Variable number tandem repeat
Variable number tandem repeats (VNTRs), also known as minisatellites, are segments of DNA in which a short sequence motif, typically 10 to 100 base pairs in length, is repeated multiple times in a head-to-tail tandem arrangement, with the number of repeats varying significantly among individuals within a population.[1][2] This variability arises from high mutation rates involving insertions or deletions of repeat units, making VNTRs highly polymorphic genetic markers that contribute substantially to human genetic diversity.[3] Discovered in the mid-1980s by Alec Jeffreys during research on inherited diseases, VNTRs were quickly recognized for their potential in individual identification due to their unique patterns in non-coding regions of the genome.[2] In forensic science, VNTR analysis, often via restriction fragment length polymorphism (RFLP), enabled the first DNA fingerprinting techniques, allowing differentiation of individuals (except identical twins) by comparing the lengths of these repeats at multiple loci.[4][5] Beyond forensics, VNTRs play key roles in population genetics, where they facilitate studies of ancestry, migration, and evolutionary relationships through their allele frequency distributions.[6] In human health, VNTRs are implicated in both Mendelian and complex diseases, as variations in repeat number can disrupt gene function or regulation; for instance, they have been associated with conditions like Alzheimer's disease, obesity, and certain familial cancers.[3] Many VNTRs occur in regulatory regions such as promoters and untranslated regions (UTRs), where changes in copy number modulate the expression of nearby genes, influencing traits and disease susceptibility with effect sizes often exceeding those of single nucleotide polymorphisms (SNPs).[3] Although largely replaced by shorter short tandem repeats (STRs) in modern genotyping due to technical advantages, VNTRs remain valuable for understanding structural variation and its biological impacts, comprising about 3% of the human genome.[7][8]Definition and Molecular Structure
Definition
Variable number tandem repeats (VNTRs) are regions of non-coding DNA characterized by tandemly repeated short sequences, typically ranging from 10 to 100 base pairs per repeat unit, in which the number of copies varies among individuals, creating polymorphic loci.[9] These variations arise from differences in the repeat copy number at specific genomic locations, distinguishing VNTRs as a key form of structural genetic polymorphism.[10] VNTRs, also known as minisatellites, were first identified in the mid-1980s by Alec Jeffreys and colleagues during investigations into repetitive DNA sequences near the human insulin and myoglobin genes, which unexpectedly revealed highly variable tandem repeat regions and paved the way for DNA fingerprinting techniques.[9] This discovery highlighted VNTRs' potential for individual identification due to their extensive allelic diversity. A defining feature of VNTRs is their hypervariability, driven by copy number differences that enhance genetic diversity across populations without impacting protein-coding regions, as these elements are predominantly located in non-coding genomic areas.[10] For instance, the VNTR in the human myoglobin gene is located in an intron, where variations in the length of the repetitive sequence may influence gene regulation.Core Structure and Repeat Units
Variable number tandem repeats (VNTRs) are genomic loci characterized by arrays of short, tandemly repeated DNA sequences arranged in a head-to-tail orientation, with no intervening nucleotides between repeat units. This tandem architecture creates contiguous blocks of repetitive DNA, where the repeat units are typically identical or highly similar, forming the core polymorphic element of the locus.[11] In VNTRs, particularly the minisatellite subclass, each repeat unit ranges from 10 to 100 base pairs (bp) in length, though commonly 10 to 60 bp, and these units are often organized around a conserved core motif such as a 10-15 bp sequence like GNN or related variants. For instance, many human minisatellites share a core sequence motif that facilitates their detection and contributes to the structural uniformity within the array. The overall array length can span 0.1 to 20 kilobases (kb), depending on the number of repeats present.[12][13] Flanking the VNTR array on both sides are unique, non-repetitive DNA sequences that serve as critical anchors for molecular analysis. These flanking regions enable targeted amplification of the VNTR locus via polymerase chain reaction (PCR) using primers designed to anneal specifically to them, allowing precise isolation of the variable repeat array for downstream characterization.[14][15] The polymorphism of VNTRs arises primarily from differences in the number of repeat units within the array, resulting in alleles of varying total lengths that can differ by hundreds to thousands of bp between individuals. This length variation can be resolved and sized using techniques such as gel electrophoresis of PCR amplicons, where alleles migrate differently based on size, or more precisely through DNA sequencing to count the exact repeat number. For example, one allele might contain 5 repeat units (shorter overall length), while another has 10 units (longer length), producing distinct banding patterns or sequence read lengths.[16][17][18] To illustrate, consider a schematic of a VNTR locus:- Flanking region A (unique sequence) – [Repeat unit 1] – [Repeat unit 2] – ... – [Repeat unit n] – Flanking region B (unique sequence)