Another excellent blog post by Josh Mitteldorf, A New Approach to Methylation Clocks, that curated the same study:
“The Levine/Horvath PhenoAge epigenetic clock was calibrated using a combination of metabolic factors that correlate with health, including inflammation, DNA transcription, DNA repair, and mitochondrial activity.
Evolution is not an engineer. Living things are not constructed out of parts that are separately optimized for exactly one function.
Every molecule has multiple functions. Every function is regulated by multiple pathways.
For clock technology, using individual CpGs for a starting point may not be optimal. We suspect that CpGs, like other biological entities, work together closely in teams.
CpGs on a team might vary slightly from one individual to the next. But the team has a function and an identity and a signature that is robust. We expect the team to function more consistently than any of its individual members.
The peer-reviewed version of her paper will be published shortly. Full details of algorithms will be available on GitHub, and script in the R programming language will be released for use of other researchers. If principal component analysis clocks correlate well with previously validated clocks but offer tighter uncertainties, we’ll know we’re on the right track.”
Best wishes for Josh to recover from a bike accident.