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Updated: Jun 25, 2026
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.
Shiwei Duan1, Wei Zhang, Nancy Jean Cox
1Section of Hematology/Oncology, Department of Medicine, The University of Chicago, IL 60637, USA.
Bioinformation
|February 25, 2009
Summary
This study identified 28,215 highly differentiated single nucleotide polymorphisms (SNPs) using genomewide fixation index (Fst) tests. These SNPs, with Fst values over 0.5, are valuable for pharmacogenetics research across diverse populations.
Area of Science:
- Genetics
- Population Genetics
- Pharmacogenetics
Background:
- The International HapMap Project provides extensive genotype data for population genetics studies.
- Phase 3 of HapMap includes data from 1,115 individuals across diverse ancestries.
- This dataset offers a rich resource for identifying population-specific genetic variations.
Purpose of the Study:
- To facilitate pharmacogenetics research by identifying highly differentiated single nucleotide polymorphisms (SNPs).
- To create a database of SNPs exhibiting significant allele frequency variation among different populations.
- To leverage the HapMap3 dataset for population differentiation analysis.
Main Methods:
- Utilized genomewide fixation index (Fst) tests to measure allele frequency variation.
- Analyzed common SNPs with minor allele frequency greater than 5 cent across 11 HapMap3 samples.
- Conducted Fst tests between all pairs and continental subgroups of HapMap3 samples.
Main Results:
- Identified 28,215 highly differentiated SNPs (Fst > 0.5) across 49 sample combinations.
- Performed 64 genomewide Fst tests to assess population differentiation.
- Included common SNPs with minor allele frequency > 5 cent in the analysis.
Conclusions:
- A significant number of highly differentiated SNPs were identified, valuable for pharmacogenetics.
- The developed database provides a resource for targeted genetic association studies.
- This work enhances the utility of HapMap3 data for understanding population-specific genetic variations.
Related Concept Videos
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%...
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.
GWAS does not require the identification of the target gene involved in...
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