We present the Canadian Open Genetics Repository (COGR) - a collaborative effort for the collection, storage, sharing and analysis of variants reported by medical diagnostics laboratories across Canada. The increasing quantity and complexity of data produced by Canadian laboratories has become difficult to analyze. There is a need for collaborative measures between institutions to better facilitate variant analysis and information transfer. The inherent collaborative structure of the COGR promotes real-time sharing between geographically distant Canadian clinical laboratories and enhances the exchange of information about DNA variants within the expert community. Each laboratory was provided a systematic Variant Assessment Tool (VAT) and a standard, structured mechanism for collecting and sharing variant level data using GeneInsight™. Participating laboratories have also been encouraged to share on both ClinVar and on VariantWire, a real-time data sharing initiative including US and Canadian laboratories.
To date, 23 Canadian institutions have become members of COGR, with 11 of these sites actively sharing data in real-time. The COGR currently contains over 17,000 single nucleotide and copy number variants being shared that encompass 90 genes and 60 genetic diseases. Members of COGR have also been provided discrepancy reports detailing differences in classification between their laboratory and other COGR sites. Additionally, consensus building meetings have begun to formalize interpretations of specific variants among the participating COGR laboratories. Recently, the COGR started an initiative to create a consensus on variants identified in the BRCA1 and BRCA2 genes, pulling in over 5,500 variants from 11 laboratories; this data is actively being reviewed. Additionally, a public-facing instance of consensus level variants has been initiated through a collaboration with the BRCA exchange. Here, we report on our methodologies for resolving variant interpretation discrepancies, a system for resolving differences, and a process for arriving at a consensus. As a continuing effort, the COGR endeavors to increase genetic knowledge and standardization through data sharing and consensus building, ultimately improving our ability to diagnose and treat genetic diseases.