Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences
| Autor: | Samantha D. Drinan, Marzieh Eslami Rasekh, Yozen Hernandez, Juan I. Fuxman Bass, Gary Benson |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
Minisatellite Repeat Population Datasets as Topic Context (language use) Data Resources and Analyses Minisatellite Repeats Biology Quantitative trait locus Genome 03 medical and health sciences 0302 clinical medicine Tandem repeat Genotype Genetics Humans education Genotyping Alleles 030304 developmental biology 0303 health sciences education.field_of_study Polymorphism Genetic Whole Genome Sequencing Genome Human Variable number tandem repeat Minisatellite Enhancer Elements Genetic Gene Expression Regulation Transcription Initiation Site 030217 neurology & neurosurgery |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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 2,770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35,638 VNTR loci and classified 5,676 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 1,096 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. |
| Databáze: | OpenAIRE |
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