期刊
PEERJ
卷 9, 期 -, 页码 -出版社
PEERJ INC
DOI: 10.7717/peerj.10762
关键词
DNA methylation; Illumina EPIC array; Bisulfite based amplicon sequencing
资金
- University of Otago Research Grant
- Health Research Council of New Zealand [16/600]
- Canterbury Medical Research Foundation
The study found that the bisulfite-based amplicon sequencing (BSAS) can effectively validate EPIC array data, but each locus must be compared on an individual basis. BSAS has advantages over the EPIC array in that it can discover novel CpG sites and differentially methylated regions that may not be present on the array.
The Illumina Infinium (R) MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are often used for hypothesis generation or pilot studies, the natural conclusion to which is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system at some loci. However, BSAS correlated less well with EPIC array data in some instances, and most notably, when the magnitude of change via EPIC array was greater than 5%. Therefore, our data suggests that BSAS can be used to validate EPIC array data, but each locus must be compared on an individual basis, before being taken forward into large scale screening. Further, BSAS does offer advantages compared to the probe-based EPIC array; BSAS amplifies a region of the genome (similar to 500 bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据