eCOMPAGT -- efficient combination and management of phenotypes and genotypes for genetic epidemiology.
BACKGROUND
High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.


METHODS
We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT) deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software.


CONCLUSIONS
eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at (http://dbis-informatik.uibk.ac.at/ecompagt).
Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria. sebastian.schoenherr@uibk.ac.at
Sebastian
S
Schönherr
Hansi
H
Weissensteiner
Stefan
S
Coassin
Günther
G
Specht
Florian
F
Kronenberg
Anita
A
Brandstätter
D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems / Q000592:standards; D005838:Genotype; D017720:Molecular Epidemiology / Q000379:methods*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface