ArticleBMC genomics2021
Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genome-wide copy number variation drives adaptive evolution inCurrent zoology · 2026Article
- Identification of Copy Number Variations in Familial Hemiplegic Migraine Genes in Suspected Hemiplegic Migraine Patients.Biomedicines · 2026Article
- Copy Number Variant Duplications Associated with Essential Tremor.Tremor and other hyperkinetic movements (New York, N.Y.) · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- CNV-Finder: streamlining copy number variation discovery.Bioinformatics advances · 2026Article
- CNV-Finder: Streamlining Copy Number Variation Discovery.bioRxiv : the preprint server for biology · 2025Article
- Monogenic diabetes: An evidence-based clinical approach.World journal of diabetes · 2025Review
- Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.BMC genomics · 2025Article
- Contribution of copy number variations to education, socioeconomic status and cognition from a genome-wide study of 305,401 subjects.Molecular psychiatry · 2025Article
- Chromosomal quality control in hPSCs: A practical guide to SNP array analysis with GenomeStudio.Frontiers in cell and developmental biology · 2025Article
- Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline.BMC bioinformatics · 2024Article
- Review
- Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN.Scientific reports · 2024Article
- The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young.Genome medicine · 2024Article
- Genome-wide investigation to assess copy number variants in the Italian local chicken population.Journal of animal science and biotechnology · 2024Article
- Cas9-targeted-based long-read sequencing for genetic screening ofFrontiers in genetics · 2024Article
- Identification of anInternational journal of molecular sciences · 2023Article
- Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies.Molecular genetics & genomic medicine · 2023Article
- Enhancing genomic mutation data storage optimization based on the compression of asymmetry of sparsity.Frontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundSNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with its own limitations and biases, many of which are well-known, but not all of them are thoroughly quantified.
resultsWe assembled an ensemble of public datasets of published CNV calls and raw data for the well-studied Genome in a Bottle individual NA12878. This assembly represents a variety of methods and pipelines used for CNV calling from array, short- and long-read technologies. We then performed cross-technology comparisons regarding their ability to call CNVs. Different from other studies, we refrained from using the golden standard. Instead, we attempted to validate the CNV calls by the raw data of each technology.
conclusionsOur study confirms that long-read platforms enable recalling CNVs in genomic regions inaccessible to arrays or short reads. We also found that the reproducibility of a CNV by different pipelines within each technology is strongly linked to other CNV evidence measures. Importantly, the three technologies show distinct public database frequency profiles, which differ depending on what technology the database was built on.
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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.