# Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left

Source: https://onco.cc/ideas/idea-same-fragment-methylation-and-mutation/  
OnCo record `idea-same-fragment-methylation-and-mutation` (Idea). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

A proposal, untested: when a blood test finds a tumour fragment after treatment, also read the chemical marks on that same piece of DNA, which might show whether the cell it came from was making the oestrogen receptor or TROP2.

## Summary

This is a proposal with no evidence yet that it works. Ultrasensitive residual disease tests find a handful of tumour-derived molecules by their mutations, and then discard everything else those molecules carry. The same fragment also carries its methylation, and TROP2 expression is controlled mainly by methylation of its gene rather than by mutation (Notini 2026). Reading a tracked tumour mutation and the methylation of nearby CpG sites on one molecule would tie each rare tumour fragment to an epigenetic state, so that even a few molecules could carry phenotype information that tumour-naive methods (Griffin, METER, cfChIP-seq) only recover at 3 to 5 per cent tumour fraction. Duplex strand reading such as SaferSeqS shows single rare molecules can be read accurately; whether their methylation can be read at the same time, and whether a few fragments near a mutation say anything about ESR1 or TACSTD2 regulation elsewhere in the genome, is unknown.

## Fields

- Kind: Idea
- Last checked: 2026-11-04
- Also known as: Same-fragment methylation and mutation; Phenotype from residual ctDNA molecules
- Tags: proposal
- Hypothesis: Methylation read on the same cell-free DNA fragments that carry tracked tumour mutations classifies oestrogen receptor and TROP2 (TACSTD2) expression status of the source tumour better than chance at tumour fractions below 0.1 per cent, where tumour-naive methylation and fragmentation methods are not validated.
- Rationale: TACSTD2 expression is inversely associated with methylation and its genomic alterations are uncommon (Notini 2026); oestrogen receptor activity is readable from cell-free DNA chromatin and methylation at percent-level tumour fractions (Doebley 2022, Paoli 2026); and ECLIPSE shows that the bottleneck for clone attribution is the number of informative molecules, so information per molecule is the lever.
- Proposed test: First, in tumour tissue and matched cell lines, check whether methylation at CpGs within a fragment's length of commonly tracked mutations differs between ER-positive and ER-negative, and TROP2-high and TROP2-low, tumours; if it does not, stop. Then, in plasma dilution series of known ER and TROP2 status (for example from metastatic breast cancer patients with paired biopsies), read mutation and methylation together with an enzymatic conversion chemistry that preserves both, and measure classification accuracy against the number of tumour molecules recovered, with matched white-cell DNA to exclude clonal haematopoiesis.
- Maturity: speculative
- Actor: research

## Sources

- Notini et al., NPJ Precis Oncol 2026 (TACSTD2 methylation): https://doi.org/10.1038/s41698-026-01523-w
- Abbosh et al., Nature 2023 (ECLIPSE): https://doi.org/10.1038/s41586-023-05776-4
- Cohen et al., Nat Biotechnol 2021 (SaferSeqS): https://doi.org/10.1038/s41587-021-00900-z

## Connected records

- ideas: [Read tumour RNA and tumour DNA from the same blood draw to find and type residual cancer](https://onco.cc/ideas/idea-stack-ctdna-and-tumour-rna-residual-disease/), [Track clones in blood with methylation patterns instead of mutations](https://onco.cc/ideas/idea-bio1-methylation-clone-tracking/), [TROP2 PET to choose and sequence TROP2 ADCs](https://onco.cc/ideas/idea-trop2-pet-selection/)
- cancers: [Breast cancer (all types)](https://onco.cc/cancers/breast-cancer/), [HR-positive / HER2-negative breast cancer](https://onco.cc/cancers/breast-hr-positive/), [Triple-negative breast cancer (TNBC)](https://onco.cc/cancers/tnbc/)
- technologies: [DNA methylation profiling](https://onco.cc/technologies/methylation-profiling/), [ECLIPSE (subclone tracking from ctDNA)](https://onco.cc/technologies/eclipse-subclone-ctdna/), [Griffin (nucleosome profiling of cell-free DNA)](https://onco.cc/technologies/griffin-nucleosome-profiling/), [METER (methylome-based ctDNA detection and subtyping)](https://onco.cc/technologies/meter-methylome-subtyping/), [MRD / molecular residual disease testing](https://onco.cc/technologies/mrd-testing/), [SaferSeqS (Watson and Crick strand sequencing)](https://onco.cc/technologies/saferseqs/)
- targets: [Estrogen receptor (ERα)](https://onco.cc/targets/estrogen-receptor/), [TROP2](https://onco.cc/targets/trop2/)
- terms: [Cell-free DNA (cfDNA)](https://onco.cc/terms/cfdna/), [Circulating tumour DNA (ctDNA)](https://onco.cc/terms/ctdna/), [Minimal / molecular residual disease (MRD)](https://onco.cc/terms/mrd/)
- bottlenecks: [Dormant cells and minimal residual disease](https://onco.cc/bottlenecks/b-dormancy-mrd/), [Naming which clone or phenotype is left after treatment](https://onco.cc/bottlenecks/b-subclone-attribution-residual-disease/), [Tumour heterogeneity and clonal evolution](https://onco.cc/bottlenecks/b-tumor-heterogeneity/)
- 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/), [A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA](https://onco.cc/key-papers/paper-doebley-griffin-nucleosome-profiling-nat-commun-2022/), [Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands](https://onco.cc/key-papers/paper-cohen-saferseqs-nat-biotechnol-2021/), [Pan-cancer multi-omic integration of Trop2 reveals biological determinants and translational implications for ADC therapy](https://onco.cc/key-papers/paper-notini-trop2-pan-cancer-multiomic-npj-precis-oncol-2026/), [Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer](https://onco.cc/key-papers/paper-coates-sacituzumab-resistance-tacstd2-cancer-discov-2021/), [Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA](https://onco.cc/key-papers/paper-abbosh-tracerx-ctdna-relapse-nature-2023/)
- roadmaps: [ctDNA tests roadmap: from a curiosity in plasma to blood tests that decide treatment](https://onco.cc/roadmaps/ctdna-tests/)

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