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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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Comparing Copy Number Variations and SNPs02:26

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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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Single Nucleotide Polymorphisms-SNPs

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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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
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Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case

Samira Bahl1, Ikhlak Ahmed,

  • 1Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi, 110 007, India.

Journal of Genetics
|May 7, 2009
PubMed
Summary

Endogamous Indian populations offer significant potential for genetic studies due to large linkage disequilibrium (LD) regions. This study successfully mapped a spinocerebellar ataxia type 12 (SCA12) gene mutation using minimal single nucleotide polymorphisms (SNPs).

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Area of Science:

  • Genetics
  • Population Genetics
  • Human Disease Genetics

Background:

  • Identifying causal genetic loci is challenging in stratified populations.
  • Linkage Disequilibrium (LD) is crucial for mapping disease genes using surrogate markers.
  • Endogamous populations exhibit extended LD regions, facilitating genetic mapping.

Purpose of the Study:

  • To demonstrate the utility of endogamous Indian populations for mapping disease-causing mutations.
  • To identify causal loci for spinocerebellar ataxia type 12 (SCA12) using minimal single nucleotide polymorphisms (SNPs).
  • To assess the transferability of genetic markers across populations.

Main Methods:

  • Utilized LD information from the Indian Genome Variation database (IGVdb).
  • Focused on the PPP2R2B gene, a candidate gene for SCA12, which contains a CAG repeat.
  • Employed a minimal set of three SNPs for mapping the causal locus.
  • Evaluated the transferability of tagSNPs from a HapMap population.

Main Results:

  • Successfully mapped the causal locus for SCA12 using a minimal set of three SNPs in an endogamous Indian population.
  • Demonstrated that LD information from IGVdb is sufficient without generating new basal data.
  • Confirmed the transferability of tagSNPs from a related HapMap population for mutation mapping.

Conclusions:

  • Endogamous Indian populations are highly valuable for genetic association studies due to extended LD.
  • Minimal SNP sets can effectively map disease-associated genes in these populations.
  • Genetic marker transferability enhances the efficiency of gene mapping studies across diverse populations.