Opal 4.20 Release Notes

Jeanette McCarthy -

8 July 2016

Opal 4.20 is live! This release delivers two major platform extensions: automated variant classification, and clinical interpretation for somatic cancer. Automated variant classification enables high-volume testing labs to automatically use previously classified variant data in new clinical reports, accelerating interpretation and improving standardization. Opal Clinical has also been extended to support somatic cancer testing, enabling labs to use one interpretation platform for hereditary and somatic NGS testing. 

Opal Clinical provides an end-to-end solution for clinical NGS testing, combining Omicia’s industry-leading Opal annotation platform with structured workflows, integrated ACMG-guided classification, full support for clinical report generation and LIS integration -- all within a secure, HIPAA-compliant environment. Contact sales@omicia.com if you’d like to try Opal Clinical.


Simpler Navigation in Opal Clinical

Automated Variant Classification for High-Volume Labs

Opal Clinical for Somatic Cancer

Opal Clinical Enhancements

HGMD & Other Annotation Enhancements

Data Source & Algorithm Versions


 Simpler Navigation in Opal Clinical

 Clinical Reporter is now the default Home Page for Opal Clinical users. Projects are still accessible using the Menu drop-down menu in the top Navigation bar.


Automated Variant Classification for High-Volume Labs

Opal Clinical's new automated variant classification feature allows high-volume testing labs to automatically use previously classified variant data in new clinical reports. Intended for focused panels, this feature accelerates interpretation and improves standardization within a lab. 

  • A master curation record is created when a variant is classified and a report is approved. When the variant is seen again in a new patient, the master curation for the variant is automatically applied, including the classification and variant description to be included the report
  • Evidence for the variant classification is automatically saved in the master curation record during the classification process. The 2015 ACMG Guidelines have been implemented within Opal Clinical for classification, and the classification criteria can be extended or customized depending on a lab's requirements.
  • A timeframe for expiring variant classifications is set for each workspace. The default expiration is six months. When the variant classification has expired, the variant needs to be rescored, either by using the previous scoring session as a starting point or starting a new session. For the former the evidence originally used to classify a variant is automatically presented when the variant needs to be re-evaluated, and can be used as a starting point for re-classification. Accepting the existing scoring session will not restart the expiration timeframe.
  • Condition-Gene associations defined in the panel allow automated classification of variants in panel genes for specific associated conditions. 


Contact support@omicia.com to enable automated variant classification in your workspace. Omicia's Customer Success team can also help you import existing classified variant data into Opal. 


Opal Clinical for Somatic Cancer

Opal Clinical has been extended to support somatic testing, providing clinical labs with a single interpretation and reporting platform for hereditary and somatic NGS testing. Opal Clinical supports hotspot and targeted gene panel tests, and provides actionable drug and clinical trials information through a partner. Opal Clinical's full interpretation and reporting capabilities including sample and report management, audit capabilities, customizable variant classification rules and lab-branded PDF reports are all available for somatic tests. 

Contact support@omicia.com to get started with somatic testing. 


Additional Opal Clinical Enhancements

Opal Clinical has been enhanced to further support high-volume labs' requirements. Updates include: 

  • Different PDF report templates are now supported for different tests in the same workspace
  • The canonical RefSeq transcript is now highlighted in yellow in the Effects dialog, accessed when clicking on the Effect hyperlink for a variant 
  • Wildcard searches can now be used when filtering based on gene symbol. Use as asterisk ("*") at the end of your search term
  • Alamut can be integrated and launched from Opal. The integration can be configured in workspace Admin Settings

Opal Clinical also provides expanded support for custom report statuses to meet your lab's specific reporting workflow requirements.  For information on configuring report statuses, please contact support@omicia.com.


HGMD & Other Annotation Enhancements

Opal 4.20 includes the following enhancements:

  • HGMD Professional - indels are now reduced and realigned, improving the accuracy of matching indel annotations. More information on Omicia's realignment approach is provided here
  • Mitochondrial variant frequencies from Thousand Genomes are now included


Data Source & Algorithm Versions

Opal Pipeline 6.0.3 - Released July 8, 2016

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded June 28, 20161)
  • ClinVar (downloaded June 6, 2016 - weekly release2)
  • COSMIC v77
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar May 26, 2016 Release
  • dbNSFP version 2.9
  • dbSNP release 147
  • ENSEMBL version 83
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO February 12, 2016 
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGMD Professional 2016.1
  • HGNC and Entrez gene synonyms (downloaded June 27, 2016)
  • Human Phenotype Ontology3 build #110
  • Human Phenotype Ontology OBO 1699 (January 13, 2016)
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded June 10, 2016)
  • 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
  • UMLS version 2015AB (November 12, 2015)
  • VAAST Variant Prioritizer v1.1


1The ClinGen update file contained a duplicate line for the SOX5 gene, with no gene_id. This was removed from the data set

2The ClinVar weekly release was used for Opal Pipeline 6.0.3 because records were missing in the ClinVar monthly June release download.

3Sebastian Köhler, Sandra C Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi:10.1093/nar/gkt1026



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