Evidence map›Paper›PMID 41365872›Full record

ArticleNature communications2025

Circulating tumor DNA refines risk stratification of neoadjuvant therapy-resistant breast tumors.

Mark Jesus M Magbanua, Nayelis A Manon, Denise M Wolf, Samuel Rivero-Hinojosa, Ziad Ahmed, Rosalyn W Sayaman, Antony Tin, Derrick Renner, Ekaterina Kalashnikova, Lamorna Brown-Swigart and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed, 2 pooled it
–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

11 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
  3. Trial
  4. Review
  5. Article
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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

25 authors.

Mark Jesus M MagbanuaDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. mark.magbanua@ucsf.edu.ORCID http://orcid.org/0000-0003-2113-3593
Nayelis A ManonDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Denise M WolfDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Samuel Rivero-HinojosaNatera Inc., Austin, TX, USA.ORCID http://orcid.org/0000-0002-3595-8273
Ziad AhmedDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Rosalyn W SayamanDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-1343-0619
Antony TinNatera Inc., Austin, TX, USA.
Derrick RennerNatera Inc., Austin, TX, USA.
Ekaterina KalashnikovaNatera Inc., Austin, TX, USA.
Lamorna Brown-SwigartDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-2076-5177
Gillian L HirstDepartment of Surgery, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-4502-0035
Christina YauDepartment of Surgery, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-1937-0859
Wen LiDepartment of Radiology, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-6584-363X
Claudine IsaacsLombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.ORCID http://orcid.org/0000-0002-9646-1260
Rebecca A ShatskyDepartment of Medicine, University of California San Diego, La Jolla, CA, USA.
Amy S ClarkDivision of Hematology/Oncology, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-3685-6535
Alexandra ZimmerDivision of Hematology/Oncology, Oregon Health and Science University, Portland, OR, USA.ORCID http://orcid.org/0000-0001-6789-0982
Amy L DelsonBreast Science Advocacy Core, University of California San Francisco, San Francisco, CA, USA.
Angel RodriguezNatera Inc., Austin, TX, USA.
Minetta C LiuNatera Inc., Austin, TX, USA.ORCID http://orcid.org/0000-0002-8206-5232
Paula R PohlmannDepartment of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0001-7914-5162
Laura J EssermanDepartment of Surgery, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-9202-4568
Hope S RugoDivision of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-6710-4814
Angela DeMicheleDivision of Hematology/Oncology, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-1297-4251
Laura van 't VeerDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9838-8298

Funding

The I SPY 2.2 TRIAL: Evolving to Imaging and Molecular Biomarker Response Directed Adaptive Sequential Treatment to Optimize Breast Cancer OutcomesP01CA210961 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANGELA DEMICHELE · 2017 to 2026
$22.9M
Strategy for combining circulating tumor DNA (ctDNA) and magnetic resonance imaging (MRI) measures of tumor burden for prediction of response and outcome in neoadjuvant-treated early breast cancerR01CA255442 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LI, WEN, MAGBANUA, MARK JESUS · 2021 to 2025
$3.3M
A systems biology approach to elucidate the biology of immune-associated outcomes in breast cancerK01CA279498 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Rosalyn Wong Sayaman · 2023 to 2026
$696k
NCI NIH HHS K01 CA279498NCI NIH HHS P01 CA210961NCI NIH HHS R01 CA255442U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P01CA210961U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA255442
6 · The paper itself

Abstract

Early-stage breast cancers resistant to neoadjuvant therapy (NAT), characterized by high residual cancer burden (RCB) after treatment, have an increased risk of metastatic recurrence. Here, we show that circulating tumor DNA (ctDNA) detected using a tumor-informed test (1) can improve risk stratification of patients with NAT-resistant tumors (RCB-II/RCB-III) and (2) predict response to NAT. Stratification using ctDNA status at pretreatment or post-NAT and ctDNA dynamics identified NAT-resistant tumors with a significantly decreased risk of metastatic recurrence. ctDNA clearance as early as week 3 across receptor subtypes predicted favorable responses to NAT, including immunotherapies. Interestingly, less than a fifth of patients with NAT-resistant tumors were ctDNA-positive post-NAT. Serial mutation profiling of NAT-resistant tumors revealed that patient-specific ctDNA assay variants remained detectable over time, including in tumors of patients ctDNA-negative post-NAT. Refining risk stratification for NAT-resistant tumors using ctDNA and understanding ctDNA shedding in these tumors could guide treatment decisions to prevent or delay metastatic recurrence.

Indexed as

Breast NeoplasmsCirculating Tumor DNADrug Resistance, NeoplasmAdultBiomarkers, TumorFemaleHumansMiddle AgedMutationNeoadjuvant TherapyNeoplasm Recurrence, LocalNeoplasm, ResidualRisk AssessmentBiomarkers, TumorCirculating Tumor DNA

Identifiers

PMID41365872
PMCPMC12690079

What OpenQuestion holds

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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.