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AmpliconDesign - 一个用于高通量靶向 DNA 甲基化检测设计的交互式网络服务器。

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

机构信息

Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.

Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.

出版信息

Epigenetics. 2021 Sep;16(9):933-939. doi: 10.1080/15592294.2020.1834921. Epub 2020 Oct 24.

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 , 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 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)的靶向 DNA 甲基化模式分析被认为是开发表观遗传生物标志物的金标准。现有的软件工具可用于引物设计、引物质量控制或引物定位的可视化。然而,BT-DNA 扩增用引物的高通量设计受到现有工具的通量和功能限制,这要求用户反复手动执行特定任务。因此,BT-DNA 的 PCR 引物设计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 ,这是一个基于 BT-DNA 的靶向 DNA 甲基化研究的设计和分析的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。该网络服务器的核心功能包括基于 Bisulfite 转化的 DNA 序列的高通量引物设计和结合位点验证、EpiTYPER MassArray 的片段化模式预测、交互式质量控制以及 ampBS-seq 的简化分析工作流程。

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