First-Generation Multi-Tissue Epigenetic Clocks
The next major milestone in the field of epigenetic aging was the development of multi-tissue epigenetic clocks. Teschendorff et al. , 201070 described a set of 69 CpGs with age-associated increases in methylation in both blood and epithelial tissue, demonstrating a pan-tissue signature of aging. Koch et al. used Illumina 27K data from four different tissue types (Table 2 ) to develop a multi-tissue clock with mean AE of 11 years71. This clock was quickly followed by two multi-tissue clocks developed by Horvath et al. : the pan-tissue53 and Skin & Blood clocks68.
Since its development, the pan-tissue Horvath clock53 has been the backbone of epigenetic aging studies. It was developed using 8,000 samples (from 51 healthy tissues) of Illumina 27K and 450K data, divided into training and validation cohorts. Elastic net with 10-fold cross validation was performed on the DNAm values of 21,369 CpG sites with a log- transformed version of CA as the dependent variable. This regression yielded a clock of 353 CpG sites with a median AE of 3.6 years in the validation cohort53. The pan-tissue Horvath clock has been repeatedly validated and has shown high accuracy, even when applied to data from the Illumina 850K EPIC array (missing 19/353 CpG sites)72, and robustness to changes in cell type composition61. However, the pan-tissue clock underestimates epigenetic age in older individuals73. In addition, while this clock is more accurate in pediatric samples than the Hannum clock61, it was predominantly developed using adult samples and may not contain the CpG sites associated with early developmental processes.
The Skin & Blood epigenetic clock is another multi-tissue clock developed by Horvath et al . It aims to improve the accuracy of the Horvath pan-tissue clock in fibroblasts68. The Skin & Blood clock consists of 391 CpG sites and was developed through a similar process as the pan-tissue clock, but using Illumina 450K or 850K array data from buccal cells, fibroblasts, keratinocytes, endothelial cells, blood, and saliva68. In addition to better performance in fibroblasts, this clock is more accurate than both the Horvath pan-tissue clock and Hannum clock in blood samples (median AE=2.5 years vs. 3.7 and 5.1 years)68.