Abstract
BackgroundWhole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genome-wide DNA methylation at single nucleotide resolution. However, the applications of WGBS are limited by low accuracy resulting from bisulfite-induced damage on DNA fragments. Although many computer programs have been developed for accurate detecting, most of the programs have barely succeeded in improving either quantity or quality of the methylation results. To improve both, we attempted to develop a novel integration of most widely used bisulfite-read mappers: Bismark, BSMAP, and BS-seeker2.ResultsA comprehensive analysis of the three mappers revealed that the mapping results of the mappers were mutually complementary under diverse read conditions. Therefore, we sought to integrate the characteristics of the mappers by scoring them to gain robustness against artifacts. As a result, the integration significantly increased detection accuracy compared with the individual mappers. In addition, the amount of detected cytosine was higher than that by Bismark. Furthermore, the integration successfully reduced the fluctuation of detection accuracy induced by read conditions. We applied the integration to real WGBS samples and succeeded in classifying the samples according to the originated tissues by both CpG and CpH methylation patterns.ConclusionsIn this study, we improved both quality and quantity of methylation results from WGBS data by integrating the mapping results of three bisulfite-read mappers. Also, we succeeded in combining and comparing WGBS samples by reducing the effects of read heterogeneity on methylation detection. This study contributes to DNA methylation researches by improving efficiency of methylation detection from WGBS data and facilitating the comprehensive analysis of public WGBS data.
Highlights
Whole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genomewide DNA methylation at single nucleotide resolution
Researchers have focused on methylation at CpG sites and found that differentially methylated regions (DMRs) among various cells are involved to cell-specific functions, aging and deceases [2,3,4,5]
We mapped the reads by Bismark, BSMAP, and BS-seeker2 and evaluated the performances of the three mappers with respect to mapping rate and accuracy; the mapping rate is the portion of mapped read number over total read number, whereas the mapping accuracy is the portion of correctly mapped read number over mapped read number
Summary
Whole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genomewide DNA methylation at single nucleotide resolution. Many computer programs have been developed for accurate detecting, most of the programs have barely succeeded in improving either quantity or quality of the methylation results. We attempted to develop a novel integration of most widely used bisulfite-read mappers: Bismark, BSMAP, and BS-seeker. To analyze the methylation modifications, highthroughput methods coupled with microarray and nextgeneration sequencing have been widely used. Bisulfite microarray is a specially designed genotyping microarray combined with bisulfite treatment. This method is a useful strategy for targeted DNA methylation analyses, it is not suitable for genome-scale studies due to low genome coverage; only 0.8% of CpGs and 0.02% of CpHs have been covered in the newest version [10]
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