亚硫酸氢盐测序
计算生物学
DNA甲基化
生物
照明菌甲基化试验
甲基化
DNA测序
CpG站点
基因组
遗传学
DNA
基因
基因表达
作者
Xin Liu,Yu Pang,Jianguo Shan,Yunfei Wang,Yanhua Zheng,Yuhang Xue,Xue‐Rong Zhou,Wenjun Wang,Yanlai Sun,Xiaojing Yan,Jiantao Shi,Xiaoxue Wang,Hongcang Gu,Fan Zhang
摘要
Abstract Deoxyribonucleic acid (DNA) methylation plays a key role in gene regulation and is critical for development and human disease. Techniques such as whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) allow DNA methylation analysis at the genome scale, with Illumina NovaSeq 6000 and MGI Tech DNBSEQ-T7 being popular due to their efficiency and affordability. However, detailed comparative studies of their performance are not available. In this study, we constructed 60 WGBS and RRBS libraries for two platforms using different types of clinical samples and generated approximately 2.8 terabases of sequencing data. We systematically compared quality control metrics, genomic coverage, CpG methylation levels, intra- and interplatform correlations, and performance in detecting differentially methylated positions. Our results revealed that the DNBSEQ platform exhibited better raw read quality, although base quality recalibration indicated potential overestimation of base quality. The DNBSEQ platform also showed lower sequencing depth and less coverage uniformity in GC-rich regions than did the NovaSeq platform and tended to enrich methylated regions. Overall, both platforms demonstrated robust intra- and interplatform reproducibility for RRBS and WGBS, with NovaSeq performing better for WGBS, highlighting the importance of considering these factors when selecting a platform for bisulfite sequencing.
科研通智能强力驱动
Strongly Powered by AbleSci AI