SNPLims: A Data Management System for Genome Wide Association Studies

Background: Recent progresses in genotyping technologies allow the generation high-densitygenetic maps using hundreds of thousands of genetic markers for each DNA sample. The availabilityof this large amount of genotypic data facilitates the whole genome search for genetic basis ofdiseases.We need a suitable information management system to efficiently manage the data flow producedby whole genome genotyping and to make it available for further analyses.Results: We have developed an information system mainly devoted to the storage andmanagement of SNP genotype data produced by the Illumina platform from the raw outputs ofgenotyping into a relational database.The relational database can be accessed in order to import any existing data and export userdefinedformats compatible with many different genetic analysis programs.After calculating family-based or case-control association study data, the results can be importedin SNPLims. One of the main features is to allow the user to rapidly identify and annotatestatistically relevant polymorphisms from the large volume of data analyzed. Results can be easilyvisualized either graphically or creating ASCII comma separated format output files, which can beused as input to further analyses.Conclusions: The proposed infrastructure allows to manage a relatively large amount ofgenotypes for each sample and an arbitrary number of samples and phenotypes. Moreover, itenables the users to control the quality of the data and to perform the most common screeninganalyses and identify genes that become "candidate" for the disease under consideration.