ArticleNature biotechnology2022
Inferring gene expression from cell-free DNA fragmentation profiles.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed.
- ctDNA and tumor-based biomarkers of giredestrant response in acelERA breast cancer.Nature communications · 2026Trial
- Exercise intensity and training alter the innate immune cell type and chromosomal origins of circulating cell-free DNA in humans.Proceedings of the National Academy of Sciences of the United States of America · 2025Trial
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring.Blood advances · 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
- Circulating Tumor DNA as a Biomarker of Treatment Response and Minimal Residual Disease in Diffuse Large B-Cell Lymphoma: A Literature Review.Journal of clinical medicine · 2026Review
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- A targeted circulating tumor DNA landscape of copy number aberrations in large B-cell lymphomas.Leukemia · 2026Article
- Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer.Genome medicine · 2026Article
- The role of circulating tumor DNA in ovarian cancer.Discover oncology · 2026Review
- Transcriptionally Informed Nucleosome Profiling of Circulating Cell-Free DNA Predicts Breast Cancer Recurrence.Cancer research communications · 2026Article
- Access to diagnosis using liquid biopsy (ADLiB): Identifying lymphoma in a tuberculosis-endemic setting.HemaSphere · 2026Article
- Noninvasive detection and prognostic stratification of biliary tract cancer using cell-free DNA fragmentomics: a model development and validation study.Molecular biomedicine · 2026Article
- A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.iScience · 2026Article
- Cell-free DNA size deconvolution resolves nucleosomal origins and reveals tumor-associated fragmentomic alterations.Nature communications · 2026Article
- Cell-free DNA fragmentomics for preeclampsia risk assessment.Nature communications · 2026Article
- Article
- Multi-modal circulating cell-free DNA profiling to predict response to docetaxel in metastatic castration-resistant prostate cancer.NPJ precision oncology · 2026Article
- Expanding role of cell-free DNA for the early diagnosis and monitoring of pulmonary diseases.Chinese medical journal · 2026Review
82 more citing papers are in PubMed but not listed here.
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28 authors.
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Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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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.