Opal 4.0 Release Notes

Jeanette McCarthy -

6 July 2014  

Omicia Opal 4.0 is a significant functional release that includes the introduction of Workspaces for collaboration, a new annotation architecture, an expanded release of our Clinical beta, and numerous other enhancements.

Opal Annotation Engine


Data Migration

Application Navigation Changes

Opal Clinical

Data Source Release Versions  

Opal Annotation Engine

Opal Annotation Engine is the backbone of Omicia’s Opal products. Incorporating a new architecture, the new pipeline annotates variants with more comprehensive gene and impact information, multiple predictive scores, as well as links to literature evidence. The architecture includes a robust, fully scalable processing engine that processes exomes in just a few minutes.

Opal Annotation Engine incorporates algorithms including VEP from Ensembl, Omicia Score Agent, and Omicia Evidence Agent, as well as data sources including dbSNP, dbNSFP and 1000 Genomes. It provides more accurate determination of variant effect and consequences including start loss/gain variants and regulatory regions. A complete, up-to-date list of curated transcripts is also provided. Literature evidence includes ClinVar, OMIM, HGMD Lite, PhamGKB, LSDB, GWAS and Locus-specific Databases.

Opal Annotation Engine annotates each variant with 19 individual scores including the Omicia score. The Omicia score is a proprietary composite score that has been published (Coonrod et al, 2013), and is more accurate over a larger number of cases. For this release, the Omicia scoring algorithm was trained on an expanded set of 12K HGMD variants, further increasing its robustness.

Users can also access the complete set of annotated scores for each variant for deeper analysis, by clicking on the variant’s Omicia score in Variant Miner. The full list of scores is provided here, and more information is provided in the User Guide.


Opal Annotation Engine Scores List

  • Omicia Score
  • phyloP - Placental
  • phyloP - Primate
  • phyloP - Vertebrate
  • PhastCons
  • CADD - Raw
  • GERP++ - NR
  • GERP++ - RS
  • SiPhy
  • MutationTaster
  • MutationAssessor
  • Polyphen-2 - HVAR
  • Polyphen-2 - HDIV
  • RadialSVM
  • LRT
  • LR
  • SIFT

Transcripts and Variant Consequences in Variant Miner

We now provide a list of potential transcripts with related protein change and effect, as well as the canonical transcript from Ensembl. This can be accessed in Variant Miner by clicking on the Effect for a variant.

Treatment of Introns and Intergenic Regions in Pipeline 3 and Opal Annotation Engine 4

The Opal Annotation 3 Variant Reports only show variants in introns or intergenic regions if they reside within or nearby genes associated with disease (OMIM or HGMD). Opal Annotation Engine 4 Variant Reports include all variants introns and intergenic regions. Modify the Exclude Filters in Variant Miner if you want to see the intronic and intergenic variants.

Re-Annotating Existing Genomes with Opal Annotation Engine 4

We are automatically re-annotating genomes uploaded to Opal within the last three months. This reprocessing is running at lower priority than annotation of new sequences, and may take several weeks to complete. If you have an older genome that needs to be re-annotated, or need a recently uploaded genome to be re-annotated more quickly, please contact support@omicia.com or upload it again.



With this release, we introduce the concept of workspaces. Workspaces facilitate collaboration and sharing. Users who share a workspace, share projects, gene sets, and filtering protocols. New projects can be set up to be automatically shared with everyone in the workspace, instead of needing to add collaborators individually to multiple projects. More granular sharing settings exist for projects, allowing projects to be shared on a selective basis, with no one, or with view only access.

Users can create multiple workspaces to facilitate different collaborations.

Payment Accounts

Payment Accounts are now associated with a Workspace instead of an individual user account. Workspace Admins manage payment accounts. The default payment method is used for genome upgrades. We also have support for POs. Contact our Support team at support@omicia.com to set up a PO.


Data Migration

Since we have expanded from an individual user account structure to a workspace structure, we have migrated data in shared projects into workspaces shared with the other users in the project. If you had shared projects with different groups of users, you now have multiple workspaces.

If you want your workspace configuration to be changed, for instance to merge workspaces, please contact our Support team at support@omicia.com for help.

Migration of Payment Accounts

Payment Accounts were previously associated with user accounts. Now, they are associated with Workspaces. Please validate the payment account associated with your Workspace(s), as this payment account will be used to upgrade genomes in any project in the Workspace.

We did not migrate existing payment accounts to a Workspace when there are multiple members in a project. A Workspace Admin will need to add a payment account so genomes can be upgraded.


Application Navigation Changes

With the introduction of Workspace, we have changed navigation in the application:

  • Filtering Protocols and Gene Sets have been moved to the Home Page
  • The other Settings features are now in Workspace
  • The Navigation bar has links to Home and Projects, and a Workspace dropdown menu to navigate to different workspaces.


Opal Clinical

We appreciate the feedback from our beta sites. We have released an expanded version of Opal Clinical, which includes Panel Builder enhancements and a new Clinical Reporter for clinical interpretation and report generation.

With Omicia Clinical you can:

  • Develop and launch new diagnostic tests
  • Deploy standardized interpretation workflows for running tests within your lab
  • Produce physician-ready reports

In this beta release, an enhanced version of Panel Builder enables you to more easily manage the curation process to rapidly build gene-based and variant-based Panels.

We are also introducing Clinical Reporter, which provides a clinical workflow for interpretation of a patient’s variant data, leveraging any curated data in the Panel. Clinical Reporter also manages the report approval workflow, and produces a final, physician-ready PDF report.

Including Your Logo in Clinical Reports

Opal Clinical enables organizations to brand Clinical Reports. To add your organization’s logo to the Clinical Report template please send a PNG version of your logo to Omicia support at support@omicia.com. The file should be 72 dpi and no larger than 200 x 65 pixels.

Panel Builder Requires Genomic Coordinates

Panel Builder requires genomic coordinates to map a variant correctly. When adding variants to a panel, variants that do not have genomic coordinates will not be included even if they are in a database such as ClinVar.

Opal Clinical Requires Annotation from Opal Annotation Engine 4

To run a sample through Opal Clinical, it requires annotation from Opal Annotation Engine 4. If the sample you want to interpret has a Pipeline 3 or older Variant Report only, please contact support@omicia.com to have it reprocessed. Note that we are automatically re-annotating genomes uploaded to Opal within the last three months. This reprocessing is running at lower priority and may take several weeks to complete.


Data Source Release Versions

  • dbSNP - release 138
  • ENSEMBL - version 73
  • ClinVar (downloaded on 6/2014)
  • HGMD Public version 7.1
  • OMIM (downloaded 3/2014)
  • PharmGKB (downloaded 1/2010)
  • 1000 Genomes - phase 1 release (downloaded 12/2011)
  • PhenCode (downloaded 05/2013)
  • GWAS catalogue (downloaded 05/2013)
  • dbNSFP - version 2.5


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