The Human Genome Project has produced an enormous amount of sequence data, based on which single base changes between individuals are being identified. Unfortunately, computer tools that were adequate for sequence assembly are less than ideal for the characterization of single nucleotide polymorphism (SNP) data and its relationship to established sequence features.
Our researchers have developed some applications as a flexible tool.
Polyrisk Model Project
The combined effect of multiple Single Nucleotide polymorphisms (SNPs) will allow diseases to be predicted and to be prevented at both individual and population levels more accurately than only a few genetic markers. The risk associated with any individual probable SNP-genotype is small, but as the effects are multiplicative, a person with several susceptibility genotypes is at high risk. Therefore additional applications have been emerging to analyze such huge GWA data with an aim to add together the impact of many such low risk factors to accomplish a cumulative risk value for the clinics. This study overlooks the combined effect of multiple risk factors (SNPs) on the disease outcome and explains how the PolyRisk model can be used for risk characterization and prediction in the population from the molecular testing of common genetic variants for any disease. The basic of the PolyRisk model is applicable to any other method of odd ratio calculation such as allelic test or logistic regression and any other risk factors such as Haplotype blocks, environmental effects or the mixed effects can be modeled in this way.
Including more SNPs (Risk factors) into the model makes more difference between the case and control population and increases the sensitivity and specificity of the model and discriminative power of the model. By increasing the number of SNPs the case and control population move to opposite directions, while the mean for the whole population can move toward the protective or risk associated site depending on the selected SNPs.
For more information please contact Mehran Meschian.
Query & Database Project
Database Management
The purpose of this project is to upload the information from different sources in SQL Server and MySql databases. The goal is to get
consistency and integrity of genetic information. To accomplish this goal, the raw data is transformed into information with a process that goes from curing data to uploading database tables. At the end of this process, the information is ready to be used by the researchers of Ozcelik Lab.
The scope of this project is to relate genes, SNPs, Pathways and Proteins with the genotype information.
For more information please contact Antonio Mendoza.
SNPs & Visualization Project
GWADview
The GWADview software is an visualization tool for interpretation of genome-wide association results, which gives the ability to analyze Genes and SNPs data in variety of ways based on the research purposes. The system is based on a Genome Wide Association database which is a logical association of data that provides a single, integrated, coherent view of multiple resources. Current version can provide the plots of SNP P-Values vs. Chromo-some position and odd ratio; however, other GWA results can be per-featly visualized using the available information in the database.
For more information please contact Yongmei Ding.
