Selecting Single-Nucleotide Polymorphisms for Association Studies With SNPbrowser™ Software

Abstract

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative muta- tion is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap Project performed a genome-wide survey of genetic variation with over 3 million SNPs typed in four populations, providing a rich resource to inform the design of associa- tion studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype- tagging SNPs. Power calculations are important at the study design stage to ensure suc- cessful results. Integrating these methods and annotations can be challenging: the algo- rithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we review the typical workflows for the selection of markers for association studies utilizing the SNPbrowser™ software, a freely available, stand-alone application that incorporates the HapMap data- base together with gene and SNP annotations. Selected SNPs are screened for their con- version potential to genotyping platforms, expediting the set up of genetic studies with an increased probability of success.