ArticleEuropean journal of human genetics : EJHG2022
Combining callers improves the detection of copy number variants from whole-genome sequencing.
Article in European journal of human genetics : EJHG, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Characterizing features of the genetic architecture underlying autism from a multi-ancestry perspective.Molecular psychiatry · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Copy number variant analysis by exome sequencing is an effective approach to optimize diagnostic yield for developmental disorders-the DDD-Africa study.European journal of human genetics : EJHG · 2026Article
- Genetic analysis of neurodegenerative diseases.The Journal of clinical investigation · 2026Review
- GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.Heredity · 2026Article
- Copy Number Variant analysis by exome sequencing is an effective approach to optimize diagnostic yield for developmental disorders - the DDD-Africa study.medRxiv : the preprint server for health sciences · 2026Article
- Case report on multilocus gene deletion and gene conversion at Y-STR loci.International journal of legal medicine · 2026Article
- Toward Graph-Based Decoding of Tumor Evolution: Spatial Inference of Copy Number Variations.Diagnostics (Basel, Switzerland) · 2025Article
- Combined genomics and proteomics unveils elusive variants and vast aetiologic heterogeneity in dystonia.Brain : a journal of neurology · 2025Article
- Copy Number Variation Shapes Structural Genomic Diversity Associated With Ecological Adaptation in the Wild Tomato Solanum chilense.Molecular biology and evolution · 2025Article
- Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome.Molecular cytogenetics · 2025Article
- CCRR: a user-friendly platform for analyzing complex chromosomal rearrangements in tumors.Bioinformatics (Oxford, England) · 2025Article
- Article
- Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.BMC genomics · 2025Article
- Genome-wide association testing beyond SNPs.Nature reviews. Genetics · 2025Review
- Copy number variant analysis improves diagnostic yield in a diverse pediatric exome sequencing cohort.NPJ genomic medicine · 2025Article
- Whole genome sequencing for copy number variant detection to improve diagnosis and management of rare diseases.Developmental medicine and child neurology · 2025Article
- Novel mutation in patients with microcephalic osteodysplastic primordial dwarfism type II (MOPD II).Metabolic brain disease · 2024Article
- A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data.Scientific reports · 2024Article
- CNVoyant a machine learning framework for accurate and explainable copy number variant classification.Scientific reports · 2024Article
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Authors and funding
10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Copy Number Variants (CNVs) are deletions, duplications or insertions larger than 50 base pairs. They account for a large percentage of the normal genome variation and play major roles in human pathology. While array-based approaches have long been used to detect them in clinical practice, whole-genome sequencing (WGS) bears the promise to allow concomitant exploration of CNVs and smaller variants. However, accurately calling CNVs from WGS remains a difficult computational task, for which a consensus is still lacking. In this paper, we explore practical calling options to reach the best compromise between sensitivity and sensibility. We show that callers based on different signal (paired-end reads, split reads, coverage depth) yield complementary results. We suggest approaches combining four selected callers (Manta, Delly, ERDS, CNVnator) and a regenotyping tool (SV2), and show that this is applicable in everyday practice in terms of computation time and further interpretation. We demonstrate the superiority of these approaches over array-based Comparative Genomic Hybridization (aCGH), specifically regarding the lack of resolution in breakpoint definition and the detection of potentially relevant CNVs. Finally, we confirm our results on the NA12878 benchmark genome, as well as one clinically validated sample. In conclusion, we suggest that WGS constitutes a timely and economically valid alternative to the combination of aCGH and whole-exome sequencing.
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