Ultra-cheap and scalable epigenetic age predictions with TIME-Seq

Epigenetic "clocks" based on DNA methylation (DNAme) are the most robust and widely employed aging biomarker. They have been built for numerous species and reflect gold-standard interventions that extend lifespan. However, conventional methods for measuring epigenetic clocks are expensive and low-throughput. Here, we describe Tagmentation-based Indexing for Methylation Sequencing (TIME-Seq) for ultra-cheap and scalable targeted methylation sequencing of epigenetic clocks and other DNAme biomarkers. Using TIME-Seq, we built and validated inexpensive epigenetic clocks based on genomic and ribosomal DNAme in hundreds of mice and human samples. We also discover it is possible to accurately predict age from extremely low-cost shallow sequencing (e.g., 10,000 reads) of TIME-Seq libraries using scAge , a probabilistic age-prediction algorithm originally applied to single cells. Together, these methods reduce the cost of DNAme biomarker analysis by more than two orders of magnitude, thereby expanding and democratizing their use in aging research, clinical trials, and disease diagnosis. ### Competing Interest Statement P.T.G. and D.A.S. are named inventors on a patent application related to TIME-Seq methods filed by Harvard Medical School and licensed to Longevity Sciences. P.T.G. is an equity owner of Longevity Sciences. D.A.S is a consultant to, inventor of patents licensed to, and in some cases board member and investor in MetroBiotech, Cohbar, Life Biosciences and affiliates, Zymo, EdenRoc Sciences and affiliates, Alterity, InsideTracker, Immetas, Segterra, and Galilei Biosciences. He is also an inventor on patent applications licensed to Bayer Crops, Merck KGaA, and Elysium Health. Additional info at sinclair.hms.harvard.edu/david-sinclairs-affiliations. A.T., C.K, V.N.G. are named inventors on a patent application related to scAge filed by Brigham and Women's Hospital. S.J.M, A.E.K, M.R.M and J.R.M. have nothing to disclose.