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Updated: Jun 13, 2025
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Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
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Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies
Xin Liu1,2, Yu Pang3, Junqi Shan4
1Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China.
Briefings in Bioinformatics
|September 10, 2024
Summary
Comparing DNA methylation sequencing, the MGI DNBSEQ-T7 showed better raw reads but lower coverage uniformity than Illumina NovaSeq 6000. NovaSeq performed better for whole-genome bisulfite sequencing (WGBS).
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- DNA methylation is crucial for gene regulation, development, and disease.
- Whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are key for genome-scale DNA methylation analysis.
- Illumina NovaSeq 6000 and MGI DNBSEQ-T7 are popular platforms, but direct performance comparisons are lacking.
Purpose of the Study:
- To systematically compare the performance of Illumina NovaSeq 6000 and MGI DNBSEQ-T7 platforms for WGBS and RRBS.
- To evaluate key metrics including read quality, genomic coverage, methylation levels, reproducibility, and differential methylation detection.
- To provide data-driven insights for selecting appropriate bisulfite sequencing platforms.
Main Methods:
- Construction of 60 WGBS and RRBS libraries across both platforms using diverse clinical samples.
- Generation of approximately 2.8 terabases of sequencing data.
- Comprehensive analysis of quality control metrics, genomic coverage, CpG methylation, inter-platform correlations, and differential methylation analysis.
Main Results:
- DNBSEQ-T7 demonstrated superior raw read quality, but potential base quality overestimation was noted.
- NovaSeq 6000 provided higher sequencing depth and more uniform coverage, especially in GC-rich regions.
- Both platforms showed high reproducibility for WGBS and RRBS, with NovaSeq excelling in WGBS performance.
- DNBSEQ-T7 tended to enrich methylated regions, impacting comparative analysis.
Conclusions:
- Both NovaSeq 6000 and DNBSEQ-T7 platforms offer robust performance for DNA methylation analysis via WGBS and RRBS.
- Platform selection should consider specific experimental needs, particularly regarding coverage uniformity and GC-rich region analysis.
- NovaSeq 6000 may be preferable for WGBS applications requiring comprehensive coverage, while DNBSEQ-T7 offers advantages in raw read quality.
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