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Single-nucleotide polymorphisms in the public domain: how useful are they?
Nature Genetics
|March 30, 2001
Summary
Researchers are identifying numerous human single-nucleotide polymorphisms (SNPs) for genomic mapping. A significant portion of candidate SNPs are confirmed as polymorphic and common, aiding in genetic research and SNP discovery.
Area of Science:
- Genomics
- Human Genetics
- Bioinformatics
Background:
- A significant global effort is underway to identify human single-nucleotide polymorphisms (SNPs).
- Public databases like dbSNP at NCBI now host millions of identified SNPs.
- Proprietary databases also maintain substantial SNP collections.
Purpose of the Study:
- To report on the scale of human SNP identification efforts.
- To assess the polymorphism and frequency of candidate SNPs from major sources.
- To contribute to the development of a high-density human genome SNP map.
Main Methods:
- Analysis of SNP data deposited in the public dbSNP database.
- Review of SNP data from the International SNP Map Working Group.
- Survey and validation of over 1,200 candidate SNPs from TSC and Washington University.
Main Results:
- As of March 2001, dbSNP contained 2.84 million SNPs, comprising 1.65 million non-redundant entries.
- A high-density map of the human genome includes 1.42 million SNPs.
- Over 80% of surveyed candidate SNPs are polymorphic, with approximately 50% classified as common SNPs (minor allele frequency >= 20%).
Conclusions:
- The ongoing identification and mapping of human SNPs are advancing rapidly.
- Candidate SNPs from major research groups demonstrate high rates of polymorphism and commonality.
- These findings support the utility of identified SNPs for genetic studies and genome-wide association studies.
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