ArticleMolecular biology and evolution2010
Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Genome-wide detection of CNVs and their association with performance traits in broilers.BMC genomics · 2021Article
- Insertion variants missing in the human reference genome are widespread among human populations.BMC biology · 2020Article
- Functional and population genetic features of copy number variations in two dairy cattle populations.BMC genomics · 2020Article
- Identification of loci associated with conception rate in primiparous Holstein cows.BMC genomics · 2019Article
- Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.American journal of human genetics · 2013Article
- Detecting highly differentiated copy-number variants from pooled population sequencing.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2013Article
- Gene copy-number polymorphism caused by retrotransposition in humans.PLoS genetics · 2013Article
- Article
- Population-genetic properties of differentiated human copy-number polymorphisms.American journal of human genetics · 2011Article
- Article
- Human copy number variation and complex genetic disease.Annual review of genetics · 2011Article
- Gene copy-number polymorphism in nature.Proceedings. Biological sciences · 2010Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have found that CNVs are less likely to be in strong LD with flanking markers. We hypothesized that this "taggability gap" can be explained by duplication events that place paralogous sequences far apart. In support of our hypothesis, we find that duplications are significantly less likely than deletions to have a "tag" SNP, even after controlling for CNV length, allele frequency, and availability of appropriate flanking SNPs. Using a novel likelihood method, we are able to show that many complex CNVs--those due to multiple duplication or deletion polymorphisms--are made up of two loci with little LD between them. Additionally, we find that many polymorphic duplications detected in a recent clone-based study are located far from their parental loci. We also examine two other common hypotheses for the taggability gap, and find that recurrent mutation of both deletions and duplications appears to have an effect on LD, but that lower SNP density around CNVs has no effect. Overall, our results suggest that a substantial fraction of CNVs caused by duplication cannot be tagged by markers flanking the parental locus because they have changed genomic location.
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