Evidence map›Paper›PMID 41225146›Full record

ArticleCommunications biology2025

Open chromatin-guided interpretable machine learning reveals cancer-specific chromatin features in cell-free DNA.

Sakuntha D Gunarathna, Aerica Nagornyuk, Nazim A Belabbaci, Regina Nguyen, Bappa Ghosh, Sabha Ganai, Tabatha Lemke, Cassy Garry, Mika Saotome, Muhan Yu and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026
    Review
  2. Article
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

13 authors.

Sakuntha D GunarathnaDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.ORCID http://orcid.org/0000-0002-0376-9742
Aerica NagornyukDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.
Nazim A BelabbaciDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.ORCID http://orcid.org/0009-0006-8380-9818
Regina NguyenDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.
Bappa GhoshDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.ORCID http://orcid.org/0000-0002-4054-0859
Sabha GanaiDivisions of Surgical Oncology and Hepatobiliary Surgery, Los Angeles General Medical Center, Los Angeles, CA, USA.
Tabatha LemkeSanford Research, Sioux Falls, SD, USA.
Cassy GarrySanford Research, Sioux Falls, SD, USA.
Mika SaotomeDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA.
Muhan YuDepartment of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.
Mamoru TakadaDepartment of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.
Xusheng WangDepartment of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-1759-9588
Motoki TakakuDepartment of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA. motoki.takaku@und.edu.ORCID http://orcid.org/0000-0002-8652-2541

Funding

Tracking and Evaluation CoreU54GM128729 · NIGMS · UNIVERSITY OF NORTH DAKOTA · PI BASSON, MARC D. · 2018 to 2022
$20.3M
American Cancer Society (American Cancer Society, Inc.) RSG-23-645952-01-DMCNational Science Foundation (NSF) ND-ACES (EPSCoR) #OIA-1946202 pilot grant awardNIGMS NIH HHS U54 GM128729U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) U54GM128729
6 · The paper itself

Abstract

Cell-free DNAs (cfDNAs) are DNA fragments found in blood, originating mainly from immune cells in healthy individuals and from both immune and cancer cells in cancer patients. While cancer-derived cfDNAs carry mutations, they also retain epigenetic features such as DNA methylation and nucleosome positioning. In this study, we examine nucleosome enrichment patterns in cfDNAs from breast and pancreatic cancer patients and find significant enrichment at open chromatin regions. Differential enrichment is observed not only at cancer cell type specific ATAC-seq peaks but also at CD4

Indexed as

Breast NeoplasmsCell-Free Nucleic AcidsChromatinMachine LearningNeoplasmsPancreatic NeoplasmsDNA MethylationFemaleHumansNucleosomesCell-Free Nucleic AcidsChromatinNucleosomes

Identifiers

PMID41225146
PMCPMC12612109

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.