ArticleNucleic acids research2021
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Tandem repeat variation within and between species reveals signatures of selection in humans and chimpanzees.bioRxiv : the preprint server for biology · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- A family portrait of the genomic factors shaping tandem repeat mutagenesis.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- Multisample motif discovery and visualization for tandem repeats.Genome research · 2025Article
- Whole Genome Variable Number Tandem Repeat Analysis in Alzheimer Disease.Neurology. Genetics · 2025Article
- Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats.PLoS computational biology · 2025Article
- Differential Impact of VNTR Polymorphism in the CBS Gene on Gastric and Breast Cancers Risk.Indian journal of clinical biochemistry : IJCB · 2025Article
- Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits.Cell genomics · 2024Article
- Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT andGenome research · 2024Article
- Modification of Huntington's disease by short tandem repeats.Brain communications · 2024Article
- Article
- Characterization of genome-wide STR variation in 6487 human genomes.Nature communications · 2023Article
- The motif composition of variable number tandem repeats impacts gene expression.Genome research · 2023Article
- Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans.Genome research · 2023Article
- A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits.American journal of human genetics · 2022Article
- Serotonin transporter functional polymorphisms potentially increase risk of schizophrenia separately and as a haplotype.Scientific reports · 2022Article
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Authors and funding
5 authors.
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Abstract
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
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