ArticleNPJ genomic medicine2022
Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer.
Article in NPJ genomic medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- DNA-Based Liquid Biopsy for Evaluating Surgical and Postsurgical Outcomes in Gynecologic Malignancies: A Systematic Review.Journal of clinical laboratory analysis · 2026Pooled it
- A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.Nature cancer · 2026Article
- Article
- Predictive value of peripheral blood cell-free DNA breast cancer gene mutation profiling for postoperative pathological malignancy in BI-RADS 4 breast nodules.Frontiers in genetics · 2026Article
- Repeatome Analysis of Plasma Circulating DNA in Patients with Cardiovascular Disease: Variation with Cell-Free DNA Integrity/Length and Clinical Parameters.International journal of molecular sciences · 2025Article
- Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection.Future oncology (London, England) · 2025Article
- Circulating Tumour DNA for Ovarian Cancer Diagnosis and Treatment Monitoring: What Perspectives for Clinical Use?International journal of molecular sciences · 2025Review
- Exploration of cfDNA landscape in NIPT and clinical utilities of cfDNA based gene expression inference in prenatal diagnostics.Frontiers in genetics · 2025Article
- Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns.Nature communications · 2024Article
- Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA.Nature communications · 2024Article
- Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors.Cancer discovery · 2024Article
- Analysis of cell free DNA to predict outcome to bevacizumab therapy in colorectal cancer patients.NPJ genomic medicine · 2024Article
- Molecular analysis for ovarian cancer detection in patient-friendly samples.Communications medicine · 2024Article
- Plasma cell-free DNA as a sensitive biomarker for multi-cancer detection and immunotherapy outcomes prediction.Journal of cancer research and clinical oncology · 2024Article
- Analysis of the primary factors influencing donor derived cell-free DNA testing in kidney transplantation.Frontiers in immunology · 2024Review
- Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors.Cancers · 2023Article
- Circulating Histones to Detect and Monitor the Progression of Cancer.International journal of molecular sciences · 2023Review
- Review
Corrections and comments
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Authors and funding
21 authors at 7 institutions in 5 countries.
Funding
Abstract
Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals. Multinomial modeling was subsequently applied to capture these deviations in a per sample nucleosome footprint score. Validation was performed in 271 cfDNAs pre-surgically collected from women with an adnexal mass. We confirmed that nucleosome scores were elevated in invasive carcinoma patients, but not in patients with benign or borderline disease. Combining nucleosome scores with chromosomal instability scores assessed in the same cfDNA improved prediction of malignancy. Nucleosome scores were, however, more reliable to predict non-high-grade serous ovarian tumors, which are characterized by low chromosomal instability. These data highlight that compared to chromosomal instability, nucleosome footprinting provides a complementary and more generic read-out for pre-surgical diagnosis of invasive disease in women with adnexal masses.
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Registered trials
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.