Epigenetic ageing clocks: statistical methods and emerging computational challenges

Baker, G. T. 3rd & Sprott, R. L. Biomarkers of aging. Exp. Gerontol. 23, 223–239 (1988).

Article  PubMed  Google Scholar 

Kirkwood, T. B. Understanding the odd science of aging. Cell 120, 437–447 (2005).

Article  PubMed  Google Scholar 

Kirkwood, T. B. L. & Cooper, C. L. Wellbeing in Later Life, Vol. IV (Wiley, 2014).

Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013). Landmark paper presenting the first pan-tissue epigenetic clock for chronological age, while also demonstrating its relevance for estimation of biological age.

Article  PubMed  PubMed Central  Google Scholar 

Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018).

Article  PubMed  Google Scholar 

Rutledge, J., Oh, H. & Wyss-Coray, T. Measuring biological age using omics data. Nat. Rev. Genet. 23, 715–727 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Lu, Y. et al. Reprogramming to recover youthful epigenetic information and restore vision. Nature 588, 124–129 (2020). A landmark paper showing how epigenetic reprogramming can rejuvenate cells in vivo.

Article  PubMed  PubMed Central  Google Scholar 

Beyret, E., Martinez Redondo, P., Platero Luengo, A. & Izpisua Belmonte, J. C. Elixir of life: thwarting aging with regenerative reprogramming. Circ. Res. 122, 128–141 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Yang, J. H. et al. Loss of epigenetic information as a cause of mammalian aging. Cell 187, 1312–1313 (2024).

Article  PubMed  Google Scholar 

Zhang, W., Qu, J., Liu, G. H. & Belmonte, J. C. I. The ageing epigenome and its rejuvenation. Nat. Rev. Mol. Cell Biol. 21, 137–150 (2020).

Article  PubMed  Google Scholar 

Bell, C. G. et al. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 20, 249 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010–1022 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Bocklandt, S. et al. Epigenetic predictor of age. PLoS One 6, e14821 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Zhang, Q. et al. Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing. Genome Med. 11, 54 (2019). This paper clearly demonstrates how increasing sample size can improve accuracy of a clock for chronological age.

Article  PubMed  PubMed Central  Google Scholar 

Hannum, G. et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell 49, 359–367 (2013).

Article  PubMed  Google Scholar 

Field, A. E. et al. DNA methylation clocks in aging: categories, causes, and consequences. Mol. Cell 71, 882–895 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Levine, M. E. et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging 10, 573–591 (2018). One of the first second-generation epigenetic clock papers, presenting a clock trained on clinical ageing biomarkers.

Article  PubMed  PubMed Central  Google Scholar 

Lu, A. T. et al. DNA methylation GrimAge version 2. Aging 14, 9484–9549 (2022).

PubMed  PubMed Central  Google Scholar 

Lu, A. T. et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging 11, 303–327 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Moran, S., Arribas, C. & Esteller, M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 8, 389–399 (2016).

Article  PubMed  Google Scholar 

Sandoval, J. et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6, 692–702 (2011).

Article  PubMed  Google Scholar 

Han, Y. et al. New targeted approaches for epigenetic age predictions. BMC Biol. 18, 71 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Griffin, P. T. et al. TIME-seq reduces time and cost of DNA methylation measurement for epigenetic clock construction. Nat. Aging 4, 261–274 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Paparazzo, E. et al. An ELOVL2-based epigenetic clock for forensic age prediction: a systematic review. Int. J. Mol. Sci. 24, 2254 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Seale, K., Teschendorff, A., Reiner, A. P., Voisin, S. & Eynon, N. A comprehensive map of the aging blood methylome in humans. Genome Biol. 25, 240 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Teschendorff, A. E. On epigenetic stochasticity, entropy and cancer risk. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 379, 20230054 (2024).

Article  Google Scholar 

Lu, A. T. et al. Universal DNA methylation age across mammalian tissues. Nat. Aging 3, 1144–1166 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Horvath, S., Zhang, J., Haghani, A., Lu, A. T. & Fei, Z. Fundamental equations linking methylation dynamics to maximum lifespan in mammals. Nat. Commun. 15, 8093 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Li, C. Z. et al. Epigenetic predictors of species maximum life span and other life-history traits in mammals. Sci. Adv. 10, eadm7273 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Bors, E. K. et al. An epigenetic clock to estimate the age of living beluga whales. Evol. Appl. 14, 1263–1273 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Marioni, R. E. et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol. 16, 25 (2015). This paper demonstrates how an epigenetic clock can be used to predict the future risk of all-cause mortality.

Article  PubMed  PubMed Central  Google Scholar 

Lu, A. T. et al. DNA methylation-based estimator of telomere length. Aging 11, 5895–5923 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Marioni, R. E. et al. The epigenetic clock and telomere length are independently associated with chronological age and mortality. Int. J. Epidemiol. 47, 356 (2018).

Article  PubMed  Google Scholar 

Yang, Z. et al. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol. 17, 205 (2016). This paper builds an epigenetic mitotic clock and shows that it correlates with literature/experimentally derived stem cell division rates.

Article  PubMed  PubMed Central  Google Scholar 

Zhou, W. et al. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat. Genet. 50, 591–602 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Youn, A. & Wang, S. The MiAge calculator: a DNA methylation-based mitotic age calculator of human tissue types. Epigenetics 13, 192–206 (2018).

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