Whole genome bisulphite sequencing using the Illumina X system [Illumina HumanMethylation450 BeadChip]

While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads. NA12878 and IMR90 cell lines assayed with Illumina Infinium MethylationEPIC BeadChip for comparison against whole genome bisulphite sequencing using BS-tagging protocol

尽管Illumina X技术已大幅降低全基因组测序的成本，但其应用于亚硫酸氢盐测序（bisulphite sequencing）时却并非易事。本研究详述了一套文库制备与测序方案的优化策略，该策略可最大化测序产出量与测序质量，同时阐明了如何消除此前未被识别的、影响数百分比亚硫酸氢盐测序读段（reads）的测序伪影。本研究针对NA12878与IMR90细胞系，采用Illumina Infinium MethylationEPIC BeadChip进行检测，以与采用BS-tagging协议的全基因组亚硫酸氢盐测序结果开展对照分析。