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) 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.

摘要

基于亚硫酸氢盐处理的基因组 DNA (BT-DNA) 的 DNA 甲基化模式靶向分析被认为是表观遗传生物标志物开发的金标准。现有的软件工具有助于引物设计、引物质量控制或引物定位的可视化。然而，BT-DNA 扩增引物的高通量设计受到现有工具通量和功能的限制，需要用户手动重复执行特定任务。因此，为 BT-DNA 设计 PCR 引物仍然是一个繁琐且耗时的过程。为了弥补这一差距，我们开发了AmpliconDesign, 一个网络服务器，为设计和分析基于 BT-DNA 的靶向 DNA 甲基化研究提供可扩展且用户友好的平台，例如深度扩增子亚硫酸氢盐测序 (ampBS-seq) 或 EpiTYPER MassArray。Web 服务器的核心功能包括高通量引物设计和基于计算机亚硫酸氢盐转换的 DNA 序列的结合位点验证、 EpiTYPER MassArray 的片段模式预测、交互式质量控制以及 ampBS-seq 的简化分析工作流程。