ArticleGenome research2012
Copy number variation detection and genotyping from exome sequence data.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 409 papers, 2 of them syntheses that pooled it.
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Who cites it
409 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A frameshift mutation in theMolecular medicine reports · 2024Pooled it
- A novel AGK splicing mutation in a patient with Sengers syndrome and left ventricular non-compaction cardiomyopathy.Pediatric research · 2023Pooled it
- Characterization of familial short stature with or without skeletal dysplasia in a Pakistani cohort reveals founder mutations as well as novel variants.Human genetics · 2026Article
- Spectrum of DNA Variants Underlying Deafness in an Ecuadorian Cohort.Biochemical genetics · 2026Article
- Genetic and hemostatic characterization of PAI-1 deficiency and isolated hyperfibrinolysis: data from the RBiN study.Research and practice in thrombosis and haemostasis · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.Bioinformatics (Oxford, England) · 2026Article
- Genotypic and phenotypic features of 23 Egyptian patients with tuberous sclerosis complex.BMC pediatrics · 2026Observational
- Integrating genomic features for prognosis in Chinese patients with diffuse large B-cell lymphoma following R-CHOP therapy.Annals of hematology · 2026Article
- Insight into Haploinsufficiency of the ERBB4 Gene: Expanding the Spectrum of Associated Phenotypes.Journal of autism and developmental disorders · 2026Article
- CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data.bioRxiv : the preprint server for biology · 2026Article
- Genetic studies identify known and novel variants for recessively inherited moderate to severe hearing loss in consanguineous families from Pakistan.Scientific reports · 2026Article
- Detection of Copy-Number Variations in CNS Tumours From Off-Target Reads of Hybrid-Capture Sequencing.Neuropathology and applied neurobiology · 2026Article
- Exploring the hereditary genetic mutational landscape of breast and ovarian cancer in Estonia.Scientific reports · 2026Article
- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
- ML-ExonCNV: a robust XGBoost multi-expert ensemble framework for rare exon CNV detection in whole-exome sequencing data.Briefings in bioinformatics · 2026Article
- Studies on intellectual disability identify variants in established genes as well as confirm candidature of new genes.Scientific reports · 2026Article
- Molecular characterization of recessively inherited ataxic and neuropathic disorders in consanguineous Pakistani families.Scientific reports · 2026Article
- Article
- BayesCNV: A Bayesian Hierarchical Model for Sensitive and Specific Copy Number Estimation in Cell Free DNA.Diagnostics (Basel, Switzerland) · 2026Article
349 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered exome-based detection and characterization of genic copy number variation. We developed a novel method using singular value decomposition (SVD) normalization to discover rare genic copy number variants (CNVs) as well as genotype copy number polymorphic (CNP) loci with high sensitivity and specificity from exome sequencing data. We estimate the precision of our algorithm using 122 trios (366 exomes) and show that this method can be used to reliably predict (94% overall precision) both de novo and inherited rare CNVs involving three or more consecutive exons. We demonstrate that exome-based genotyping of CNPs strongly correlates with whole-genome data (median r(2) = 0.91), especially for loci with fewer than eight copies, and can estimate the absolute copy number of multi-allelic genes with high accuracy (78% call level). The resulting user-friendly computational pipeline, CoNIFER (copy number inference from exome reads), can reliably be used to discover disruptive genic CNVs missed by standard approaches and should have broad application in human genetic studies of disease.
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Registered trials
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