# Liquid biopsy epigenomic profiling for cancer subtyping

Source: https://onco.cc/key-papers/paper-baca-plasma-epigenomic-profiling-nat-med-2023/  
OnCo record `paper-baca-plasma-epigenomic-profiling-nat-med-2023` (Key paper). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Reading chemical marks on DNA and its packaging from 1 mL of blood let researchers infer which genes advanced cancers had switched on, including the targets of some drugs.

## Summary

An immunoprecipitation-based method targeting histone modifications and DNA methylation measured 1,268 epigenomic profiles in plasma from 433 people with one of 15 cancers. It served as a proxy for transcriptional activity, inferring expression of diagnostic markers and drug targets, the activity of targetable transcription factors, and epigenetic mechanisms of resistance.

## Fields

- Kind: Key paper
- Last checked: 2026-11-04
- Journal: Nature Medicine
- Year: 2023
- DOI: 10.1038/s41591-023-02605-z
- Authors: Baca SC, Seo JH, Davidsohn MP, et al.
- Findings: 1,268 plasma epigenomic profiles from 433 individuals with 15 cancers, from 1 mL of plasma.; Inferred expression of drug targets and activity of targetable transcription factors.
- What it means: Blood can show what a tumour is doing, not only what mutations it has. It is a proof of concept in advanced cancer.
- Caveats: Advanced cancers; analyses were restricted to samples above 3 per cent ctDNA in the full text.; TROP2 is not among the targets reported.

## Sources

- Baca et al., Nat Med 2023: https://doi.org/10.1038/s41591-023-02605-z
- PubMed: https://pubmed.ncbi.nlm.nih.gov/37865722/

## Connected records

- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/)
- technologies: [Liquid biopsy (ctDNA)](https://onco.cc/technologies/liquid-biopsy/), [Plasma epigenomic profiling (cfChIP-seq)](https://onco.cc/technologies/plasma-epigenomic-profiling/)
- terms: [Cell-free DNA (cfDNA)](https://onco.cc/terms/cfdna/), [Circulating tumour DNA (ctDNA)](https://onco.cc/terms/ctdna/)
- journals: [Nature Medicine](https://onco.cc/journals/nature-medicine/)

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