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Experimental validation of data mined single nucleotide polymorphisms from several databases and consecutive dbSNP
Hege Edvardsen1, Grethe Irene Grenaker Alnaes, Anya Tsalenko
1Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Faculty Division of the University of Oslo, Oslo, Norway. hedvards@medisin.uio.no
Pharmacogenetics and Genomics
|February 24, 2006
Summary
Selecting single nucleotide polymorphisms (SNPs) for genetic studies is challenging. This workflow efficiently identifies functional SNPs in candidate genes for pharmacogenetic research in Caucasian populations.
Area of Science:
- Genetics
- Pharmacogenomics
Background:
- The rapid increase in human genetic variation data, particularly single nucleotide polymorphisms (SNPs), presents challenges in selecting informative markers for disease association and treatment response studies.
- Efficiently identifying functionally relevant SNPs within candidate genes is crucial for advancing genetic research and personalized medicine.
Purpose of the Study:
- To develop and validate a workflow for selecting single nucleotide polymorphisms (SNPs) with putative function and population frequency from candidate genes.
- To create a verified set of candidate SNPs suitable for pharmacogenetic studies in Caucasian populations.
Main Methods:
- A workflow was designed to identify SNPs based on function and frequency in candidate genes sourced from PubMed.
- SNP annotation and frequency in Caucasian populations were assessed using multiple databases.
- In silico identified SNPs were validated through genotyping 193 individuals from a Caucasian population.
Main Results:
- Approximately 4000 SNPs were identified from an initial 233 candidate genes.
- A case study successfully genotyped 710 out of 1030 selected SNPs across 213 genes.
- Only 12% of the genotyped SNPs were found to be monomorphic, indicating a high success rate for identifying variable markers.
Conclusions:
- The described in silico workflow effectively selects validated candidate SNPs for pharmacogenetic studies.
- The identified and genotyped SNPs provide a valuable resource for investigating genetic variations influencing drug response in Caucasian populations.