期刊
EPIGENETICS
卷 16, 期 9, 页码 933-939出版社
TAYLOR & FRANCIS INC
DOI: 10.1080/15592294.2020.1834921
关键词
DNA methylation; bisulfite sequencing; targeted sequencing; massarray; epityper; primer design; analysis pipeline
资金
- Deutsche Krebshilfe [DKH project] [70112574]
- Deutsche Forschungsgemeinschaft [FOR2674, LI 2492/3-1]
- AMPro Project of the Helmholtz Association [ZT00026]
AmpliconDesign is a webserver that provides scalable and user-friendly platform for designing and analyzing targeted DNA methylation studies based on bisulfite-treated genomic DNA (BT-DNA). Core functionalities include high-throughput primer design and binding site validation, prediction of fragmentation patterns for EpiTYPER MassArray, interactive quality control, and a streamlined analysis workflow for deep amplicon bisulfite sequencing (ampBS-seq).
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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