In: Epigenetics
Year: 2021, Volume: 16, Issue: 9, Pages: 933-939
ISSN:1559-2308
DOI:10.1080/15592294.2020.1834921
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1080/15592294.2020.1834921
Verlag, kostenfrei, Volltext: https://www.tandfonline.com/doi/full/10.1080/15592294.2020.1834921
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Author Notes:Maximilian Schönung, Jana Hess, Pascal Bawidamann, Sina Stäble, Joschka Hey, Jens Langstein, Yassen Assenov, Dieter Weichenhan, Pavlo Lutsik, and Daniel B. Lipka
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Summary:Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq) or EpiTYPER MassArray. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq.
Item Description:"Published online: 24 Oct 2020".- Artikelvorschau
Gesehen am 15.08.2024
Physical Description:Online Resource
ISSN:1559-2308
DOI:10.1080/15592294.2020.1834921

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