SNPLims: a data management system for genome wide association studies

Background: Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypic data facilitates the whole genome search for genetic basis of diseases. We need a suitable information management system to efficiently manage the data flow produced by whole genome genotyping and to make it available for further analyses. Results: We have developed an information system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database. The relational database can be accessed in order to import any existing data and export userdefined formats compatible with many different genetic analysis programs. After calculating family-based or case-control association study data, the results can be imported in SNPLims. One of the main features is to allow the user t...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano Milanesi
• Keywords: BMCBI 2008, Genotyping, Relational Database, SNP Genotype Data