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Published on: June 23, 2012
Tag SNPs chosen from HapMap perform well in several population isolates
Susan Service1, , Chiara Sabatti
1Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095-1761, USA.
Genetic Epidemiology
|February 27, 2007
Summary
Tag single nucleotide polymorphisms (SNPs) selected from the HapMap reference panel are transferable and effective for genetic association studies in diverse population isolates. This finding supports their utility in complex trait research across different human populations.
Area of Science:
- Population genetics
- Genomic association studies
- Human complex traits
Background:
- Population isolates offer unique advantages for studying complex traits due to reduced genetic heterogeneity.
- The effectiveness of genome-wide association studies (GWAS) in these isolates relies on the transferability of genetic markers, such as tag single nucleotide polymorphisms (SNPs).
- Reference panels like HapMap are crucial for selecting tag SNPs, but their applicability in genetically distinct populations is a key concern.
Purpose of the Study:
- To evaluate the transferability and performance of tag SNPs selected from the HapMap reference panel in various population isolates.
- To determine if genetic factors characterizing population isolates, like genetic drift, impact the utility of HapMap-derived tag SNPs.
- To assess the applicability of standard GWAS approaches in population isolates using established reference data.
Main Methods:
- Selection of tag SNPs from the HapMap reference panel based on established criteria.
- Genotyping of selected tag SNPs in multiple, diverse population isolate samples.
- Analysis of tag SNP performance, including allele frequency distributions and linkage disequilibrium patterns, in comparison to HapMap data.
- Statistical evaluation of tag SNP transferability across different population groups.
Main Results:
- Tag SNPs chosen from the HapMap panel demonstrated good performance across several population isolates.
- The utility of HapMap tag SNPs was maintained even in populations with substantial differences in linkage disequilibrium levels compared to the HapMap sample.
- SNP allele frequency distributions in population isolates did not significantly impede the performance of HapMap-derived tag SNPs.
Conclusions:
- Tag SNPs derived from the HapMap reference panel are transferable and perform well in population isolates for association studies.
- Genetic drift and other population-specific factors in isolates do not necessarily hinder the effectiveness of standard tag SNP selection strategies.
- These findings validate the use of HapMap-based tag SNPs for genetic research in diverse population isolates, facilitating the study of complex traits.
Related Concept Videos
01:11Genome-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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GWAS does not require the identification of the target gene involved in...
01:05Single 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,...
02:26Comparing Copy Number Variations and SNPs
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%...
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%...