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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| Main Authors: | , , , , , , , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
2021
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| 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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| 520 | |a 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. | ||
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| 650 | 4 | |a DNA methylation | |
| 650 | 4 | |a epityper | |
| 650 | 4 | |a massarray | |
| 650 | 4 | |a primer design | |
| 650 | 4 | |a targeted sequencing | |
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