27 August 2014
Opal Annotation Engine 4
With this release, we included performance and scalability enhancements as well as these new features:
- Addition of COSMIC as an Evidence source for point mutations
- Additional VCF file format compatibility for including Ref and Alt read data:
- Genotype field - AD (Complete Genomics) NR/NV, and RR/VR/VP
- INFO field - FRO/FAO
Evidence - COSMIC
COSMIC is now available as an Evidence source for point mutations in both Variant Miner and Clinical Reporter.
Workspaces are a new in Opal 4. Workspaces facilitate collaboration and sharing, allowing users to easily share share projects, gene sets, filtering protocols and more.
In Opal 4.1 we simplified the navigation for managing Workspaces. The Manage Workspaces option on the Workspace dropdown menu (top navigation bar) provides a list of all the Workspaces you have access to. You can manage or view the information for any workspace using the Actions dropdown menu.
Projects now have a sharing setting. Projects can be shared with all members of a Workspace as Admins, Members or Viewers, or on a Restricted basis with select members of the workspace. From the Project list view Actions dropdown menu you can:
- Change project settings by selecting Edit
- Add, remove or change permissions for individual users by selecting Share
Change your Opal password by clicking on your login name in the top navigation bar, then clicking on the Reset Password link.
Filtering Protocols - Public Filters
We have added Public Filtering Protocols: filtering protocols published by Omicia. These are automatically accessible throughout the application. You can review the filter criteria by selecting Filtering Protocols from the Home page then clicking the Public Filters link.
Opal Clinical - Public Panels
We have added Public Panels: panels published by Omicia and third parties. You can review the list of available panels and curated content in the Panel Builder Panels list view. Click on the Public Panels link. These are automatically available for use in Clinical Reporter.
Opal Clinical - Panel Builder
Copy Published Panels
Published Panels can now be copied to create a new version of the panel using the Clone Panel feature. If at any time you want to confirm which panel your new panel was cloned from, click “View History” in the Actions dropdown menu.
Export Variants to CSV
The Export Variants to CSV feature allows you to export the curated variants in your panel to a comma separated file.
Accept Source Classifications
The Accept Source Classifications feature enables you to accept the Classifications from the variant source data, for example ClinVar, when curating your panel. This feature will not overwrite any manual classifications assigned to variants in your panel.
Gene-Disease Associations can now be captured within Panels. You can include multiple disease associations for a gene, and specify the strength of each association as high/medium/low.
Opal Clinical - Clinical Reporter
Filters have been added to the Select Variants page. You can filter by Curation Status, Reviewed Status, Classification, Condition and Effect.
Data Source Release Versions
- dbSNP - release 138
- ENSEMBL - version 75
- ClinVar - downloaded on 7/2014
- HGMD Public - version 7.1
- OMIM - downloaded 3/2014
- PharmGKB - downloaded 1/2010
- 1000 Genomes - phase 1 release
- PhenCode - downloaded 05/2013
- GWAS catalogue - downloaded 05/2013
- dbNSFP - version 2.5