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-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 <b><i>AmpliconDesign</i></b>, 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 <i>in silico</i> 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.

基于亚硫酸氢盐处理基因组DNA（bisulfite-treated genomic DNA, BT-DNA）的DNA甲基化模式靶向分析，被视为表观遗传生物标志物开发的金标准。现有软件工具可实现引物设计、引物质量控制或引物定位可视化。然而，现有工具在通量与功能上存在局限，阻碍了BT-DNA扩增引物的高通量设计，使用者需反复手动执行特定任务。因此，针对BT-DNA的PCR引物设计仍是一项繁琐且耗时的工作。为填补这一研究空白，我们开发了AmpliconDesign，一款可扩展且用户友好的网络服务器，为基于BT-DNA的靶向DNA甲基化研究的设计与分析提供平台，例如深度扩增子亚硫酸氢盐测序（deep amplicon bisulfite sequencing, ampBS-seq）或EpiTYPER MassArray。该网络服务器的核心功能包括：基于计算机模拟（in silico）亚硫酸氢盐转化的DNA序列的高通量引物设计与结合位点验证、EpiTYPER MassArray的片段化模式预测、交互式质量控制，以及针对ampBS-seq的简化分析工作流。