Software

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

Jinho Yoo^1,2 , Youngbok Lee⁵ , Yujung Kim⁵ , Sun Young Rha^1,2,3 and Yangseok Kim⁴

¹  Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea

²  Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea

³  Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea

⁴  College of Oriental Medicine, KyungHee University, Seoul, Republic of Korea

⁵  Bioinformatics Division, ISTECH Inc., Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea

author email corresponding author email

BMC Bioinformatics 2008, 9:290doi:10.1186/1471-2105-9-290

Published:	23 June 2008

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.

Results

We have developed an advanced tool to perform linkage disequilibrium analysis, and genetic association analysis between disease and SNPs/haplotypes in an integrated web interface. It comprises of four main analysis modules: (i) data import and preprocessing, (ii) haplotype estimation, (iii) LD blocking and (iv) association analysis. Hardy-Weinberg Equilibrium test is implemented for each SNPs in the data preprocessing. Haplotypes are reconstructed from unphased diploid genotype data, and linkage disequilibrium between pairwise SNPs is computed and represented by D', r² and LOD score. Tagging SNPs are determined by using the square of Pearson's correlation coefficient (r²). If genotypes from two different sample groups are available, diverse genetic association analyses are implemented using additive, codominant, dominant and recessive models. Multiple verified algorithms and statistics are implemented in parallel for the reliability of the analysis.

Conclusion

SNPAnalyzer 2.0 performs linkage disequilibrium analysis and genetic association analysis in an integrated web interface using multiple verified algorithms and statistics. Diverse analysis methods, capability of handling huge data and visual comparison of analysis results are very comprehensive and easy-to-use.