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

Authors
 Jinho Yoo  ;  Youngbok Lee  ;  Yujung Kim  ;  Sun Young Rha  ;  Yangseok Kim 
Citation
 BMC BIOINFORMATICS, Vol.9 : 290, 2008 
Journal Title
BMC BIOINFORMATICS
Issue Date
2008
MeSH
Algorithms ; Data Interpretation, Statistical ; Haplotypes ; Humans ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide* ; Software*
Keywords
Linkage Disequilibrium ; Linkage Disequilibrium Block ; Linkage Disequilibrium Analysis ; Genetic Association Analysis ; Haplotype Estimation
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.
Files in This Item:
T200800517.pdf Download
DOI
10.1186/1471-2105-9-290
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
Yonsei Authors
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/106702
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