snpStorage: A database to store and share experimental SNPs data sets

The last years have seen a continuous improvement in sequencing and genotyping technologies. These improvements have spawned a rapid advancement in bioinformatics databases and software relating to the collection and analysis of genetic data. Genetic data holds several types of variations such as: indels, microsatellites, copy number variants (CNV), and Single Nucleotide Polymorphisms (SNPs). SNPs are the most abundant type of genetic variation and are now the principals raw material underlying most genetic studies and databases. SNPs can be used as potential biomarkers to investigate cancer growth or progression, and planning more effective treatment regimens. To make data quickly accessible to the users, e.g., to face the burden related to the relation of several experiments and to allow an easy and controlled sharing of genotyping data among different labs, the need for specialized SNP databases arises. For these reasons, we developed snpStorage (and related querying service), a database to collect experimental SNPs data integrated with clinical data if available. snpStorage collects experimental SNPs data in pharmacogenomics studies, obtained by using DMET (Drug Metabolism Enzymes and Transporters) platform and subsequently enriched with clinical data. The main contributions of snpStorage are i) automatic translation, normalization and integration of SNP data sets with clinical data and mapping in relational schema. ii) A repository where research laboratories can store data (anonymously), merge and handle SNP data sets for more specific analysis; iii) To provide medical professionals a software instrument to facilitate clinical decisions based on the individual’s genome, and tailoring health care services to the patient’s genotype.