ArticleNucleic acids research2013
ParseCNV integrative copy number variation association software with quality tracking.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders.Genome medicine · 2017Pooled it
- Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.Circulation research · 2014Trial
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Genetic analysis of two bladder exstrophy populations of South Asian and North American origin.Journal of pediatric urology · 2025Article
- Copy Number Variant Architecture of Child Psychopathology and Cognitive Development in the ABCD Study.The American journal of psychiatry · 2025Article
- Integrated Genomic Approaches to Elucidate the Genetic Basis of Brugada Syndrome in Taiwanese Patients.Bioinformatics and biology insights · 2025Article
- Genome-wide association studies for economically important traits in mink using copy number variation.Scientific reports · 2024Article
- Article
- Rare recurrent copy number variations in metabotropic glutamate receptor interacting genes in children with neurodevelopmental disorders.Journal of neurodevelopmental disorders · 2023Article
- ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies.European journal of human genetics : EJHG · 2023Article
- ParseCNV2: a versatile and integrated tool for copy number variation association studies.European journal of human genetics : EJHG · 2023Article
- Article
- MONTAGE: a new tool for high-throughput detection of mosaic copy number variation.BMC genomics · 2021Article
- Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep.Frontiers in genetics · 2021Article
- Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations.Nature communications · 2020Article
- Article
- Deletions in Genes Participating in Innate Immune Response Modify the Clinical Course of Andes Orthohantavirus Infection.Viruses · 2019Article
- Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2019Article
- Microduplications at the 15q11.2 BP1-BP2 locus are enriched in patients with anorexia nervosa.Journal of psychiatric research · 2019Article
- A comprehensive screening of copy number variability in dementia with Lewy bodies.Neurobiology of aging · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A number of copy number variation (CNV) calling algorithms exist; however, comprehensive software tools for CNV association studies are lacking. We describe ParseCNV, unique software that takes CNV calls and creates probe-based statistics for CNV occurrence in both case-control design and in family based studies addressing both de novo and inheritance events, which are then summarized based on CNV regions (CNVRs). CNVRs are defined in a dynamic manner to allow for a complex CNV overlap while maintaining precise association region. Using this approach, we avoid failure to converge and non-monotonic curve fitting weaknesses of programs, such as CNVtools and CNVassoc, and although Plink is easy to use, it only provides combined CNV state probe-based statistics, not state-specific CNVRs. Existing CNV association methods do not provide any quality tracking information to filter confident associations, a key issue which is fully addressed by ParseCNV. In addition, uncertainty in CNV calls underlying CNV associations is evaluated to verify significant results, including CNV overlap profiles, genomic context, number of probes supporting the CNV and single-probe intensities. When optimal quality control parameters are followed using ParseCNV, 90% of CNVs validate by polymerase chain reaction, an often problematic stage because of inadequate significant association review. ParseCNV is freely available at http://parsecnv.sourceforge.net.
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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.