ArticleNucleic acids research2015
CODEX: a normalization and copy number variation detection method for whole exome sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Consensus-based detection of aetiologic copy number variants for syndromic orofacial clefts utilising whole exome sequencing of case parent trios.BMC genomic data · 2026Article
- Consensus-based Detection of Aetiologic Copy Number Variants For Syndromic Orofacial Clefts Utilising Whole Exome Sequencing of Case Parent Trios.Research square · 2026Article
- A convolutional attention model classifies copy number variants from whole exome sequencing.Scientific reports · 2026Article
- Developing an interpretable machine learning model via SHAP to predict HCC postoperative survival based on tumor immune microenvironment CODEX immunomics and MRI.Cancer imaging : the official publication of the International Cancer Imaging Society · 2026Article
- BayesCNV: A Bayesian Hierarchical Model for Sensitive and Specific Copy Number Estimation in Cell Free DNA.Diagnostics (Basel, Switzerland) · 2026Article
- CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization.Nucleic acids research · 2026Article
- <italic>WT1</italic> Deletion in 46,XY DSD: The Importance of Copy Number Variant Analysis.Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation · 2026Article
- Article
- EMcnv: enhancing CNV detection performance through ensemble strategies with heterogeneous meta-graph neural networks.Briefings in bioinformatics · 2025Article
- Diagnostic Utility of Trio-Exome Sequencing for Children With Neurodevelopmental Disorders.JAMA network open · 2025Article
- CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.Bioinformatics (Oxford, England) · 2024Article
- Eukaryotic translation initiation factorExperimental and therapeutic medicine · 2024Article
- HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.Nucleic acids research · 2024Article
- labelSeg: segment annotation for tumor copy number alteration profiles.Briefings in bioinformatics · 2024Article
- GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data.Nature genetics · 2023Article
- Article
- A novel missense mutation inMolecular medicine reports · 2023Article
- Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning.Nucleic acids research · 2022Article
- Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data.BMC bioinformatics · 2022Article
23 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases. Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from exome sequencing is challenging due to the high level of biases and artifacts. We propose CODEX, a normalization and CNV calling procedure for whole exome sequencing data. The Poisson latent factor model in CODEX includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data. CODEX is compared to existing methods on a population analysis of HapMap samples from the 1000 Genomes Project, and shown to be more accurate on three microarray-based validation data sets. We further evaluate performance on 222 neuroblastoma samples with matched normals and focus on a well-studied rare somatic CNV within the ATRX gene. We show that the cross-sample normalization procedure of CODEX removes more noise than normalizing the tumor against the matched normal and that the segmentation procedure performs well in detecting CNVs with nested structures.
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