ArticleProceedings of the National Academy of Sciences of the United States of America2023
Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.
Erratum issuedOpen access · greenAbstract read
In one paragraph
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 49 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
49citing papers in PubMed, 1 pooled it
17.0field-weighted citation impact, top 1% of its field
What it found
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- AI-guided meta-analysis of non-invasive prenatal testing platforms for trisomy 21 screening: comparative evaluation of cffDNA and fetal cell-based approaches.BMC pregnancy and childbirth · 2026Pooled it
- Liquid surrogates of spatial tumor ecosystems.Cell research · 2026Article
- NICE: A Two-Step Non-Invasive Framework for Embryo cfDNA Read Enrichment and Quality Assessment.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- UCtracker: A Deep Learning-Based DNA Methylation Model for Noninvasive Diagnosis and Recurrence Surveillance of Urothelial Carcinoma in a Prospective Study.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors.International journal of molecular sciences · 2026Article
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- A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.iScience · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- DADA-EV: domain-adaptive diffusion autoencoder for estimating tissue- and cell-type-specific origin in extracellular vesicle transcriptomes.Briefings in bioinformatics · 2026Article
- Toward the simultaneous detection of multiple diseases with a highly cost-effective cell-free DNA methylome test.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell types.Cell reports methods · 2026Article
- Harnessing viral footprints in circulating free DNA (cfDNA) for early cancer detection: A focus on liquid-biopsy-based screening.International journal of cancer · 2026Review
- Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA.Genome medicine · 2026Article
- The INSPECTOR study: enhanced feasibility for clinical translation of a multi-cancer early detection method based on enzyme-assisted high signal-to-noise ratio sequencing of methylated circulating tumor DNA.Cancer communications (London, England) · 2025Article
- Cell type inference in cell-free nucleic acid liquid biopsy.Nature biotechnology · 2025Review
- Tracing the tissue origin of cell-free DNA through open chromatin footprint.Communications biology · 2025Article
- Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression.Genome medicine · 2025Article
- Genetic Deconvolution of Embryonic and Maternal Cell-Free DNA in Spent Culture Medium of Human Preimplantation Embryo Through Deep Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Read-level DNA methylation deconvolution enhances circulating tumor DNA detection.Briefings in bioinformatics · 2025Article
- A new class of human CpG Island promoters with primate-specific repeats.Scientific reports · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
22 authors at 4 institutions in 1 country.
Shuo LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.ORCID 0000-0002-1960-6016
Weihua ZengDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.ORCID 0009-0006-8727-0055
Xiaohui NiEarlyDiagnostics Inc., Los Angeles, CA 90095.
Qiao LiuDepartment of Statistics, Stanford University, Stanford, CA 94305.ORCID 0000-0002-9781-3360
Wenyuan LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.ORCID 0000-0002-5029-8525
Mary L StackpoleDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.ORCID 0000-0003-4432-6718
Yonggang ZhouDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Arjan GowerDepartment of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA 90095.
Kostyantyn KrysanDepartment of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA 90095.
Preeti AhujaDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
David S LuDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Steven S RamanDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
William HsuDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Denise R AberleDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Clara E MagyarDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Samuel W FrenchDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Steven-Huy B HanDepartment of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA 90095.
Edward B GaronDepartment of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA 90095.
Vatche G AgopianJonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA 90095.ORCID 0000-0003-0130-9838
Wing Hung WongDepartment of Statistics, Stanford University, Stanford, CA 94305.ORCID 0000-0001-7466-2339
Steven M DubinettDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
Xianghong Jasmine ZhouDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095.
University of California, Los Angeles · USQB3 · USStanford University · USVPDiagnostics (United States) · US
Funding
Special EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2MThe UCLA Center in Early Detection of Liver CancerU01CA230705 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Vatche Agopian, Samuel Wheeler French · 2018 to 2026
$6.6MHCC EV Digital Scoring Assay for assessing treatment response in HCC patientsR01CA253651 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TSENG, HSIAN-RONG, ZHU, YAZHEN · 2020 to 2024
$3.3MDetecting and locating cancer for patients with CT-detected lung nodulesR01CA264864 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZHOU, XIANGHONG JASMINE · 2022 to 2025
$3.2MHLA B44 motif neoepitopes in NSCLC: Evaluating their effects on the TME and adding them to established markers in a model to predict durable benefit from PD- 1 inhibition with and without chemotherapyR01CA276917 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI EDWARD B GARON · 2023 to 2026
$2.9MIntegrated analysis of HCC CTCs for Liver Transplant Candidate SelectionR01CA246304 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AGOPIAN, VATCHE, TSENG, HSIAN-RONG · 2020 to 2024
$2.8MNovel 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
$2.2MStatistical methods for gene regulatory analysis and single cell genomicsR01HG010359 · NHGRI · STANFORD UNIVERSITY · PI WONG, WING H. · 2019 to 2022
$1.5MInformatics resources for liquid biopsy researchU01CA237711 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, WENYUAN · 2019 to 2021
$1.1MNCI NIH HHS R01 CA246304NCI NIH HHS R01 CA246329NCI NIH HHS R01 CA253651NCI NIH HHS R01 CA264864NCI NIH HHS R01 CA276917NCI NIH HHS U01 CA230705NCI NIH HHS U01 CA237711NHGRI NIH HHS P50 HG007735NHGRI NIH HHS R01 HG010359
Abstract
Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Despite the great promise, the sensitive and accurate quantification of tissue-derived cfDNA remains challenging to existing methods due to the limited characterization of tissue methylation and the reliance on unsupervised methods. To fully exploit the clinical potential of tissue-derived cfDNA, here we present one of the
Indexed as
Cell-Free Nucleic AcidsDeep LearningBiomarkersBiomarkers, TumorDNA MethylationHumansPromoter Regions, GeneticBiomarkersBiomarkers, TumorCell-Free Nucleic Acidscell-free DNAdisease diagnosisdisease monitoringDNA methylationtissue deconvolution
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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.