ArticleScience translational medicine2024
Genome-wide repeat landscapes in cancer and cell-free DNA.
Article in Science translational medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
What it found
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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.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it, 46 citations in OpenAlex.
- The Predictive Role of ctDNA and CTCs in Patients with Advanced Non-Small Cell Lung Cancer Receiving Immunotherapy: A Systematic Review and Meta-Analysis.International journal of molecular sciences · 2026Pooled it
- [Liquid Biopsy Revolutionizes the Precise Management of Tumors Across the Entire Course: Current Situation and Future Prospects].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026Pooled it
- Viral mimicry escape as a necessary feature of malignant transformation.Nature reviews. Cancer · 2026Review
- Noninvasive detection and differentiation of gastric malignancy using cell-free DNA biomarkers.Journal of advanced research · 2026Article
- Liquid Biopsy for Molecular Residual Disease Detection and Postoperative Surveillance in Gastric Cancer: Current Evidence and Future Directions.International journal of molecular sciences · 2026Review
- Multidimensional 5-hydroxymethylcytosine features in cell-free DNA enable the detection, staging and subtyping of pancreatic ductal adenocarcinoma.Biomarker research · 2026Article
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Circulating Tumor DNA Sequencing for Early Diagnosis and Detection of Treatment Response, Minimal Residual Disease, and Recurrence in Gastroesophageal Cancer.Journal of gastrointestinal cancer · 2026Review
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Advances in In Vitro Diagnostics for Cholangiocarcinoma: From Biomarker Discovery to Artificial Intelligence.International journal of molecular sciences · 2026Review
- Fragmentomic liquid biopsy enables early breast cancer detection, molecular subtyping and lymph node assessment.Nature communications · 2026Article
- Cell-free DNA fragmentomes for noninvasive detection of liver cirrhosis and other diseases.Science translational medicine · 2026Article
- Review
- TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.Nucleic acids research · 2026Article
- Leveraging cfDNA fragmentomic features for the early detection of colorectal cancer.Frontiers in immunology · 2026Article
- Article
- Liquid biopsies across the cancer care continuum.Nature medicine · 2025Review
- Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy.International journal of molecular sciences · 2025Review
- Long read sequencing reveals novel genomic and epigenomic alterations in repetitive regions of high grade serous ovarian cancer.Scientific reports · 2025Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer. We identified tumor-specific changes in these patients in 1280 repeat element types from the LINE, SINE, LTR, transposable element, and human satellite families. These included changes to known repeats and 820 elements that were not previously known to be altered in human cancer. Repeat elements were enriched in regions of driver genes, and their representation was altered by structural changes and epigenetic states. Machine learning analyses of genome-wide repeat landscapes and fragmentation profiles in cfDNA detected patients with early-stage lung or liver cancer in cross-validated and externally validated cohorts. In addition, these repeat landscapes could be used to noninvasively identify the tissue of origin of tumors. These analyses reveal widespread changes in repeat landscapes of human cancers and provide an approach for their detection and characterization that could benefit early detection and disease monitoring of patients with cancer.
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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.