ArticleNature communications2022
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
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Article in Nature communications, 2022. 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 64 papers.
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64citing papers in PubMed
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Who cites it
64 citing papers in PubMed.
- Decomposition-driven biomarker identification enhances non-invasive early cancer detection.iScience · 2026Article
- DNAmBERT: a transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data.Briefings in bioinformatics · 2026Article
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Liquid biopsy-based multi-omics approach for early detection of hepatocellular carcinoma (ASCEND-Hep): a multiphase prospective development and validation study.BMC medicine · 2026Article
- Enriched methylomes of low-input and fragmented DNA using fragment ligation EXclusive methylation sequencing.Nucleic acids research · 2026Article
- Expanding role of cell-free DNA for the early diagnosis and monitoring of pulmonary diseases.Chinese medical journal · 2026Review
- 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
- Circulating tumor DNA methylation-based method for noninvasive detection and stage stratification of colorectal tumor.Clinical epigenetics · 2026Article
- A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.Nature cancer · 2026Article
- A targeted DNA methylation method for detecting gastrointestinal cancer in circulating cell-free DNA.iScience · 2026Article
- Global Hypomethylation in Cell-Free DNA Enables Noninvasive Colorectal Cancer Screening: Results from a Retrospective Validation Study.Computational and structural biotechnology journal · 2026Article
- Article
- Epigenetic profiling of circulating cell-free DNA for early detection and minimal residual disease assessment in lung cancer: a focus on DNA methylation.Frontiers in oncology · 2026Review
- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
- Whole-genome profiling of age- and sex-associated DNA methylation signatures in human plasma cell-free DNA.Communications medicine · 2025Article
- RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.Scientific reports · 2025Article
- Advances and challenges in circulating tumor DNA-based early detection of lung cancer.Translational cancer research · 2025Review
- Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression.Genome medicine · 2025Article
- Review
- Read-level DNA methylation deconvolution enhances circulating tumor DNA detection.Briefings in bioinformatics · 2025Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
40 authors.
Mary L Stackpole *Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0003-4432-6718
Weihua Zeng *Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Shuo Li *Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-1960-6016
Chun-Chi LiuEarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA.
Yonggang ZhouDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Shanshan HeDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Angela YehDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Ziye WangDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Fengzhu SunDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.ORCID http://orcid.org/0000-0002-8552-043X
Qingjiao LiThe Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China.ORCID http://orcid.org/0000-0002-7816-123X
Zuyang YuanDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Asli YildirimDepartment of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Pin-Jung ChenDepartment of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Paul WinogradDepartment of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Benjamin TranDepartment of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Yi-Te LeeDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-8177-0407
Paul Shize LiWestlake High School, 100N Lakeview Cyn Road, Westlake Village, CA, 91362, USA.
Zorawar NoorDepartment of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Megumi YokomizoDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Preeti AhujaDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Yazhen ZhuDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-2130-8085
Hsian-Rong TsengDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0003-0942-5905
James S TomlinsonDepartment of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Edward GaronDepartment of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0001-7077-8801
Samuel FrenchDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0002-7611-881X
Clara E MagyarDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Sarah DryDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Clara LajonchereJonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Daniel GeschwindInstitute for Precision Health, University of California at Los Angeles, Los Angeles, CA, 90095, USA.ORCID http://orcid.org/0000-0003-2896-3450
Gina ChoiDepartment of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Sammy SaabDepartment of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Frank AlberDepartment of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Wing Hung WongDepartment of Statistics, Stanford University, Stanford, CA, 94305, USA.ORCID http://orcid.org/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, USA.
Denise R AberleDepartment of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
Vatche AgopianDepartment of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA. vagopian@mednet.ucla.edu.ORCID http://orcid.org/0000-0003-0130-9838
Steven-Huy B HanDepartment of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA. steven.han@ucla.edu.ORCID http://orcid.org/0000-0003-1459-8763
Xiaohui NiEarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA. xiaohui.ni@earlydx.com.ORCID http://orcid.org/0000-0002-3626-3588
Wenyuan LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA. wenyuanli@mednet.ucla.edu.ORCID http://orcid.org/0000-0002-5029-8525
Xianghong Jasmine ZhouDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA. xjzhou@mednet.ucla.edu.ORCID http://orcid.org/0000-0002-4522-7490
Funding
Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Samuel Wheeler French · 1985 to 2026
$134.5MMultiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4MThe 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
$3.3MExtracellular Vesicle-Based Digital Scoring Assay for Detecting Early-stage Hepatocellular CarcinomaR01CA255727 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZHU, YAZHEN · 2021 to 2025
$3.2MMolecular and Imaging Biomarkers for Early Lung Cancer Detection in the Setting of Indeterminate Pulmonary NodulesR01CA210360 · NCI · BOSTON UNIVERSITY MEDICAL CAMPUS · PI ABERLE, DENISE R., LENBURG, MARC ELLIOTT · 2016 to 2021
$3.1MThe Boston University-UCLA Lung Cancer Biomarker Development LabU01CA214182 · NCI · BOSTON UNIVERSITY MEDICAL CAMPUS · PI ABERLE, DENISE R., DUBINETT, STEVEN M. · 2016 to 2021
$3.1MIntegrated 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
$2.2MInformatics resources for liquid biopsy researchU01CA237711 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, WENYUAN · 2019 to 2021
$1.1MAn Accurate, Non-invasive, and Cost-effective Methylome Test for Early Cancer DetectionR43CA246941 · NCI · EARLYDIAGNOSTICS, INC. · PI NI, XIAOHUI · 2020 to 2020
$352kNCI NIH HHS P30 CA016042NCI NIH HHS R01 CA210360NCI NIH HHS R01 CA246304NCI NIH HHS R01 CA246329NCI NIH HHS R01 CA253651NCI NIH HHS R01 CA255727NCI NIH HHS R43 CA246941NCI NIH HHS U01 CA214182NCI NIH HHS U01 CA230705NCI NIH HHS U01 CA237711NHGRI NIH HHS UM1 HG011593
Abstract
Early cancer detection by cell-free DNA faces multiple challenges: low fraction of tumor cell-free DNA, molecular heterogeneity of cancer, and sample sizes that are not sufficient to reflect diverse patient populations. Here, we develop a cancer detection approach to address these challenges. It consists of an assay, cfMethyl-Seq, for cost-effective sequencing of the cell-free DNA methylome (with > 12-fold enrichment over whole genome bisulfite sequencing in CpG islands), and a computational method to extract methylation information and diagnose patients. Applying our approach to 408 colon, liver, lung, and stomach cancer patients and controls, at 97.9% specificity we achieve 80.7% and 74.5% sensitivity in detecting all-stage and early-stage cancer, and 89.1% and 85.0% accuracy for locating tissue-of-origin of all-stage and early-stage cancer, respectively. Our approach cost-effectively retains methylome profiles of cancer abnormalities, allowing us to learn new features and expand to other cancer types as training cohorts grow.
Indexed as
Cell-Free Nucleic AcidsStomach NeoplasmsCost-Benefit AnalysisEarly Detection of CancerEpigenomeHumansCell-Free Nucleic Acids
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