SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

Abstract

Background: Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories. The efforts of finding or interpreting genetic association between disease and SNPs/haplotypes have been on-going widely. So, the necessity of the capability to analyze huge data and diverse interpretation of the results are growing rapidly.

A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group

“…Linkage disequilibrium (LD) analysis for all pair-wise InDel loci was performed using the SNPAnalyzer v2.0 (Istech, South Korea)20. Fst and p values for pairwise interpopulation comparisons were calculated based on allele frequencies of 30 InDels by analysis of molecular variance (AMOVA) performed with ARLEQUIN version 3.1 software (http://cmpg.unibe.ch/software/arlequin3).…”

Original article Paraoxonase 1 (PON1) gene -108C>T and p.Q192R polymorphisms and arylesterase activity of the enzyme in patients with dementia

“…Linkage disequilibrium (LD) statistics (D' and r 2 ) for genetic polymorphisms and the haplotype frequency were determined using the SNPAnalyzer v2.0 (ISTECH Inc, Goyang, Korea) software [34]. All other statistical analyses were performed using Statistica version 9.…”

Population genetic data of 38 insertion–deletion markers in South East Spanish population

“…Matching probability (MP) and typical paternity index (TPI) were calculated for each locus using the PowerStats v12 software [15]. The statistical significance of linkage disequilibrium among loci pairs was measured by exact tests to estimate p values using Arlequin 3.11 software and SNPAnalyzer 2 [16].…”