期刊
STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY
卷 15, 期 1, 页码 69-81出版社
WALTER DE GRUYTER GMBH
DOI: 10.1515/sagmb-2015-0077
关键词
bisulfite sequencing; cancer; differential methylation; hidden Markov model
资金
- Dr. Shuying Sun's start-up funds by Texas State University
- Research Enhancement Program by Texas State University
DNA methylation is an epigenetic modification involved in organism development and cellular differentiation. Identifying differential methylations can help to study genomic regions associated with diseases. Differential methylation studies on single-CG resolution have become possible with the bisulfite sequencing (BS) technology. However, there is still a lack of efficient statistical methods for identifying differentially methylated (DM) regions in BS data. We have developed a new approach named HMM-DM to detect DM regions between two biological conditions using BS data. This new approach first uses a hidden Markov model (HMM) to identify DM CG sites accounting for spatial correlation across CG sites and variation across samples, and then summarizes identified sites into regions. We demonstrate through a simulation study that our approach has a superior performance compared to BSmooth. We also illustrate the application of HMM-DM using a real breast cancer dataset.
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