Academic research project on a complex disease

The customer is an academic genetic research group studying a complex disease. For their research, they collect and maintain a patient cohort with high prevalence of the disease. Research nurses meet the patients once a year, collect comprehensive patient data using questionnaires and produce laboratory data. They also record patient family relations by drawing pedigrees. In addition to collecting new data, they give the patients reports on laboratory and other results produced by the research center. To reach as many patients as possible, data is collected in many centers around the country. High-throughput genotyping and sequencing efforts are outsourced to a genome center, but smaller re-sequencing projects are performed at the customer’s own laboratory.

All the project data is collected to a BC server hosted by the university IT department. For computing intensive data analyses, the server is connected to a university calculation cluster. As the group uses patient health and genomic data, high level data security measures for both the BC platform and applications, as well as server hardware are in place.

Patient questionnaires, pedigrees, and laboratory values are directly entered or uploaded to the server by the nurses. The system also provides an application for pedigree drawing. Genotype and processed sequence data from the genome center are uploaded to the BC|GENOME database by researchers. For locally produced sequence data, alignment and variation calling are performed by the BC|GENOME application.

For statistical genetic data analyses, the researcher can choose between many different academic packages supported by the system and their own scripts and tools. Some users prefer the easy-to-use web-interface, while others prefer the command line tools provided. In addition to producing input files for different packages, BC|GENOME splits analysis tasks to small segments, and runs them in parallel in the university calculation cluster.