SNPAnalyzer-Pro Feature

Feature - Preprocess

Perform data preprocess after importing and transforming client’s SNP data Data Import Affymetrix GeneChip® Genotype Series ABI - TaqMan® SNP Genotyping Assays

Feature - Cross Tabulation Analysis

Evaluate statistically significant SNPs or haplotypes of which frequencies are different between control sample and case sample by using goodness of fit test and likelihood ratio test 2x2 Contingency Table OR, AR, PAR SNP Analysis / Haplotype Analysis Risk Allele : Minor Allele / Major Allele Using Haplotypes in LD block Genetic Model : Additive / CoDominant / Dominant / Recessive / OverDominant

Feature - Classification Analysis

Discriminate appropriate SNPs or haplotypes that classify the observed two classes as the must-be classes by using logistic regression Logistic Regression Model Classify samples by using genotypes or haplotypes Candidate markers are extracted from the result of cross tabulation analysis Classification Power Evaluate the accumulated power of classification by using SNPs or haplotypes step by step Variable Selection Select the most appropriate markers that maximize the classification power

Feature - LD Analysis

Measure linkage disequilibrium between pairwise SNPs, estimate tagging SNPs and haplotypes, and construct LD blocks Pairwise LD Calculation LD Index : D’, R2, LOD, p-value, four-gamete Estimate tagging SNPs Haplotype Estimation EM algorithm / PL-EM algorithm LD Blocking Estimate haplotypes in the LD block Crossover rate, multi-allelic D’

Feature - Biological Annotation

Provide important biological annotation about SNPs and genes for the functional study SNP Annotation Extract the physical position of SNPs in the chromosome or gene Extract the functional classes of SNPs Gene Annotation Extract gene annotation in which the SNPs reside Gene Symbol, Gene ID, GO ID, GO Term