ArticleNature medicine2023
Liquid biopsy epigenomic profiling for cancer subtyping.
Erratum issuedOpen access · hybridAbstract read
In one paragraph
Article in Nature medicine, 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 90 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
90citing papers in PubMed, 1 pooled it
15.5field-weighted citation impact, top 1% of its field
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.
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.
Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it, 102 citations in OpenAlex.
- Personalised Approach in Oncology to Improve the Efficiency of Patient Diagnosis and Treatment.Asian Pacific journal of cancer prevention : APJCP · 2025Pooled it
- ctDNA and tumor-based biomarkers of giredestrant response in acelERA breast cancer.Nature communications · 2026Trial
- Plasma nucleosome profiling reports on tumor burden and molecular subtypes in small cell lung cancer.The Journal of clinical investigation · 2026Article
- Circulating Cell-Free DNA Methylation Profiling Enables Detection, Distinction, and Estrogen Receptor Status Classification of Advanced Breast Cancer.Cancer research · 2026Article
- A serum-clinical composite model for prostate cancer diagnosis: multicenter validation and CRISPR/Cas13a-based detection.The journal of liquid biopsy · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- The next generation of antibody-drug conjugates.Nature medicine · 2026Review
- Using Disease-Agnostic Genomic Liquid Biopsy in Complex Diagnoses: Real-Life Example of cfChIP-Seq in a Fever of Unknown Origin.JCO precision oncology · 2026Article
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- Advancements and Clinical Applications Prospects of Epigenetic Biomarkers in Liquid Biopsy for Oral Squamous Cell Carcinoma.Current issues in molecular biology · 2026Review
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- Epigenetic plasticity in cancer drug resistance: mechanistic insights and strategies for therapeutic intervention.Acta pharmacologica Sinica · 2026Review
- The seventh kidney cancer research summit: progress in accelerating cures.The oncologist · 2026Article
- Plasma histone monomers as novel diagnostic markers in adult glioblastoma.The journal of liquid biopsy · 2026Article
- Circulating cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) in oncology: from technological advances to clinical applications.NPJ precision oncology · 2026Review
- Circulating Tumor DNA as Emerging Predictive and Prognostic Biomarker in Prostate Cancer.Cancers · 2026Review
- Integrative analysis of tumor-educated platelets for stage-specific diagnosis, prognosis, and therapy in ovarian cancer.Discover oncology · 2026Article
- Predicting immunotherapy benefit in leiomyosarcoma through active chromatin cfDNA profiling.NPJ precision oncology · 2026Article
- Article
- mChIP-seq for Multiplex and Multifactorial Epigenomic Profiling Uncovers Cancer-specific Histone Features in Cellular and Circulating Nucleosomes.bioRxiv : the preprint server for biology · 2026Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
43 authors at 8 institutions in 3 countries.
Sylvan C BacaDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Ji-Heui SeoDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Matthew P DavidsohnDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Brad FortunatoDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Karl SemaanDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Shahabbedin SotudianDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-5864-6192
Gitanjali LakshminarayananDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Miklos DiossyComputational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
Xintao QiuDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-8560-7017
Talal El ZarifDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Hunter SavignanoDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
John CanniffDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Ikenna MaduekeDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Renee Maria SalibyDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-9241-597X
Ziwei ZhangDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Rong LiDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0009-0000-1046-9580
Yijia JiangDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Len TaingDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Mark AwadLowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Cindy H ChauMolecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-6928-3833
James A DeCaprioDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-0896-167X
William D FiggMolecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0003-2428-5613
Tim F GretenLiver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-0806-2535
Aaron N HataMassachusetts General Hospital Cancer Center, Boston, MA, USA.ORCID 0000-0002-6127-318X
F Stephen HodiDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Melissa E HughesDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Keith L LigonDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-7733-600X
Nancy LinDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Kimmie NgDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0003-0631-1494
Matthew G OserDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0003-2047-0969
Catherine MeadorMassachusetts General Hospital Cancer Center, Boston, MA, USA.
Heather A ParsonsDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-8178-6612
Mark M PomerantzDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Arun RajanThoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.ORCID 0000-0003-2776-3385
Jerome RitzDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-5526-4669
Manisha ThakuriaDepartment of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Sara M TolaneyDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-5940-8671
Patrick Y WenCenter for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Henry LongDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-6849-6629
Jacob E BerchuckDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-7607-2428
Zoltan SzallasiComputational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.ORCID 0000-0001-5395-7509
Toni K ChoueiriDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-9201-3217
Matthew L FreedmanDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. matthew_freedman@dfci.harvard.edu.ORCID 0000-0002-0151-1238
Dana-Farber Cancer Institute · USBroad Institute · USBrigham and Women's Hospital · USHarvard University · USNational Institutes of Health · USBoston Children's Hospital · USNational Cancer Institute · USSemmelweis University · HU
Funding
U Mass Boston / DFHCC U54 Partnership (1 of 2)U54CA156732 · NCI · DANA-FARBER CANCER INST · PI Nikhil Wagle · 2010 to 2026
$25.6MUMass Boston-DF/HCC U54 Partnership (2 of 2)U54CA156734 · NCI · UNIVERSITY OF MASSACHUSETTS BOSTON · PI ADAN COLON-CARMONA, Jill A. Macoska · 2010 to 2026
$24.9MCancer Immune Monitoring and Analysis CenterU24CA224331 · NCI · DANA-FARBER CANCER INST · PI FRANK S HODI, Catherine Ju-Ying Wu · 2017 to 2026
$18.4MPhysician Scientist Training in Cancer ResearchT32CA009172 · NCI · DANA-FARBER CANCER INSTITUTE · PI Jennifer R Brown, James A. DeCaprio · 1985 to 2026
$17.1MThe Impact of DNA Damage Repair Abnormalities in Prostate CancerP01CA228696 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI OFFIT, KENNETH, POMERANTZ, MARK M. · 2019 to 2024
$8.7MThe DREAM B-Myb-MuvB complex controls sensitivity to DNA replication activators and inhibitorsR35CA232128 · NCI · DANA-FARBER CANCER INST · PI DECAPRIO, JAMES A. · 2019 to 2025
$7.2MThe Activation of ERBB3 Signaling as a Resistance Mechanism to Targeted TherapiesR01CA137008 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI Aaron N Hata, ZOFIA PIOTROWSKA · 2009 to 2026
$5.7MNovel randomized controlled trials of vitamin D supplementation in patients with colorectal cancer: Impact on survival and biologyR01CA205406 · NCI · DANA-FARBER CANCER INST · PI Kimmie Ng · 2017 to 2026
$4.9MNCI NIH HHS P01 CA228696NCI NIH HHS R01 CA137008NCI NIH HHS R01 CA205406NCI NIH HHS R35 CA232128NCI NIH HHS T32 CA009172NCI NIH HHS U24 CA224331NCI NIH HHS U54 CA156732NCI NIH HHS U54 CA156734
Abstract
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.
Indexed as
Circulating Tumor DNANeoplasmsBiomarkers, TumorEpigenomicsHumansLiquid BiopsyMutationBiomarkers, TumorCirculating Tumor DNA
Identifiers
What OpenQuestion 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 OpenQuestion graph.