ArticleGenome biology2015
CopywriteR: DNA copy number detection from off-target sequence data.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
What it found
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Who cites it
146 citing papers in PubMed.
- Molecular Profiling and Tumor Biomarker Analysis of GOG281/LOGS: A Positive Late-Phase Trial of Trametinib for Recurrent/Persistent Low-Grade Serous Ovarian Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Trial
- Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers.Cell reports. Medicine · 2025Trial
- Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures.Scientific reports · 2019Trial
- Neoadjuvant tamoxifen synchronizes ERα binding and gene expression profiles related to outcome and proliferation.Oncotarget · 2016Trial
- From stem cells to somites: Revealing genetic and exogenous factors of human embryogenesis.Stem cell reports · 2026Article
- Gene mutant dosage is associated with prognosis and metastatic tropism in 60,000 clinical cancer samples.Nature genetics · 2026Article
- Performance Evaluation of Whole-Genome Amplification Platforms for Clinical Next-Generation Sequencing with Minimal Nucleic Acid Input.Annals of laboratory medicine · 2026Article
- Detection of Copy-Number Variations in CNS Tumours From Off-Target Reads of Hybrid-Capture Sequencing.Neuropathology and applied neurobiology · 2026Article
- PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.Bioinformatics (Oxford, England) · 2026Article
- Evaluation of quantitative polymerase chain reaction for detecting BRCA1 or BRCA2 copy number loss in high-grade serous ovarian cancer.Scientific reports · 2026Article
- The Added Value of Genome-Wide Copy Numbers to Objectively Resolve Clonality of Multiple Tumors With Pulmonary Involvement and Ambiguous or Inconclusive Mutational Diagnosis.JTO clinical and research reports · 2025Article
- Circulating chromatin reveals the effects of disease-associated variants on gene regulation.bioRxiv : the preprint server for biology · 2025Article
- Functional genomics and tumor microenvironment analysis reveal prognostic biological subtypes in Mantle cell lymphoma.Nature communications · 2025Article
- Unique molecular assay (UMA): a next-generation sequencing targeted panel for efficient and comprehensive genomic profiling and risk stratification of multiple myeloma.Haematologica · 2025Article
- Article
- RCANE: a deep learning algorithm for whole-genome pan-cancer somatic copy number aberration prediction using RNA-seq data.Communications biology · 2025Article
- Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer.Cell reports. Medicine · 2025Article
- Respiration defects limit serine synthesis required for lung cancer growth and survival.Nature communications · 2025Article
- Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts.Genome research · 2025Article
- Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.BMC genomics · 2025Article
86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
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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.