An efficient classification for single nucleotide polymorphism (SNP) dataset

Abstract

Recently, a Single Nucleotide Polymorphism (SNP) which is a unit of genetic variations has caught much attention as it is associated with complex diseases. Various machine learning techniques have been applied on SNP data to distinguish human individuals affected with diseases from healthy ones or predict their predisposition. However, due to its data format and enormous feature space SNP analysis is a complicated task. In this research an efficient method is proposed to facilitate the SNP data classification. The aim was to find the most effective way of SNP data analysis by combining various existing techniques. The experiment was conducted on four SNP datasets obtained from the NCBI Gene Expression Omnibus (GEO) website, two of them are from patients with mental disorders and their healthy parents; and the other two are cancer related data. The analysis process consists of three stages: first, reduction of feature space and selection of informative SNPs; next, generation of an artificial feature from the selects SNPs; and last but not least, classification and validation. The proposed approach proved to be effective by distinguishing two groups of individuals with high accuracy, sometimes even reaching 100% preciseness. © Springer International Publishing Switzerland 2013.