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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

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,...
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.
GWAS does not require the identification of the target gene involved in...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping.

Chao Tian1, David A Hinds, Russell Shigeta

  • 1Rowe Program in Human Genetics, Department of Biochemistry, University of California Davis, Davis, CA 95616, USA.

American Journal of Human Genetics
|June 15, 2007
PubMed
Summary

We developed a genomewide panel of ancestry-informative markers (AIMs) for Mexican Americans to identify chromosomal segments of Amerindian or European ancestry. This tool enhances admixture mapping studies for complex diseases like type 2 diabetes.

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Published on: June 23, 2012

Area of Science:

  • Genetics
  • Population Genetics
  • Genomic Medicine

Background:

  • Admixture mapping studies are crucial for identifying disease-associated genetic variants in admixed populations.
  • Mexican Americans (MAM) represent a complex admixed group with Amerindian (AMI) and European (EUR) ancestry, necessitating specific genetic tools.
  • Existing SNP panels may not adequately distinguish between diverse AMI ancestries within the MAM population.

Purpose of the Study:

  • To develop and validate a genomewide single-nucleotide-polymorphism (SNP) panel of ancestry-informative markers (AIMs) for admixture mapping in Mexican Americans.
  • To assess the power of the developed AIMs panel for detecting disease-associated chromosomal segments.
  • To provide a resource for studying the genetic architecture of diseases with differential ancestry-associated susceptibility in MAM.

Main Methods:

  • Genotyping of >400,000 SNPs in European and two Amerindian (Pima, Mayan) populations to identify AIMs.
  • Selection of AIMs based on high EUR/AMI FST values (>0.30) and low inter-AMI FST values (<0.05).
  • Simulation studies using realistic parameters to evaluate the power of the AIMs panel for admixture mapping.

Main Results:

  • A panel of 8,144 SNP AIMs was established, effectively distinguishing between Amerindian and European ancestry segments in Mexican Americans.
  • A reduced set of 5,287 AIMs retained most of the admixture mapping information.
  • The AIMs panel demonstrated good power for detecting disease-associated segments, particularly for genes with modest ethnicity risk ratios.

Conclusions:

  • The developed SNP AIMs panel is a valuable tool for precise admixture mapping in Mexican Americans.
  • This resource will facilitate genetic studies of complex diseases, including type 2 diabetes and rheumatoid arthritis, in this population.
  • The panel's ability to distinguish ancestral segments enhances the power to identify disease-susceptibility loci influenced by population history.