How do I join the COGR?

Please send us an email at cogr@opengenetics.ca and we will arrange an introduction to the project.

What is the relationship between the GeneInsight software platform and the COGR Project?

COGR has been given funding for a 3 year licensing agreement with GeneInsight such that the software can be freely provided to all COGR members. Talks are in place to extend the licensing agreement.

How is the COGR different from other tools already on the market?

The COGR will allow for real-time sharing of variant classifications and interpretations across Canadian laboratories. In addition, the COGR provides members with resources such as the Variant Assessment Tool, with the aim of creating a final database of consensus variant information to be shared publically.

What kind of variant information is COGR looking for? What fields should we be uploading?

For the upload process the required fields are: gene and cDNA change for intragenic variants, genome build and genomic  coordinates for CNVs. A variant classification and interpretation statement is highly encouraged. For research labs on the system, in place of classification we suggest the addition of frequency data for the variant found in your cohorts. The COGR will also accept other fields (see “Aggregate Variant-Level Data Fields Shared among Network” under Policies/Guidelines) for labs that wish to include additional information.

Do I have to reformat my export from the database myself?

No, the COGR management team is creating scripts to help semi-automate the upload process. Simply send us your raw export file with the information you want uploaded. Please be sure to include your genome
build and your variant classification terminology. We will follow up with additional questions.

My variants have been uploaded – how do I start sharing?

Variant information is not shared by default. Simply send us an email explicitly stating your intention to start sharing. E.g. “I agree to share with the other COGR labs” and that functionality will be enabled. If you are also interested in sharing with the VariantWire (an international consortium of clinical labs), please let us know and we will send additional information.

What information is shared as part of variant sharing?

Once variant sharing has been requested and enabled, basic variant information and approved variant interpretations are shared with other labs via the GeneInsight application. The following fields are visible to other labs: variant including gene, DNA change, amino acid change, transcript, category, evidence text, disease associations (if applicable), date of interpretation approval and name of the individual who approved the variant. If a variant has never been approved it will not be shared with other labs. If the variant was previously approved, but a new category was proposed and not yet approved, the category will display as “under review”.

How do I approve my uploaded variants?

When variants are uploaded in bulk by the COGR team, they are left in an unapproved state for review by a laboratory director (unless requested otherwise). Variants can be approved by users with the Geneticist or Site administrator roles. Variants can be approved individually or in bulk. To approve variants one by one, from each individual variant page click the “Approve” button in the upper right hand corner. To do a bulk approval, from the search results page highlight the variant rows you want to approve (shift/ctrl + click), then click “Approve Proposed Interp” in the upper right corner.

What do the user roles in the GeneInsight application do?

Users in GeneInsight are assigned roles which specify what items they can edit, propose or approve. For example: The Genetic Counselor and Fellow roles can add genes and propose variant interpretations, but they cannot approve variant interpretations. Geneticists can do the above and also approve variant interpretations. Site administrators can do all the above and add new users. The Research Assistant and Operations Manager are less commonly used and have read-only access to variant interpretation information.

What is the VAT?

The VAT (short for Variant Assessment Tool), is an Excel based aid for the classification of variants. It can be downloaded as a .zip file from our Resources page. Please contact the COGR management team for support with the tool.