Epigenetic Age Monitoring is a Different Paradigm from Genetic Testing
The study of DNA methylation is very different from genetic testing, in large part because your epigenetics are modifiable, enabling you to determine if your health is improving over time. Age is the strongest risk factor for most major killers today (cancer, cardiovascular disease, dementia), and biological age based on epigenetic aging clocks is a much better predictor than your actual age.
Physicians and treatment developers in U.S. and internationally (thousands of organizations) and patients (millions) routinely try new interventions or experimental treatments, despite the absence of means to rigorously ascertain their long-term efficacy. Until recently biomarkers simply were not available to readily and reliably determine which treatments work and which do not. As a result, the healthcare field today is littered with promising yet fragmented and piecemeal experimental interventions and diagnostics.
Unlike many other clinical biomarkers or tests, epigenetic age monitoring is also not “simply a number”. Most individual clinical biomarkers are too variable and they oversimply the biology of aging. Epigenetic aging clocks on the other hand are robust composite measures, more akin to composite measures of frailty. However, unlike frailty measures, epigenetic aging can be monitored reliably throughout lifespan. Due to this, for the first time, reliable monitoring of biological aging is becoming possible at far younger ages. This holds much promise as it means that new preventive medicine treatments could be started and reliably tested early in life, helping to delay or prevent significant functional decline and onset of major age-related diseases.
Which Epigenetic Clock Should I Use for Human Studies?
2019 GrimAge Clock – Developed in Steve Horvath’s lab at UCLA by Ake Lu. This clock strongly predicts future healthspan and lifespan and performs very well across large diverse populations. GrimAge also performs well for predicting functional decline and onset of major age-related diseases, including heart disease, cancer onset, multi-modal measures of brain health, kidney disease, fatty liver, respiratory function, and more (Lu 2019, Hillary 2018, Hillary 2020, McCrory 2020).
2018 PhenoAge Clock – Developed in Steve Horvath’s lab at UCLA by Morgan Levine. This clock enables prediction of healthspan and lifespan and has an analogous measure that can be used based on plasma biomarkers.
2013 Horvath Pan-Tissue Clock – This clock is predictor of chronological age that is accurate across all human tissues. Because it is representative of the aging process across all tissues, it may represent a more fundamental measure of biological aging than clocks that are only trained on blood samples or saliva samples.
2018 Skin & Blood Age Clock – Developed by Steve Horvath with Ken Raj. This clock is a highly accurate predictor of chronological age, and as the name suggests, is based on use of both skin and blood cells. It is effective for in vitro cell culture studies and also can be used with buccal (cheek) swabs.
There are important differences between these clocks. Some like GrimAge are designed specifically for predicting mortality and perform remarkably well for predicting a wide variety of health outcomes. However, to answer the question about which clock you should use, the answer is all of them! All of these epigenetic clocks can be measured conveniently using the same Illumina EPIC methylation array, i.e. with no added cost or inconvenience. When it comes to understanding the aging process, it’s best to analyze in as many dimensions as possible.
I Want to Study DNA Methylation & Epigenetic Clocks. Where Do I Start?
Sample Collection
Epigenetic clocks are based on many types of samples, however the best validated epigenetic aging clocks and most robust predictors of mortality require blood samples to be collected. For a clinical trial, or testing of a new intervention, it is recommended to include at least two baseline samples prior to treatment, as well as two sample after treatment. Whole blood EDTA can be collected through venous or capillary collection, and buffy coat or PBMCs can be isolated and stored for later testing. For testing of interventions, ideally samples will be batched and processed together at the end of the study, however an interim analysis may also be performed if desired by the study coordinators. The Clock Foundation can assist with custom study designs and sample collection methods.
Raw Methylation Testing
Raw methylation analysis methods require dedicated infrastructure but they can be performed in many different laboratories. Proven Illumina array technology and platforms are used enabling low technical variance, routine processing, and the ability to scale applications to meet the needs of large studies. If desirable, the process can be overseen and managed by the Clock Foundation. For human samples, the Illumina Infinium MethylationEPIC BeadChip array enables the quantitative interrogation of more than 850,000 CpG methylation loci per sample spread across the genome, including calculation of the most widely accepted and validated epigenetic aging clocks described above.
Results & Interpretation
For researchers, many different software packages are available to assist in analysis of raw methylation data including mainly in R. Raw methylation data (IDAT files) can be submitted to the Clock Foundation or the Horvath lab (http://dnamage.genetics.ucla.edu/) for routine analysis of epigenetic clocks.
Use of the EPIC array for human samples enables ready calculation of the most informative epigenetic aging clocks including GrimAge, PhenoAge, the original pan-tissue Horvath clock, and newer measures such as the Skin & Blood Age clock. Data analysis through the Clock Foundation enables many additional quality control measures to be performed as well as calculation of the latest DNA methylation based surrogate measures, e.g. predicting status of the immune system, plasma biomarkers, and more.