Journal Article

Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing

Sun, Yuan, Duan, Shumeng, Chen, Qingwang, Zhang, Yujing, Zhang, Zhihong, Shi, Leming, Dong, Lianhua, Zhang, Yuanfeng, Wang, Jianxin, Liu, Yaqing, Ni, Peng, Ren, Luyao, Qiu, Fujun, Yu, Ying, Zheng, Yuanting, Guo, Xiaorou, Ma, Ruiwen, Xu, Weihong, Hou, Wanwan, Li, Bingsi, Ma, Yu, Fang, Xiang, Li, Jinming, Zhang, Rui, He, Bo

2025

Overview

The lack of quantitative methylation reference datasets (ground truth) and cross-laboratory reproducibility assessment hinders clinical translation of epigenome-wide sequencing technologies. Using certified Quartet DNA reference materials, here we generate 108 epigenome-sequencing datasets across three mainstream protocols (whole-genome bisulfite sequencing, enzymatic methyl-seq, and TET-assisted pyridine borane sequencing) with triplicates per sample across laboratories. We observe strand-specific methylation biases across all protocols and libraries. Cross-laboratory reproducibility analyses reveal high quantitative methylation levels agreement (mean Pearson correlation coefficient (PCC) = 0.96) but low detection concordance (mean Jaccard index = 0.36). Using consensus voting, we construct genome-wide quantitative methylation reference datasets serving as ground truth for proficiency testing. Key technical parameters–including mean CpG depth, coverage, and strand consistency–correlate strongly with reference-dependent quality metrics (recall, PCC, and RMSE). Collectively, these resources establish foundational standards for benchmarking emerging epigenomic technologies and analytical pipelines, enabling robust, standardized quality control in research and clinical applications. Quality control for epigenomic datasets requires robust ground truths. Here, authors generate genome-wide quantitative methylation reference datasets from the publicly available Quartet DNA reference materials, which could serve as a resource for the standardised benchmarking of emerging technologies.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45 / 45/23 / 45/61 / 631/114/2416 / 631/1647/2210/2213 / 631/208/177 / 631/61/514/1948 / Accuracy / Benchmarking / Benchmarks / Bias / Bisulfite / Correlation coefficient / Correlation coefficients / CpG islands / CpG Islands - genetics / Datasets / Deoxyribonucleic acid / DNA / DNA - genetics / DNA methylation / DNA Methylation - genetics / Epigenome - genetics / Epigenomics - methods / Epigenomics - standards / Gene sequencing / Genomes / High-Throughput Nucleotide Sequencing - methods / Humanities and Social Sciences / Humans / Laboratories / Methylation / multidisciplinary / Quality control / Reference materials / Reference Standards / Reproducibility / Reproducibility of Results / Robust control / Science / Science (multidisciplinary) / Sequence Analysis, DNA - methods / Sequence Analysis, DNA - standards