ArticleAmerican journal of human genetics2011
Population-genetic properties of differentiated human copy-number polymorphisms.
Article in American journal of human genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 93 citations in OpenAlex.
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- Whole genome sequencing of 1427 Mexican individuals from the oriGen cohort.Nature communications · 2026Article
- Machine learning-based prediction of human structural variation and characterization of associated sequence determinants.bioRxiv : the preprint server for biology · 2026Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
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- Genomic structural variation: A complex but important driver of human evolution.American journal of biological anthropology · 2023Review
- Frequent copy number variants in a cohort of Mexican-Mestizo individuals.Molecular cytogenetics · 2023Article
- The individual and global impact of copy-number variants on complex human traits.American journal of human genetics · 2022Article
- Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- Multi-allelic positional Burrows-Wheeler transform.BMC bioinformatics · 2019Article
- Effector variation at tandem gene arrays in tissue-dwelling coccidia: who needs antigenic variation anyway?Current opinion in microbiology · 2018Review
- POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Article
- Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations.Frontiers in genetics · 2018Article
- Benign, Pathogenic and Copy Number Variations of Unknown Clinical Significance in Patients with Congenital Malformations and Developmental Delay.Balkan journal of medical genetics : BJMG · 2017Article
- Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse.Cancer medicine · 2017Article
- CNV discovery for milk composition traits in dairy cattle using whole genome resequencing.BMC genomics · 2017Article
- Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children.BioMed research international · 2017Article
- Human adaptation and evolution by segmental duplication.Current opinion in genetics & development · 2016Review
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Copy-number variants (CNVs) can reach appreciable frequencies in the human population, and recent discoveries have shown that several of these copy-number polymorphisms (CNPs) are associated with human diseases, including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. We developed a method based on single-channel intensity data and benchmarked against copy numbers determined from sequencing read depth to successfully obtain CNP genotypes for 1495 CNPs from 487 human DNA samples of diverse ethnic backgrounds. This microarray contained CNPs in segmental duplication-rich regions and insertions of sequences not represented in the reference genome assembly or on standard SNP microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that biallelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although biallelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multicopy CNPs do not (40% with r > 0.8). We selected a subset of CNPs for further characterization in 1876 additional samples from 62 populations; this revealed striking population-differentiated structural variants in genes of clinical significance such as OCLN, a tight junction protein involved in hepatitis C viral entry. Our microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that cannot be imputed from SNP genotypes) might have contributed disproportionately to human diversity and selection.
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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.