26 February 2015
We have just released Omicia Opal 4.7! This Opal release provides a number of new annotations, numerous functional and performance enhancements, with a focus on accelerating comprehensive clinical variant interpretation and report creation.
Opal Clinical provides an end-to-end solution for clinical NGS, combining Omicia’s industry-leading Opal annotation platform with structured interpretation workflows, full support for clinical report generation, and LIS integration -- all within a secure, HIPAA-compliant environment. Contact firstname.lastname@example.org if you’d like to try Opal Clinical.
Opal Clinical - New Annotations
We have added a number of new annotations to Opal Clinical:
- NNSplice. NNSplice (Reese at al, 1997) predicts splice sites, supporting analysis of splice site disruption. In Opal Clinical, NNSplice data is available for splice sites in the Interpret Variant modal, Additional Annotations.
- Genotype Quality. In addition to Quality and Coverage, we now display Genotype Quality. Genotype Quality (GQ) measures confidence in the genotype assignment, and it is derived from the uploaded variant file.
- Allelic Balance. The ratio of Alt reads / Total reads is now provided in the Interpret Variant modal, Additional Annotations. Heterozygote calls should be ~0.5; homozygote calls should be ~1.0.
- Previously Seen flag. A flag indicating this variant was classified in a previously approved patient report is provided in the Interpret Variant table.
- Disease-Gene Associations. Disease-Gene associations defined in a panel are displayed in Interpret Variant modal, Additional Annotations, for variants within a relevant gene.
Opal Clinical - Family Test
The Family Test workflow has been enhanced:
- VAAST can be launched as part of the family test setup, instead of needing to be run before
- The Interpret Variant table has been expanded to include all variants fitting a mode of inheritance, in addition to the VAAST top 20 ranked candidates.
Variant Miner Updates
NNSplice and Genotype Quality were also added to Variant Miner:
- NNSplice data is available in the Effect hyperlink.
- Genotype Quality is displayed with Quality and Coverage
You can create Filtering Protocols within Variant Miner. Use Variant Miner's interactive filters to create a filter you want to save, then click the Filters button.
We significantly expanded the Workspace Admin's capabilities in our January release. We have added two additional capabilities:
- Workspace Admin visibility. Workspace Admins can see all projects by default. This allows them to more easily administer projects, project data and user visibility
- Upgrade Permissions. Workspace admins have the option of allowing any member in the workspace to upgrade genomes to Pro, or requiring admin to upgrade. By default, any workspace member can upgrade genomes in the workspace. To require that only admins upgrade genomes, uncheck the "Allow workspace members to upgrade genomes" checkbox in the Payment Accounts tab.
Data Source Release Versions
- 1000 Genomes phase 3 version 5 (downloaded 5/2/2013)
- ClinVar (downloaded 2/2015)
- COSMIC v71
- dbNSFP version 2.5
- dbSNP release 142
- ENSEMBL version 75
- ExAC 0.2 release
- Exome Variant Server version 6500
- GWAS catalogue (downloaded 05/21/2014)
- HGMD Public version 7.1
- OMIM (downloaded 2/12/2015)
- PharmGKB (downloaded 1/2010)
- PhenCode / LSDB (downloaded 05/2013)