17 posts
A technical guide to DNA methylation testing — arrays versus whole-genome bisulfite sequencing versus nanopore, what the raw files look like, how to process them, and how much of the signal is real.
A homocysteine test measures total plasma homocysteine, a sensitive readout of B12/folate status, renal function, and methylation flux. Here is how to order it so the number is real, what to run alongside it, and how genotype fits in.
A technical read on GRAIL's methylation-based multi-cancer early detection test: the assay, sensitivity by stage, and why the NHS trial result matters.
A technical read on epigenetic clocks, blood-chemistry clocks, and survey-based 'bio age' calculators: what each one measures, how precise it is, and how to compute one yourself from your own data.
Two different tests share the name methylation testing: genotyping of one-carbon metabolism genes like MTHFR, and direct measurement of DNA methylation across the genome. This explains what each one measures, how to extract the data yourself, and where the interpretation stops.
A technical walkthrough of DNA methylation testing. Compares arrays, bisulfite sequencing and nanopore, then covers the IDAT pipeline and clocks.
Two very different assays are sold under the name 'methylation panel': a one-carbon biochemistry blood panel and a DNA methylation assay. Here is what each one measures, which files you get, and how to process them yourself.
Three different things get called a DNA clock. This page covers the epigenetic age clock, which assay to run and how to compute the score yourself.
There are two products sold as a 'methylation report': an MTHFR-style SNP panel from genotyping data, and a genome-wide DNA methylation array read out as epigenetic clocks. They measure different things, and only one of them is a measurement of your current biology.
DNA age tests read cytosine methylation at a few hundred CpG sites and regress it onto chronological age. Here is how the assay works, which clocks are worth running, what the error bars really are, and how to process the raw data yourself.
A consumer epigenetics kit measures DNA methylation at CpG sites on an array, then feeds those values into a regression model that outputs an age-like number. Here is what the assay does, what the error bars are, and how to work with the raw IDAT files yourself.
Most online biological age calculators are quizzes. Here is what the published estimators take as input, how to compute them from your own blood panel or methylation array, and how much weight the output deserves.
Levine's PhenoAge is a nine-marker blood algorithm you can compute yourself in about twenty lines of Python. Here is the formula, the unit conversions that break it, and how it compares to the methylation clocks from the same lab.
A practical protocol for estimating functional age from physical performance tests, blood chemistry algorithms, and DNA methylation clocks, with the reliability problems that make most single-timepoint results uninterpretable.
What biological age tests measure and which clocks are worth running. Covers computing them from IDATs and a blood panel, and how much is noise.
Genetic Genie's methylation panel reads about two dozen genotypes out of a consumer array file. This guide shows how to extract and verify those calls yourself, what they can and cannot tell you, and how to measure actual DNA methylation if that is what you were after.
The Sinclair-associated biological age test is a buccal DNA methylation clock. Here is what methylation clocks measure, how noisy they are, and how to get data you can analyze yourself.