A study of the variability of minisatellite tandem repeat loci in the human genome based on high-throughput sequencing data
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Abstract
Variable Number Tandem Repeats (VNTRs) are repetitive sequences of DNA which exhibit polymorphism in the number of copies of the repeating pattern. As with the better known SNPs, CNVs, and other mutations, VNTRs are a form of variation in the genome. Diseases such as Fragile X syndrome, and even behavioral disorders, such as ADHD, have been attributed to VNTR polymorphisms, where changes in copy number affect chromosome and protein structure, and gene expression. Microsatellite (TRs with a pattern length <7 nt) VNTRs are well-characterized and have been used for DNA fingerprinting. Minisatellite VNTRs (pattern length ≥7 nt), however, are a relatively understudied source of genetic variation; computational complexity and the lack of specialized tools available make detecting and studying them difficult. The traditional method for examining these features involves targeted amplification and gel electrophoresis to distinguish array lengths. In this work, I discuss our effort to discover a comprehensive set of VNTRs using VNTRseek, a tool developed in Dr. Gary Benson's lab for detecting VNTRs in silico using whole genome sequencing reads. I further discuss the curation and analyses we have performed in order to build a researcher-oriented tool, the VNTRdb, which allows other researchers access to this work and enables them to perform similar analyses. Having a tool with which VNTRs can be detected with relative ease, alongside a well-curated resource for VNTR alleles, will help promote further research into how they may be related to complex diseases, natural variation, or other areas of study.
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Attribution 4.0 International