Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

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 order to detect minisatellite VNTRs, i.e., those with pattern sizes ?7 bp. We detected 35 638 VNTR and classified 5676 as commonly polymorphic (i.e. non-reference alleles occurring >5% of the population). Commonly were found be enriched genomic regions regulatory function, i.e. transcription start sites enhancers. Investigation VNTRs context population ancestry revealed 1096 contained population-specific could used classify into super-populations near-perfect accuracy. Search for quantitative trait (eQTLs), among proximal genes, indicated 187 genes expression differences correlated genotype. validated predictions several ways, including experimentally, through identification predicted long reads, by comparisons showing consistency between platforms. This study is most comprehensive analysis date.