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Large-scale validation of single nucleotide polymorphisms in gene regions
Matthew R Nelson1, George Marnellos, Stefan Kammerer
1Sequenom Inc., San Diego, California 92121, USA.
Genome Research
|August 4, 2004
Summary
Researchers developed a large collection of single nucleotide polymorphisms (SNPs) for genetic research. This curated SNP set aids in identifying genes linked to common diseases through genome-wide association studies.
Area of Science:
- Genetics
- Genomics
- Molecular Biology
Background:
- Genome-wide association studies (GWAS) are crucial for identifying genes associated with common diseases.
- A comprehensive collection of single nucleotide polymorphisms (SNPs) is essential for effective large-scale association studies.
Purpose of the Study:
- To create a robust SNP collection for large-scale genetic association studies.
- To evaluate the utility of publicly available SNPs for disease gene discovery.
Main Methods:
- Designed and validated assays for 226,099 publicly available SNPs, primarily in gene regions.
- Estimated allele frequencies in 92 CEPH Caucasian samples using pooled DNA and MALDI-TOF mass spectrometry.
- Identified 101,729 uniquely mapping, polymorphic SNPs (minor allele frequency > 0.02).
Main Results:
- Successfully designed functional assays for 204,200 SNPs.
- Confirmed 125,799 SNPs as polymorphic.
- 101,729 SNPs mapped uniquely to the human genome.
- The final SNP set is located within 10 kb of 66% of known and predicted genes.
Conclusions:
- A significant set of uniquely mapping, polymorphic SNPs has been assembled.
- This SNP collection is well-suited for large-scale disease association studies.
- Publicly available SNP annotations can predict polymorphic status, improving SNP selection for genetic research.