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Finding the causative genes for common diseases using SNP (single nucleotide polymorphism) markers is now becoming a real challenge. Although traditional statistical SNP association tests exist, these tests could not explain the effects of SNP combinations or probable recombination histories from ancestral chromosomes. Haplotype analysis of disease associated site provides more powerful markers than individual SNP analysis, and can help identify probable causative mutations. In this paper, we introduce a new method for effective haplotype pattern mining to detect disease associated mutations. Using this procedure, we can discover some of the new disease associated SNPs, which can not be detected by traditional methods. We will introduce a powerful tool for implementing this procedure with some worked examples.