ArticleGenome biology2018
CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Genomic alterations are associated with response to aromatase inhibitor therapy for ER-positive postmenopausal ductal carcinoma in situ: (CALGB 40903, Alliance).Breast cancer research : BCR · 2025Trial
- The association of complex genetic background with the prognosis of acute leukemia with ambiguous lineage.Scientific reports · 2021Trial
- Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing.The Journal of clinical investigation · 2021Trial
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- A UniqueInternational journal of molecular sciences · 2026Article
- CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data.bioRxiv : the preprint server for biology · 2026Article
- PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.Bioinformatics (Oxford, England) · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.Nucleic acids research · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.bioRxiv : the preprint server for biology · 2025Article
- Beyond the obvious: targeting the SLC transportome and non-canonical drug transport mechanisms in cancer therapy.Investigational new drugs · 2025Review
- Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.BMC genomics · 2025Article
- Detection of germline CNVs from gene panel data: benchmarking the state of the art.Briefings in bioinformatics · 2024Article
- Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis.Scientific reports · 2024Article
- Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads.American journal of human genetics · 2024Article
- Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield.Scientific reports · 2024Article
- Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility.Cell reports methods · 2023Article
- Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases.Human genomics · 2023Article
- Article
- ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets.Molecular therapy. Nucleic acids · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.
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