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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.
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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.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Updated: Aug 31, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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A comprehensive meta-analysis and prioritization study to identify vitiligo associated coding and non-coding SNV

Tithi Dutta1, Sayantan Mitra2, Arpan Saha1

  • 1Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India.

Scientific Reports
|August 25, 2022
PubMed
Summary

This study prioritizes vitiligo-associated genetic variants (SNVs) and their target genes. It identifies novel genes like FGFR10P, SUOX, CDK5RAP1, and RERE potentially contributing to vitiligo pathogenesis.

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Area of Science:

  • Genetics
  • Dermatology

Background:

  • Vitiligo is a common skin depigmentation disorder affecting approximately 1% of the population.
  • Genome-Wide Association Studies (GWAS) and Candidate Gene Association Studies (CGAS) have identified numerous single nucleotide variants (SNVs) linked to vitiligo risk.
  • The functional significance of these SNVs in disease development remains largely unclear.

Purpose of the Study:

  • To prioritize single nucleotide variants (SNVs) associated with vitiligo from existing GWAS and CGAS data.
  • To identify and functionally annotate the underlying or target genes of these prioritized SNVs.
  • To explore the potential contribution of these genes to vitiligo pathogenesis.

Main Methods:

  • Extensive data mining and downstream analysis of experimentally validated datasets (e.g., GTEx Portal).
  • Utilized web tools (rSNPBase, RegulomeDB, HaploReg, STRING) for variant and gene prioritization.
  • Functional annotation of prioritized SNVs and their associated genes in the context of vitiligo.

Main Results:

  • Prioritized 13 significant SNVs from an initial set of 291 reported vitiligo-associated SNVs.
  • Identified underlying/target genes for these SNVs, including FGFR10P, SUOX, CDK5RAP1, and RERE.
  • These genes, previously not linked to vitiligo, show strong potential for disease contribution.

Conclusions:

  • This research represents the first effort to functionally annotate vitiligo-associated GWAS and CGAS SNVs and their genes using public domain data.
  • Highlights novel candidate genes (FGFR10P, SUOX, CDK5RAP1, RERE) implicated in vitiligo pathogenesis.
  • Provides a foundation for future research into the functional mechanisms underlying vitiligo.