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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Human Genetics01:28

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
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Updated: Aug 11, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3).

Abner T Apsley1,2, Emma R Domico1, Max A Verbiest3,4,5

  • 1Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA.

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|February 8, 2023
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Researchers characterized novel variable number tandem repeats (VNTRs) in the dopamine transporter gene (SLC6A3). A newly identified hyper-VNTR in intron 8 may function as a recombination hotspot due to its sequence and PRDM9 binding sites.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Neuroscience

Background:

  • The dopamine transporter gene (SLC6A3) is crucial for neurotransmission and has been studied in various genetic association studies.
  • Previous genetic association studies of SLC6A3 have yielded inconsistent results, particularly concerning variable number tandem repeats (VNTRs).

Purpose of the Study:

  • To characterize previously unexamined VNTRs within the SLC6A3 gene.
  • To investigate the sequence properties and potential functional significance of these VNTRs, including novel variants.

Main Methods:

  • Utilized the Tandem Repeat Annotation Library to analyze 64 long-read haplotype-phased SLC6A3 sequences.
  • Characterized sequence similarity, allele correlations (SNP-SNP, SNP-VNTR, VNTR-VNTR), and identified a novel hyper-VNTR (hyVNTR).
  • Performed in silico prediction and circular dichroism spectroscopy to assess G-quadruplex formation and identified PRDM9 binding sites.

Main Results:

  • Identified five VNTRs in SLC6A3, reporting sequence similarity and allele correlations.
  • Discovered a novel hyVNTR in intron 8 with a variable repeat copy number (3.4-133.4) and high G+C content (82%).
  • Confirmed the hyVNTR's potential to form G-quadruplexes and identified multiple PRDM9 binding sites, suggesting it as a potential recombination hotspot.

Conclusions:

  • The characterization of novel VNTRs in SLC6A3 provides new genetic markers for association studies.
  • The identified hyVNTR in intron 8 exhibits unique structural and functional properties, including G-quadruplex formation and PRDM9 binding.
  • The hyVNTR's characteristics suggest a potential role as a recombination hotspot, influencing SLC6A3 genetic diversity and association study outcomes.