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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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Related Experiment Video

Updated: Jul 9, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

HapMap coverage for SNPs in the Japanese population.

Fumihiko Takeuchi1,2, Masakuni Serizawa3, Norihiro Kato4

  • 1Department of Medical Ecology and Informatics, Research Institute, International Medical Center of Japan, Tokyo, Japan.

Journal of Human Genetics
|November 29, 2007
PubMed
Summary
This summary is machine-generated.

The HapMap database offers good, but not complete, single nucleotide polymorphism (SNP) coverage for Japanese populations. This impacts genome-wide association study (GWAS) success and requires careful interpretation of results.

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Area of Science:

  • Human Genomics
  • Population Genetics
  • Genetic Epidemiology

Background:

  • Genome-wide association studies (GWAS) rely on comprehensive human genomic variation data.
  • The HapMap database is a key resource for SNP coverage in population studies.
  • Assessing SNP coverage in specific populations, like the Japanese, is crucial for accurate genetic research.

Purpose of the Study:

  • To evaluate the single nucleotide polymorphism (SNP) coverage provided by the HapMap database within the Japanese population.
  • To determine the extent to which common genetic variations in Japanese individuals are represented in the HapMap.
  • To inform the interpretation of GWAS results in the Japanese population based on HapMap coverage.

Main Methods:

  • Combined resequencing and high-density genotyping of 1,304 Japanese subjects.
  • Resequencing of 86 genes in 48 subjects to identify novel SNPs.
  • Genotyping and imputation of SNPs in an additional 1,256 subjects using HapMap data.

Main Results:

  • Identified 738 common genic SNPs in the Japanese population.
  • 58% of identified SNPs were directly genotyped in HapMap.
  • 31% had a proxy SNP in HapMap (r² > 0.8), while 11% were unrepresented.

Conclusions:

  • HapMap database provides substantial, but not exhaustive, SNP coverage for the Japanese population.
  • Coverage is lower compared to Caucasians, necessitating caution when interpreting GWAS findings.
  • Further efforts may be needed to enhance SNP representation for Japanese populations in genomic databases.