# METER (methylome-based ctDNA detection and subtyping)

Source: https://onco.cc/technologies/meter-methylome-subtyping/  
OnCo record `meter-methylome-subtyping` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

A computer method that reads chemical marks on DNA in the blood to measure how much breast cancer is there and whether it still carries the oestrogen receptor.

## Summary

METER (Paoli et al., Genome Medicine 2026) uses tumour-type-specific DNA methylation patterns in low-pass (0.5 to 1x) whole-methylome sequencing of plasma to detect, quantify and subtype ctDNA without tumour tissue. In longitudinal samples from metastatic breast cancer it was more strongly associated with outcome than other ctDNA methods and matched circulating tumour cell counts, including below 3 per cent tumour content. In the full text, oestrogen receptor calls on samples with at least 5 per cent tumour content had an accuracy of 0.93 when the two cohorts were combined (80 ER-positive against 12 ER-negative samples). The authors state that subtype accuracy depends on tumour content.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-11-04
- Also known as: METER
- Principle: Plasma methylation is deconvolved into reference components, including oestrogen receptor positive and negative breast cancer, and the predominant component assigns the subtype.
- Since: 2026
- Strengths: Quantifies and subtypes from one low-cost assay; Open source
- Limitations: Subtyping validated at 5 per cent tumour content and above, in metastatic disease; Only 12 ER-negative samples in the combined validation

## Sources

- Paoli et al., Genome Med 2026 (METER): https://doi.org/10.1186/s13073-026-01603-3
- METER code: https://github.com/caos-lab-unifi/METER

## Connected records

- technologies: [Cell-free DNA methylation tests](https://onco.cc/technologies/cfdna-methylation-testing/), [DNA methylation profiling](https://onco.cc/technologies/methylation-profiling/), [Griffin (nucleosome profiling of cell-free DNA)](https://onco.cc/technologies/griffin-nucleosome-profiling/), [Liquid biopsy (ctDNA)](https://onco.cc/technologies/liquid-biopsy/)
- cancers: [HR-positive / HER2-negative breast cancer](https://onco.cc/cancers/breast-hr-positive/)
- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/)
- targets: [Estrogen receptor (ERα)](https://onco.cc/targets/estrogen-receptor/)
- terms: [Cell-free DNA (cfDNA)](https://onco.cc/terms/cfdna/), [Circulating tumour DNA (ctDNA)](https://onco.cc/terms/ctdna/)
- bottlenecks: [Naming which clone or phenotype is left after treatment](https://onco.cc/bottlenecks/b-subclone-attribution-residual-disease/)
- key papers: [A computational framework for sensitive tumor detection and accurate subtyping using shallow cell-free DNA methylome sequencing](https://onco.cc/key-papers/paper-paoli-meter-methylome-subtyping-genome-med-2026/)
- ideas: [Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left](https://onco.cc/ideas/idea-same-fragment-methylation-and-mutation/)

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