ArticleeLife2020
CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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
36 citing papers in PubMed, 76 citations in OpenAlex.
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- Malignant triton tumor of the common bile duct.Clinical journal of gastroenterology · 2025Review
- The difference in tumor immune microenvironment and IFN-γ response between solid and non-solid adenocarcinoma.Translational lung cancer research · 2025Article
- CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.BMC bioinformatics · 2025Article
- Modelling Acral Melanoma in Admixed Brazilians Uncovers Genomic Drivers and Targetable Pathways.medRxiv : the preprint server for health sciences · 2025Article
- Ancestry and somatic profile predict acral melanoma origin and prognosis.medRxiv : the preprint server for health sciences · 2025Article
- Mutational landscape of pure ductal carcinoma in situ and associations with disease prognosis and response to radiotherapy.Breast cancer research : BCR · 2025Article
- Glioma-neuronal circuit remodeling induces regional immunosuppression.Nature communications · 2025Article
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- A Comparative Genomic Study of Conventional and Undifferentiated Melanoma.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2024Article
- Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level.Nature communications · 2024Article
- Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations.Nature communications · 2024Article
- Dual-loss of PBRM1 and RAD51 identifies hyper-sensitive subset patients to immunotherapy in clear cell renal cell carcinoma.Cancer immunology, immunotherapy : CII · 2024Article
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- Somatic Copy Number Alterations in Colorectal Cancer Lead to a Differentially Expressed ceRNA Network (ceRNet).Current issues in molecular biology · 2023Article
- Innovative Approach to Isolate and Characterize Glioblastoma Circulating Tumor Cells and Correlation with Tumor Mutational Status.International journal of molecular sciences · 2023Article
- Identification of New Potential Prognostic and Predictive Markers in High-Grade Osteosarcoma Using Whole Exome Sequencing.International journal of molecular sciences · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, a web-based tool that allows a comprehensive exploration of CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to the TCGA pan-cancer dataset of 10,635 genomes showing that CNAs classify cancer types according to their tissue-of-origin, and that each cancer type shows specific ranges of broad and focal CNA scores. Moreover, CNApp reproduces recurrent CNAs in hepatocellular carcinoma and predicts colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and discrete genomic imbalances. In summary, CNApp facilitates CNA-driven research by providing a unique framework to identify relevant clinical implications. CNApp is hosted at https://tools.idibaps.org/CNApp/.
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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.