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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Related Experiment Video

Updated: Sep 18, 2025

Measurement of BK-polyomavirus Non-Coding Control Region Driven Transcriptional Activity Via Flow Cytometry
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Single-nucleotide polymorphisms within the BK polyomavirus non-coding control region are genotype-associated.

Tiana A Walder1, Elizabeth A Odegard1, Heidi L Meeds1

  • 1Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.

Microbiology Spectrum
|June 24, 2025
PubMed
Summary

Genotype-associated polymorphisms (GAPs) in the BK polyomavirus (BKPyV) non-coding control region are linked to specific genotypes. These GAPs can identify BKPyV strains and offer insights into viral disease mechanisms.

Keywords:
BK polyomavirusgenotypehematopoietic cell transplantationnon-coding control regionsingle-nucleotide polymorphismssubtypetranscription factor binding sitesviral diversity

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Area of Science:

  • Virology
  • Molecular Biology
  • Genetics

Background:

  • BK polyomavirus (BKPyV) is a significant cause of complications in transplant recipients, including hemorrhagic cystitis and nephropathy.
  • Understanding the genetic diversity of BKPyV is crucial for improving transplant outcomes and exploring disease mechanisms.

Purpose of the Study:

  • To investigate genotype-associated polymorphisms (GAPs) within the non-coding control region (NCCR) of BKPyV.
  • To determine if GAPs can be used for genotyping clinical BKPyV strains and identify potential functional sites.

Main Methods:

  • Analysis of BKPyV genome sequences to identify mutations within the NCCR.
  • Correlation of identified mutations with known BKPyV genotypes.
  • Bioinformatic prediction of transcription factor binding sites within the NCCR.

Main Results:

  • Many point mutations in the BKPyV NCCR are genotype-associated, termed genotype-associated polymorphisms (GAPs).
  • GAPs correlate with hypervariable regions and are inherent to specific BKPyV genotypes.
  • GAPs were found within predicted transcription factor binding sites, suggesting functional relevance.

Conclusions:

  • GAPs in the BKPyV NCCR are reliable markers for genotyping clinical strains.
  • These GAPs represent potential targets for functional studies into BKPyV pathogenesis.
  • Understanding BKPyV genomic diversity, including GAPs, can enhance screening and elucidate disease factors.