22 December 2014
Omicia Opal 4.5 is now live. This release of Opal includes various functional and performance enhancements, extending our analysis capabilities for both clinical and research users. Opal Clinical continues to be enhanced. 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.
- Omicia Curated Panels
- NLP Phenotype Mapper
- Add Patient Information via File Upload
- Retiring Published Panels
ExAC and EVS6500 Subpopulation Frequencies
We have extended our population frequencies to include the ExAC and EVS6500 subpopulations. These are accessible by clicking on the overall ExAC or EVS6500 frequency in Opal Clinical or Variant Miner. The subpopulation frequencies are also available in the Opal Clinical Interpret Variants modal, Additional Annotations tab.
Reminder: Opal Annotation Engine 4.1 - New Annotations and Analyses
Opal Annotation Engine was upgraded in the December 8 release.Opal Annotation Engine 4.1 includes new population frequencies, a new VAAST Variant Prioritization Score, an updated Clinical Grade, and a new Regions of Homozygosity Viewer. For more information on these features, please see the Opal 4.4 Release Notes.
Accessing these new capabilities requires re-annotation of any sequences already in Opal. If you want to re-annotate any of your sequences with Opal Annotation Engine 4.1, please contact email@example.com. Any newly uploaded sequences are automatically annotated using 4.1.
Omicia Curated Panels
Omicia develops Curated Panels to accelerate your panel creation effort. These panels have been curated based on strength of disease association and published guidelines. Information on currently available panels is provided here. The Omicia Curated Panels are available in Panel Builder, under Public Panels. If you want to use any of these panels, click the Actions dropdown menu and select the “Clone Panel” option. Now, it will be available in your Workspace Panels, and can be edited and updated as needed. Note that a clinical report cannot be created off a public panel; you will need to clone the panel before you can use it.
NLP Phenotype to Gene Mapper
The Natural Language Processing (NLP) Phenotype Mapper is now available in Opal Clinical. NLP Phenotype Mapper provides a list of conditions associated with this gene, strength of association and prioritized list of PubMed abstracts, generated through natural language processing. NLP Phenoytpe Mapper is available in the Gene Summary, accessed by clicking on the Gene hyperlink in a Clinical Reporter variant table.
Add Patient Information via File Upload
In addition to manually entering patient information, now you can opt to upload patient information from a file. To do this, in Clinical Reporter, click the Actions dropdown menu for your report, and select “Edit Patient Information”. In the Edit Patient Information page, click the Upload File link. Templates for Excel and CSV are provided in the Upload File dialog. Patient information can also be uploaded via Omicia's API. Please contact firstname.lastname@example.org if you would like information on Omicia's API.
Retiring Published Panels
A Retired Panel status is now available. If you want to retire a published panel, select the “Retire Panel” option from the Actions dropdown menu. A retired panel cannot be used for new clinical tests.
Internal ID Field for Tracking Samples Across Multiple Systems
An Internal ID field is now available. This field can be used to cross-reference a unique ID field in another system, such as an LIS. The Internal ID can be specified in the Upload Genome page, and can be updated in the Rename Genome dialog, accessible in the Actions dropdown menu of the project view. The Genome ID field in Clinical Reporter displays the Internal ID in this format: “<Opal Genome ID> - <Internal ID>”.
Variant Miner Filters
Your active Variant Miner filters are now listed at the top right of the Variant Miner window, allowing you to easily see all currently applied filters.
VAAST Case-Control Workflow - Default Background
The VAAST Case-Control Workflow we introduced in the Opal 4.4 release has been updated to use "Control Genomes" as the default background. This is recommended, especially with smaller sets of control samples, as VAAST uses the entire set of background sequences to calculate allele frequency.
Data Source Release Versions
- dbSNP release 138
- Exome Variant Server version 6500
- ExAC November release
- ENSEMBL version 75
- ClinVar (downloaded 11/2014)
- HGMD Public version 7.1
- OMIM (downloaded 11/13/2014)
- PharmGKB (downloaded 1/2010)
- 1000 Genomes phase 1 release (downloaded 12/2011)
- PhenCode (downloaded 05/2013)
- GWAS catalogue (downloaded 05/14/2014)
- dbNSFP version 2.5