ArticleHuman heredity2011
Copy number variation accuracy in genome-wide association studies.
Article in Human heredity, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- CNV-Finder: streamlining copy number variation discovery.Bioinformatics advances · 2026Article
- Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Identification of novel variants underlying non-syndromic primary ovarian insufficiency using a targeted NGS gene panel.Frontiers in endocrinology · 2025Article
- Chromosomal quality control in hPSCs: A practical guide to SNP array analysis with GenomeStudio.Frontiers in cell and developmental biology · 2025Article
- A novel scatterplot-based method to detect copy number variation (CNV).Frontiers in genetics · 2023Article
- A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer.Molecular oncology · 2021Article
- A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data.Genome medicine · 2020Article
- The Role of Constitutional Copy Number Variants in Breast Cancer.Microarrays (Basel, Switzerland) · 2015Review
- The association of copy number variation and percent mammographic density.BMC research notes · 2015Article
- On the association of common and rare genetic variation influencing body mass index: a combined SNP and CNV analysis.BMC genomics · 2014Article
- A genome-wide association study on copy-number variation identifies a 11q11 loss as a candidate susceptibility variant for colorectal cancer.Human genetics · 2014Article
- Biological relevance of CNV calling methods using familial relatedness including monozygotic twins.BMC bioinformatics · 2014Article
- Identifying Potential Regions of Copy Number Variation for Bipolar Disorder.Microarrays (Basel, Switzerland) · 2014Article
- Copy number variations in 6q14.1 and 5q13.2 are associated with alcohol dependence.Alcoholism, clinical and experimental research · 2012Article
- Detectable clonal mosaicism from birth to old age and its relationship to cancer.Nature genetics · 2012Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
BACKGROUND/
aimCopy number variations (CNVs) are a major source of alterations among individuals and are a potential risk factor in many diseases. Numerous diseases have been linked to deletions and duplications of these chromosomal segments. Data from genome-wide association studies and other microarrays may be used to identify CNVs by several different computer programs, but the reliability of the results has been questioned.
methodsTo help researchers reduce the number of false-positive CNVs that need to be followed up with laboratory testing, we evaluated the relative performance of CNVPartition, PennCNV and QuantiSNP, and developed a statistical method for estimating sensitivity and positive predictive values of CNV calls and tested it on 96 duplicate samples in our dataset.
resultsWe found that the positive predictive rate increases with the number of probes in the CNV and the size of the CNV, with the highest positive predicted rates in CNVs of at least 500 kb and at least 100 probes. Our analysis also indicates that identifying CNVs reported by multiple programs can greatly improve the reproducibility rate and the positive predicted rate.
conclusionOur methods can be used by investigators to identify CNVs in genome-wide data with greater reliability.
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