An university hospital has a growing biobank collecting clinical data and DNA samples. To add to the value of the biobank by facilitating pharmaceutical companies to run availability queries for feasibility studies as well as facilitating high scale genomic research, they have decided to produce genotype data for 100 000’s of patients. They will also perform whole genome sequencing for 2 000 patients to build a population specific imputation panel.
For performing high throughput genotyping, they have built a lab with Illumina LIMS as well as multiple Illumina iScan machines. BC Platforms has delivered them a fully automated system for extracting genotype information from Illumina Autocaller binary files, performing QC/QA steps, and finally performing imputation. The results of the imputation are stored to a high performance tiled data architecture for fast data access.
For analyzing the data, principal investigators can apply for an access to clinical data relevant for their studies. They then use the BC|GENOME application to integrate clinical and genotype data together, and for performing various statistical genomics analyses, including GWAS, PheWAS, CVAS, RVAS, Linkage, eQTL, imputing etc. BC|GENOME is linked to the university HPC cluster, anprivate cloud storage system, as well as the university authentication system.