Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies
文献类型：期刊论文
| 作者 | Liu, Xin1,2; Pang, Yu3; Shan, Junqi4; Wang, Yunfei5; Zheng, Yanhua6; Xue, Yuhang6; Zhou, Xuerong6; Wang, Wenjun5; Sun, Yanlai4; Yan, Xiaojing6 |
| 刊名 | BRIEFINGS IN BIOINFORMATICS
 |
| 出版日期 | 2024-09-10 |
| 卷号 | 25 |
| 关键词 | sequencing performance DNB Illumina coverage uniformity methylation |
| ISSN号 | 1467-5463 |
| DOI | 10.1093/bib/bbae440 |
| 通讯作者 | Wang, Xiaoxue(xx-wang119@hotmail.com) ; Gu, Hongcang(gu_hongcang@cmpt.ac.cn) ; Zhang, Fan(fzhang@cmpt.ac.cn) |
| 英文摘要 | 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. |
| WOS关键词 | QUALITY-CONTROL ; PLATFORMS ; PERFORMANCE ; FRAMEWORK ; TOOLS |
| 资助项目 | CASHIPS |
| WOS研究方向 | Biochemistry & Molecular Biology ; Mathematical & Computational Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001308963500001 |
| 出版者 | OXFORD UNIV PRESS |
| 资助机构 | CASHIPS |
| 源URL | [http://ir.hfcas.ac.cn:8080/handle/334002/135170]  |
| 专题 | 中国科学院合肥物质科学研究院 |
| 通讯作者 | Wang, Xiaoxue; Gu, Hongcang; Zhang, Fan |
| 作者单位 | 1.Chinese Acad Sci, Inst Hlth & Med Technol, Hefei Inst Phys Sci, Anhui Prov Key Lab Med Phys & Technol, Hefei 230031, Anhui, Peoples R China 2.Chinese Acad Sci, Hefei Canc Hosp, Hefei 230031, Anhui, Peoples R China 3.Capital Med Univ, Beijing Chest Hosp, Beijing TB & Thorac Tumor Res Inst, Dept Bacteriol & Immunol, Beijing 101149, Peoples R China 4.Shandong First Med Univ & Shandong Acad Med Sci, Shandong Canc Hosp & Inst, Dept Gastrointestinal Surg, Jinan 250117, Shandong, Peoples R China 5.Hangzhou ShengTing Biotech Co Ltd, Hangzhou 310018, Zhejiang, Peoples R China 6.China Med Univ, Hosp 1, Dept Hematol, Shenyang 110001, Liaoning, Peoples R China 7.Chinese Acad Sci, Shanghai Inst Biochem & Cell Biol, Ctr Excellence Mol Cell Sci, State Key Lab Mol Biol, Shanghai 200031, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Xin,Pang, Yu,Shan, Junqi,et al. Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies[J]. BRIEFINGS IN BIOINFORMATICS,2024,25. |
| APA | Liu, Xin.,Pang, Yu.,Shan, Junqi.,Wang, Yunfei.,Zheng, Yanhua.,...&Zhang, Fan.(2024).Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies.BRIEFINGS IN BIOINFORMATICS,25. |
| MLA | Liu, Xin,et al."Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies".BRIEFINGS IN BIOINFORMATICS 25(2024). |
入库方式： OAI收割
来源：合肥物质科学研究院
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