Evidence map›Paper›PMID 40454229›Full record

ArticleBioinformatics advances2025

cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.

Ran Hu, Shuo Li, Mary L Stackpole, Qingjiao Li, Xianghong Jasmine Zhou, Wenyuan Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics advances, 2025. 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

6 authors.

Ran HuDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.ORCID https://orcid.org/0000-0002-0563-8957
Shuo LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.
Mary L StackpoleDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.
Qingjiao LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.
Xianghong Jasmine ZhouDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.
Wenyuan LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, United States.

Funding

The UCLA Center in Early Detection of Liver CancerU01CA230705 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Vatche Agopian, Samuel Wheeler French · 2018 to 2026
$6.6M
Multi-cancer early detection using cell-free DNA methylome analysisU01CA285010 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ROBERT S BRESALIER, Wenyuan Li · 2023 to 2026
$3.3M
Detecting and locating cancer for patients with CT-detected lung nodulesR01CA264864 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZHOU, XIANGHONG JASMINE · 2022 to 2025
$3.2M
Novel Computation Methods for the Analysis of Cell-Free DNA Sequence DataR01CA246329 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M., LI, WENYUAN · 2019 to 2022
$2.2M
Informatics resources for liquid biopsy researchU01CA237711 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, WENYUAN · 2019 to 2021
$1.1M
Comprehensive monitoring of diverse cancer outcomes using genomic and epigenomic sequencing of cfDNAK99CA290092 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Shuo Li · 2025 to 2026
$259k
NCI NIH HHS K99 CA290092NCI NIH HHS R01 CA246329NCI NIH HHS R01 CA264864NCI NIH HHS U01 CA230705NCI NIH HHS U01 CA237711NCI NIH HHS U01 CA285010
6 · The paper itself

Abstract

Motivation: Cell-free DNA (cfDNA) released by dying cells from damaged or diseased tissues can lead to elevated tissue-specific DNA, which is traceable and quantifiable through unique DNA methylation patterns. Therefore, tracing cfDNA origins by analyzing its methylation profiles holds great potential for detecting and monitoring a range of diseases, including cancers. However, deconvolving tissue-specific cfDNA remains challenging for broader applications and research due to the scarcity of specialized, user-friendly bioinformatics tools. Results: To address this, we developed cfTools, an R package that streamlines cfDNA tissue-of-origin analysis for disease detection and monitoring. Integrating advanced cfDNA tissue deconvolution algorithms with R/Bioconductor compatibility, cfTools offers data preparation and analysis functions with flexible parameters for user-friendliness. By identifying abnormal cfDNA compositions, cfTools can infer the presence of underlying pathological conditions, including but not limited to cancer. It simplifies bioinformatics tasks and enables users without advanced expertise to easily derive biologically interpretable insights from standard preprocessed sequencing data, thus increasing its accessibility and broadening its application in cfDNA-based disease studies. Availability and implementation: cfTools and its supplementary package cfToolsData are freely available at Bioconductor: https://bioconductor.org/packages/release/bioc/html/cfTools.html and https://bioconductor.org/packages/release/data/experiment/html/cfToolsData.html. The development version of cfTools is maintained on GitHub: https://github.com/jasminezhoulab/cfTools.

Identifiers

PMID40454229
PMCPMC12124914

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.