插补(统计学)
计算机科学
DNA甲基化
计算生物学
CpG站点
亚硫酸氢盐测序
纳米孔测序
数据挖掘
生物
DNA测序
遗传学
DNA
缺少数据
基因
机器学习
基因表达
作者
Miljana Tanić,Ismail Moghul,Simon Rodney,Pawan Dhami,Heli Vaikkinen,John C. Ambrose,James E. Barrett,Andrew Feber,Stephan Beck
标识
DOI:10.1038/s41587-022-01336-9
摘要
Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms-three hybridization capture-based (Agilent, Roche and Illumina) and two reduced-representation-based (Diagenode and NuGen)-across 11 samples. Two samples were also compared with whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed workflow complexity, on/off-target performance, coverage, accuracy and reproducibility. Although all platforms produced robust and reproducible data, major differences in the number and identity of the CpG sites covered make it difficult to compare datasets generated on different platforms. To overcome this limitation, we applied imputation and show that it improves interoperability from an average of 10.35% (0.8 million) to 97% (7.6 million) common CpG sites. Our study provides guidance on which TBS platform to use for different methylome features and offers an imputation-based harmonization solution that allows comparative, integrative analysis.
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