MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research
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- 作者：Ram Vinay Pandey ; Pulverer Walter ; Rainer Kallmeyer…
- 关键词：PCR ; Primer design ; DNA methylation ; Methylation sensitive restriction enzyme ; High ; throughput ; CpG islands ; MSRE ; PCR
- 刊名：Clinical Epigenetics
- 出版年：2016
- 出版时间：December 2016
- 年：2016
- 卷：8
- 期：1
- 全文大小：2,569 KB
- 刊物主题：Human Genetics; Gene Function;
- 出版者：BioMed Central
- ISSN：1868-7083
文摘
Background Methylation-sensitive restriction enzymes—polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discovery studies provide many candidate regions for which the MSREqPCR approach can be very effective to confirm the findings. MSREqPCR provides high multiplexing capabilities also when starting with limited amount of DNA-like cfDNA to validate many targets in a time- and cost-effective manner. Multiplex design is challenging and cumbersome to define specific primers in an effective manner, and no suitable software tools are freely available for high-throughput primer design in a time-effective manner and to automatically annotate the resulting primers with known SNPs, CpG, repeats, and RefSeq genes. Therefore a robust, powerful, high-throughput, optimized, and methylation-specific primer design tool with great accuracy will be very useful.