血沉棕黄层、外周血单个核细胞及唾液样本中Infinium甲基化EPIC v1与EPIC v2之间的DNA甲基化年龄差异。

DNAm age differences between infinium methylationEPICv1 vs EPICv2 in buffy coat, PBMC, and saliva samples.

作者信息

Tay Jian Hua, Chew Yi Ern, Wang Weilan, Lim Zhi Meng, Guan Lihuan, Dorajoo Rajkumar, Kennedy Brian K, Brooke Robert, Gordevicius Juozas, Horvath Steve, Sandalova Elena, Maier Andrea B

机构信息

Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore.

NUS Academy for Healthy Longevity, National University of Singapore, 10 Medical Drive, 117597, Singapore, Singapore.

出版信息

Commun Biol. 2025 Apr 23;8(1):654. doi: 10.1038/s42003-025-08021-y.

DOI:10.1038/s42003-025-08021-y

PMID:40269264

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12019316/

Abstract

This study aims to evaluate differences between Infinium MethylationEPIC (EPICv1) and Infinium MethylationEPICv2 (EPICv2) arrays in estimating DNAm age with eleven DNAm clocks using buffy coat, peripheral blood mononuclear cell (PBMC), and saliva from 16 healthy middle-aged individuals. DNAm ages were estimated using six principal component-based (PC) clocks (PCHorvath1, PCHorvath2, PCHannum, PCPhenoAge, PCGrimAge, and PCDNAmTL) and five non-PC clocks (DunedinPACE, DNAmFit, YingCausAge, YingAdaptAge, and YingDamAge) across all biological samples. Agreement between arrays was assessed using Spearman correlation, Bland-Altman plots, and Wilcoxon Signed-Rank test. The 16 individuals with median age of 48 [43.5;53.8] years, were predominantly female, Chinese and non-smokers. High correlations (ρ > 0.8) were observed between EPICv1 and EPICv2 except for DunedinPACE, YingDamAge and YingAdaptAge. PC-based clocks showed lower systematic bias (MAPE:0.118-8.98%) compared to non-PC-based clocks (MAPE:5.31-21.2%). Saliva samples demonstrated greatest variability between arrays. EPICv2 introduces systematic biases especially in non-PC-based clocks and between different biological samples.

摘要

本研究旨在评估Illumina甲基化EPIC（EPICv1）芯片与Illumina甲基化EPICv2（EPICv2）芯片在使用11种DNA甲基化时钟从16名健康中年个体的血沉棕黄层、外周血单核细胞（PBMC）和唾液中估计DNA甲基化年龄方面的差异。使用六种基于主成分（PC）的时钟（PCHorvath1、PCHorvath2、PCHannum、PCPhenoAge、PCGrimAge和PCDNAmTL）和五种非PC时钟（达尼丁PACE、DNAmFit、YingCausAge、YingAdaptAge和YingDamAge）对所有生物样本估计DNA甲基化年龄。使用斯皮尔曼相关性、布兰德-奥特曼图和威尔科克森符号秩检验评估芯片之间的一致性。这16名个体的年龄中位数为48[43.5；53.8]岁，主要为女性、中国人且不吸烟。除达尼丁PACE、YingDamAge和YingAdaptAge外，EPICv1和EPICv2之间观察到高度相关性（ρ>0.8）。与非基于PC的时钟（平均绝对百分比误差：5.31-21.2%）相比，基于PC的时钟显示出较低的系统偏差（平均绝对百分比误差：0.118-8.98%）。唾液样本在芯片之间表现出最大的变异性。EPICv2引入了系统偏差，尤其是在非基于PC的时钟以及不同生物样本之间。