How to select tag SNPs in genetic association studies? The CLONTagger method with parameter optimization

Selection of genetic variants is a crucial first step in the rational design of studies aimed at explaining individual differences in susceptibility to complex human diseases or health intervention outcomes; for example, in the emerging fields of pharmacogenomics, nutrigenomics, and vaccinomics. While single nucleotide polymorphisms (SNPs) are frequently employed in these studies, the cost of genotyping a huge number of SNPs remains a limiting factor, particularly in low and middle income countries. Therefore, it is important to detect a subset of SNPs to represent the rest of SNPs with maximum possible accuracy. The present study introduces a new method, CLONTagger with parameter optimization, which uses Support Vector Machine (SVM) to predict the rest of SNPs and Clonal Selection Algorithm (CLONALG) to select tag SNPs. Furthermore, the Particle Swarm Optimization algorithm is preferred for the optimization of C and γ parameters of the Support Vector Machine. Additionally, using many datasets, we compared the proposed new method with the tag SNP selection algorithms present in literature. Our results suggest that the CLONTagger with parameter optimization can identify tag SNPs with better prediction accuracy than other methods. Application-oriented studies are warranted to evaluate the utility of this method in future research in human genetics and study of the genetic components of variable responses to drugs, nutrition, and vaccines.