ArticleCommunications medicine2025
Leveraging sequences missing from the human genome to diagnose cancer.
Article in Communications medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Factors Associated with Stage at Diagnosis in Pancreatic Cancer: Implications for Precision Screening and Early Detection.Biomedicines · 2026Review
- neomerDB: a comprehensive database of neomer biomarkers in cancer.Database : the journal of biological databases and curation · 2026Article
- A foundational quantum framework for multi-pattern string matching in k-mer detection.Frontiers in bioinformatics · 2026Article
- Quantum implementation of multi-pattern string matching for k-mer detection.bioRxiv : the preprint server for biology · 2025Article
- Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response.Genomics, proteomics & bioinformatics · 2025Article
- Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA.Bioinformatics (Oxford, England) · 2025Article
- Identification of the shortest species-specific oligonucleotide sequences.Genome research · 2025Article
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- Predicting Disease Progression in Inoperable Localized NSCLC Patients Using ctDNA Machine Learning Model.Cancer medicine · 2024Observational
- Detecting pulmonary malignancy against benign nodules using noninvasive cell-free DNA fragmentomics assay.ESMO open · 2024Article
- Utilizing nullomers in cell-free RNA for early cancer detection.Cancer gene therapy · 2024Article
- Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.BMC genomics · 2023Article
Corrections and comments
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Authors and funding
27 authors.
Funding
Abstract
backgroundCancer diagnosis using cell-free DNA (cfDNA) has the potential to improve treatment and survival but has several technical limitations.
methodsIn this study, we developed a prediction model based on neomers, DNA sequences 13-17 nucleotides in length that are predominantly absent from the genomes of healthy individuals and are created by tumor-associated mutations.
resultsWe show that neomer-based classifiers can accurately detect cancer, including early stages, and distinguish subtypes and features. Analysis of 2577 cancer genomes from 21 cancer types shows that neomers can distinguish tumor types with higher accuracy than state-of-the-art methods. Generation and analysis of 465 cfDNA whole-genome sequences demonstrates that neomers can precisely detect lung and ovarian cancer, including early stages, with an area under the curve ranging from 0.89 to 0.94. By testing various promoters or over 9000 candidate enhancer sequences with massively parallel reporter assays, we show that neomers can identify cancer-associated mutations that alter regulatory activity.
conclusionsCombined, our results identify a sensitive, specific, and simple cancer diagnostic tool that can also identify cancer-associated mutations in gene regulatory elements.
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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.