ArticleNucleic acids research2019
EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide association meta-analysis and rare copy number variant analysis of treatment-resistant depression.Molecular psychiatry · 2025Pooled it
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.Bioinformatics (Oxford, England) · 2026Article
- CNValidatron: accurate and efficient validation of PennCNV calls using computer vision.BMC bioinformatics · 2026Article
- CNValidatron: Accurate And Efficient Validation of PennCNV Calls Using Computer Vision.bioRxiv : the preprint server for biology · 2025Article
- The Eating Disorders Genetics Initiative 2 (EDGI2): study protocol.BMC psychiatry · 2025Article
- Genome-wide copy number variation association study in anorexia nervosa.Molecular psychiatry · 2025Article
- Transcriptomic and genetic analysis suggests a role for mitochondrial dysregulation in schizophrenia.medRxiv : the preprint server for health sciences · 2025Article
- EMcnv: enhancing CNV detection performance through ensemble strategies with heterogeneous meta-graph neural networks.Briefings in bioinformatics · 2025Article
- Copy Number Variations in Neuropsychiatric Disorders.International journal of molecular sciences · 2023Review
- Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis.Schizophrenia bulletin · 2023Article
- BMI-CNV: a Bayesian framework for multiple genotyping platforms detection of copy number variants.Genetics · 2022Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Multiclass Cancer Prediction Based on Copy Number Variation Using Deep Learning.Computational intelligence and neuroscience · 2022Article
- Patient Endothelial Colony-Forming Cells to Model Coronary Artery Disease Susceptibility and Unravel the Role of Dysregulated Mitochondrial Redox Signalling.Antioxidants (Basel, Switzerland) · 2021Article
- Implications of germline copy-number variations in psychiatric disorders: review of large-scale genetic studies.Journal of human genetics · 2021Review
- A Novel Computational Framework to Predict Disease-Related Copy Number Variations by Integrating Multiple Data Sources.Frontiers in genetics · 2021Article
- A genome-wide analysis of copy number variation in Murciano-Granadina goats.Genetics, selection, evolution : GSE · 2020Article
- The Personal Genome Project-UK, an open access resource of human multi-omics data.Scientific data · 2019Article
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Authors and funding
11 authors.
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Abstract
The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose a novel ensemble learning framework, ensembleCNV, to detect and genotype CNVs using single nucleotide polymorphism (SNP) array data. EnsembleCNV (a) identifies and eliminates batch effects at raw data level; (b) assembles individual CNV calls into CNV regions (CNVRs) from multiple existing callers with complementary strengths by a heuristic algorithm; (c) re-genotypes each CNVR with local likelihood model adjusted by global information across multiple CNVRs; (d) refines CNVR boundaries by local correlation structure in copy number intensities; (e) provides direct CNV genotyping accompanied with confidence score, directly accessible for downstream quality control and association analysis. Benchmarked on two large datasets, ensembleCNV outperformed competing methods and achieved a high call rate (93.3%) and reproducibility (98.6%), while concurrently achieving high sensitivity by capturing 85% of common CNVs documented in the 1000 Genomes Project. Given this CNV call rate and accuracy, which are comparable to SNP genotyping, we suggest ensembleCNV holds significant promise for performing genome-wide CNV association studies and investigating how CNVs predispose to human diseases.
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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.