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High-density single-nucleotide polymorphism maps of the human genome
Raymond D Miller1, Michael S Phillips, Inho Jo
1Washington University, Division of Dermatology, St. Louis, MO, USA.
Genomics
|June 18, 2005
Summary
This study characterized over 55,000 human single-nucleotide polymorphisms (SNPs) across diverse populations. Results show significant shared genetic variation, with some SNPs useful for admixture studies, but caution is advised for complex trait studies using mixed populations.
Area of Science:
- Human Genetics
- Population Genetics
- Genomics
Background:
- Single-nucleotide polymorphisms (SNPs) are crucial markers for understanding human genetic variation.
- Characterizing allele frequencies across diverse populations is essential for genetic association studies.
Purpose of the Study:
- To create a comprehensive, well-characterized set of human genome SNPs.
- To determine allele frequencies for a large SNP set in African Americans, Asians, and European Americans.
- To provide a valuable resource for genetic research and population modeling.
Main Methods:
- Genotyping of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans.
- Characterization of 8,333 SNPs in Koreans.
- Analysis of allele frequencies and genetic variation across populations.
Main Results:
- Significant genetic variation is shared among human populations.
- 44% of autosomal SNPs had a minor allele frequency >=10% in each population.
- Average allele frequency differences between continental populations were <19%, but smaller differences existed among closely related Asian populations.
- Approximately 7% of SNPs were private (<1% minor allele frequency).
- A subset of SNPs with large allele frequency differences (>60%) was identified for admixture studies.
Conclusions:
- The characterized SNP set is a valuable resource for genetic studies, particularly for modeling and admixture analysis.
- Caution is recommended when using mixed populations for case-control studies of complex traits due to subtle allele frequency differences.
- High-density maps of characterized SNPs are freely available.