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

Schoenung, M.; Hess, J.; Bawidamann, P.; Staeble, S.; Hey, J.; Langstein, J.; Assenov, Y.; Weichenhan, D.; Lutsik, P.; Lipka, D. B.

doi:10.1101/2020.05.23.043448

bioRxiv · 10.1101/2020.05.23.043448

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

Schoenung, M.·Hess, J.·Bawidamann, P.·Staeble, S.·Hey, J.·Langstein, J.·Assenov, Y.·Weichenhan, D.·Lutsik, P.·Lipka, D. B.

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Abstract

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), EpiTYPER MassArray, or pyrosequencing. 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. Availability and ImplementationThe AmpliconDesign webserver is freely available online at: https://amplicondesign.dkfz.de/. AmpliconDesign has been implemented using the R Shiny framework (Chang et al., 2018). The source code is publicly available under the GNU General Public License v3.0 (https://github.com/MaxSchoenung/AmpliconDesign). ContactDaniel B. Lipka (d.lipka@dkfz.de) & Maximilian Schonung (m.schoenung@dkfz.de)

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Schoenung, M., Hess, J., Bawidamann, P., Staeble, S., Hey, J., Langstein, J., Assenov, Y., Weichenhan, D., Lutsik, P., Lipka, D. B.. 2020-05-27. AmpliconDesign - An interactive web server for the design of high-throughput targeted DNA methylation assays. https://doi.org/10.1101/2020.05.23.043448

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