ArticleNature genetics2023
GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 92 papers, 1 of them a synthesis that pooled it.
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Who cites it
92 citing papers in PubMed, 1 synthesis or guideline pooled it, 105 citations in OpenAlex.
- Contribution of copy number variants to schizophrenia in East Asian populations.Nature genetics · 2026Pooled it
- Whole-exome sequencing in individuals with obsessive-compulsive disorder and chronic tic disorders identifies 36 large-effect risk genes.Nature neuroscience · 2026Article
- Sequencing approaches in hereditary cancer testing: strengths, limitations and future directions.European journal of human genetics : EJHG · 2026Review
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- Systematic analysis of homozygous autosomal copy number losses in exomes improves diagnostic yield and uncovers ultra-rare recessive disorders.European journal of human genetics : EJHG · 2026Article
- Automated reanalysis of genomic data for rare disease diagnostics at scale.Nature medicine · 2026Article
- A blended genome and exome sequencing method captures genetic variation in an unbiased and cost-effective manner.Nature genetics · 2026Article
- Germline determinants of risk and molecular subtype in young-onset lung cancer.medRxiv : the preprint server for health sciences · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 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
- Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.Bioinformatics (Oxford, England) · 2026Article
- Genetic architecture of two novel chicken breeds from Xinjiang: A whole-genome sequencing study on Ili gamecock and Yemili Chicken.Poultry science · 2026Article
- Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank.American journal of human genetics · 2026Article
- Comprehensive analysis ofmedRxiv : the preprint server for health sciences · 2026Article
- A novel compound heterozygosity in AAAS gene in two Greek siblings: expanding the genotypic landscape of Allgrove syndrome.Neurogenetics · 2026Article
- Article
- Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor.Nature communications · 2026Article
- Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
15 authors at 1 institution in 1 country.
Funding
Abstract
Copy number variants (CNVs) are major contributors to genetic diversity and disease. While standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short variants, technical challenges have confounded uniform large-scale CNV analyses from whole-exome sequencing (WES) data. Given the profound impact of rare and de novo coding CNVs on genome organization and human disease, we developed GATK-gCNV, a flexible algorithm to discover rare CNVs from sequencing read-depth information, complete with open-source distribution via GATK. We benchmarked GATK-gCNV in 7,962 exomes from individuals in quartet families with matched genome sequencing and microarray data, finding up to 95% recall of rare coding CNVs at a resolution of more than two exons. We used GATK-gCNV to generate a reference catalog of rare coding CNVs in WES data from 197,306 individuals in the UK Biobank, and observed strong correlations between per-gene CNV rates and measures of mutational constraint, as well as rare CNV associations with multiple traits. In summary, GATK-gCNV is a tunable approach for sensitive and specific CNV discovery in WES data, with broad applications.
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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.