Evidence map›Paper›PMID 41634848›Full record

ArticleGenome medicine2026

A computational framework for sensitive tumor detection and accurate subtyping using shallow cell-free DNA methylome sequencing.

Marta Paoli, Francesca Galardi, Agostina Nardone, Chiara Biagioni, Dario Romagnoli, Samantha Di Donato, Gian Marco Franceschini, Luca Livraghi, Marta Pestrin, Giuseppina Sanna and 7 more

Abstract read
In one paragraph

Article in Genome medicine, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Marta Paoli *Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
Francesca Galardi *Translational Research Unit, Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Agostina NardoneTranslational Research Unit, Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Chiara BiagioniDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Dario RomagnoliDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Samantha Di DonatoDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Gian Marco FranceschiniDepartment of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
Luca LivraghiDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Marta PestrinMedical Oncology Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Gorizia, Italy.
Giuseppina SannaMedical Oncology, Ospedale Civile SS Annunziata, Sassari, Italy.
Emanuela RisiDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Ilenia MigliaccioTranslational Research Unit, Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Erica MorettiDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Luca MalorniDepartment of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Laura Biganzoli *Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy.
Francesca Demichelis *Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
Matteo Benelli *Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy. matteo.benelli@unifi.it.

Funding

Fondazione AIRC per la ricerca sul cancro ETS 27036Fondazione AIRC per la ricerca sul cancro ETS 29370Ministero della Salute GR-2018-12365195
6 · The paper itself

Abstract

Plasma circulating tumor DNA (ctDNA) enables non-invasive monitoring of metastatic cancer. However, the detection of low tumor content (TC) via tumor tissue-agnostic approaches remains challenging. We introduce METER, a computational strategy exploiting tumor-type specific DNA methylation patterns for sensitive ctDNA detection, accurate quantification, and subtyping from plasma low-pass (0.5-1x) whole-methylome sequencing. In longitudinal samples from metastatic breast cancer patients, METER demonstrated a stronger association with clinical outcomes than both state-of-the-art ctDNA methods and matched circulating tumor cell (CTC) counts, even at TC below 3%. METER ( https://github.com/caos-lab-unifi/METER ) integrates TC estimation and subtyping in a single framework, enabling sensitive and accurate analyses for precision oncology.

Indexed as

Biomarkers, TumorCirculating Tumor DNAComputational BiologyDNA MethylationEpigenomeBreast NeoplasmsFemaleHumansSequence Analysis, DNABiomarkers, TumorCirculating Tumor DNABiomarkerBreast cancerCirculating tumor DNADNA methylationEstrogen receptorLiquid biopsyMethylomePrecision oncologyTumor subtyping

Identifiers

PMID41634848
PMCPMC12958694

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.