ArticleCancers2021
A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data.
Article in Cancers, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
- Trial
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- 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
- CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data.bioRxiv : the preprint server for biology · 2026Article
- Prenatal Whole-Genome Sequencing for Fetal Anomalies: Diagnostic Performance, Challenges, and Clinical Implications.International journal of molecular sciences · 2026Review
- Consensus-based Detection of Aetiologic Copy Number Variants For Syndromic Orofacial Clefts Utilising Whole Exome Sequencing of Case Parent Trios.Research square · 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
- An NGS-based investigation of copy number variants in the diagnosis and severity of adult polycystic kidney disease.European journal of human genetics : EJHG · 2026Article
- Digital multiplex ligation-dependent probe amplification identifies exon-level copy number variants in patients with suspected hereditary cancer and negative next-generation sequencing results.Molecular biology reports · 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
- Association of Y-chromosomal gr/gr deletions with testicular germ cell tumor: whole-genome analysis of 198,306 individuals.medRxiv : the preprint server for health sciences · 2026Article
- CNValidatron: accurate and efficient validation of PennCNV calls using computer vision.BMC bioinformatics · 2026Article
- Article
- Replication stress increases de novo CNVs across the malaria parasite genome.Nucleic acids research · 2026Article
- Genetic variations associated with immediate hypersensitivity reactions to iodinated contrast media: A whole exome sequencing study.PloS one · 2026Article
- Article
- Past, present, and future of genomic technologies in cerebellar ataxias.Journal of neurology · 2025Review
- Recommendations for bioinformatics in clinical practice.Genome medicine · 2025Review
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard-SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.
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Registered trials
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