Abstract
BackgroundSince 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.ResultsWe 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.ConclusionSNPAnalyzer 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.
Highlights
Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories
We have developed an advanced analysis software program, SNPAnalyzer 2.0, which performs sample-specific linkage disequilibrium analysis and implements genetic association analysis using multiple genetic models in an integrated web interface
2.1 Data import Genotypes of biallelic SNPs should be coded in a tab delimited text file
Summary
Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories. The necessity of the capability to analyze huge data and diverse interpretation of the results are growing rapidly. The efforts of finding or interpreting genetic association between disease and SNPs/ haplotypes have been on-going widely, and the necessity of the capability to analyze huge data and diverse interpretation of the result are growing rapidly. We have developed an advanced analysis software program, SNPAnalyzer 2.0, which performs sample-specific linkage disequilibrium analysis and implements genetic association analysis using multiple genetic models in an integrated web interface. It can handle hundreds of thousands of SNPs and thousands of samples in a rather manageable time as compared with other software programs
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
