ArticleHuman molecular genetics2010
Population-genetic nature of copy number variations in the human genome.
Article in Human molecular genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Article
- Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- Copy number variation in human genomes from three major ethno-linguistic groups in Africa.BMC genomics · 2020Article
- Functional and population genetic features of copy number variations in two dairy cattle populations.BMC genomics · 2020Article
- Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer.Royal Society open science · 2017Article
- Genomic and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumors.Genes, chromosomes & cancer · 2017Article
- High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.Scientific reports · 2017Article
- Copy Number Variations in Tilapia Genomes.Marine biotechnology (New York, N.Y.) · 2017Article
- 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
- Population-genetic properties of differentiated copy number variations in cattle.Scientific reports · 2016Article
- Article
- Article
- Estrogen receptor 1 gene (TA)n polymorphism is associated with lone atrial fibrillation in men.Croatian medical journal · 2014Article
- Identification of genomic loci associated with Rhodococcus equi susceptibility in foals.PloS one · 2014Article
- Impact of constitutional copy number variants on biological pathway evolution.BMC evolutionary biology · 2013Article
- Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene.Genome biology and evolution · 2013Article
- Both positive and negative selection pressures contribute to the polymorphism pattern of the duplicated human CYP21A2 gene.PloS one · 2013Article
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.Frontiers in genetics · 2013Article
- Association of genetic copy number variations at 11 q14.2 with brain regional volume differences in an alcohol use disorder population.Alcohol (Fayetteville, N.Y.) · 2012Article
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Authors and funding
10 authors.
Funding
Abstract
Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000-4000 CNVs (4-6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV-SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV-SNP linkage disequilibrium (LD) for 500-900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP-SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.
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