29 October 2015
We are excited to announce that Opal 4.14 is live! In this release, we continue to augment our clinical product with expanded report review capabilities, and we have broadened our Opal API to further support high-throughput labs' requirements. We have also upgraded and unified our variant analysis table views across the Opal application, including Variant Miner and VAAST.
Opal Clinical provides an end-to-end solution for clinical NGS testing, combining Omicia’s industry-leading Opal annotation platform with structured interpretation workflows, full support for clinical report generation, curated gene panels 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 - Review Approved Report Data
Opal Clinical now allows data from approved reports to be reviewed, including reported and unreported variants, as well as internal notes. This new read-only view for approved reports is accessible using the View Interpretation menu option in the Clinical Reports page.
Upgrades to Variant Analysis Table Views - Clinical Variant Miner, Variant Miner, VAAST and Flex
We have upgraded and unified all of the variant analysis table views in Clinical Variant Miner, Variant Miner, VAAST and Flex.
For those users who also use Opal Clinical, the new variant table views will be familiar as we are now leveraging the same architecture and look and feel as Clinical Reporter. This change accelerates our ability to deliver new capabilities to both our clinical and research users.
- Comprehensive and consistent filters allow you to filter data using gene symbol, variant type, ClinVar class, allele frequency, coverage, saved Filtering Protocols, Panels and more
- Simplified Gene Set selection so all available gene sets are selectable from the same menu, and only workspace gene sets are provided
- Streamlined Genome Operations, allowing you to find shared or unique variants between samples more easily (Variant Miner only)
- Improved color palette for users with color vision deficiency
- Mouse-over help for fields and data in the variant table.
Review Priority Field
A new Review Priority Field has been introduced in the variant table views. The Review Priority field provides three separate color-coded assessments for each variant: ClinVar Classification, Allele Frequency and Effect.
>Review Priority upgrades and replaces Predicted Class, giving the interpreter more detail while still providing a single field for prioritization and sorting. Samples annotated with Opal pipeline 4.4 or greater will display Review Priority. Samples annotated with Opal pipeline 4.3 or lower will not be changed.
More details on Review Priority are available in Appendix 3.
The Omicia Opal API continues to be expanded to support high throughput requirements. In this release, we have added support for inclusion of phenotype terms as direct input into the Phevor algorithm for exome and genome tests.
Higher-throughput labs will benefit from using the Omicia API to integrate with existing lab systems and automate processes including:
- Uploading genomes
- Setting up clinical tests including upload of patient and phenotype information
- Uploading quality control data from sequencing and/or alignment
- Sanger confirmation of variants
- Export of final report results
- Creation and editing of panels
If you are interested in using the Omicia API in your lab, please contact email@example.com.
Annotation Pipeline - tRNA Variants
In our September release, we added annotation support for transcripts for ribosomal DNA in both mitochondrial and nuclear DNA. In this release, we also add annotation support for mitochondrial tRNA variants.
Data Source & Algorithm Versions
Opal Pipeline 4.4 - Released October 29, 2015
- 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
- CADD v1.0
- ClinVar (downloaded October 2015)
- COSMIC v71
- dbNSFP version 2.9
- dbSNP release 144
- ENSEMBL version 75
- ExAC 0.3 release
- Exome Variant Server 6500 v0.0.30
- Gene Ontology OBO October 28, 2015 15:00
- GERP++ 2010 release
- Genome Reference Consortium Human Genome Build v37
- GWAS catalogue (downloaded May 21, 2014)
- HGMD Public version 7.1
- Human Phenotype Ontology build #98
- Human Phenotype Ontology OBO 1698
- MutationTaster (dbNSFP v2.9)
- Omicia Score v2.0
- OMIM (downloaded September 19, 2015)
- PhastCons - phastCons46way (October 8, 2012)
- PhenCode / LSDB (download April 30, 2014)
- PolyPhen-2 v2.2.2 (dbNSFP v2.9)
- SIFT (dbNSFP v2.9)
- SiPhy v0.5
- VAAST Variant Prioritizer v0.0.2