Opal 4.8 Release Notes

Charlene Son-Rigby -

1 April 2015

Opal 4.8 is now live! This release provides a significant architectural upgrade, delivering substantial performance improvements for interactive variant analysis as well as annotating larger sequence files including full genomes. As part of this upgrade, data and reports generated prior to the release of Opal Annotation Engine 4 have been retired. Opal 4.8 also includes enhancements to Opal Clinical and Opal Research's Flex Cohort Analysis.

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 sales@omicia.com if you’d like to try Opal Clinical.

Opal Clinical Enhancements

Panels available within Variant Miner Filters

Flex Cohort Analysis Update

Data Source Release Versions


Opal Clinical Enhancements

We have added a number of new annotations to Opal Clinical:

  • Evidence. Links to evidence in the Interpret Variant table are now broken out by icons. At a glance you can see the evidence sources available for a particular variant.
  • Gene Summary. For the Exome test, the Gene Summary now shows all variants in a gene related to the patient, not just variants displayed in the Interpret Variant table

 


Panels available within Variant Miner Filters

Clinical panels built in Panel Builder are now available as filters within Variant Miner, under Panel Set. Panels in the current workspace are accessible.  


Flex Cohort Analysis Update

Opal Research's Flex Cohort Analysis allows you to analyze cohorts and case-controls, providing a visual tree map so you can easily identify shared disease-causing candidates. Flex Cohort has been updated. Now, you can specify sophisticated filters including match thresholds, frequency, gene sets, allelic balance and Omicia score. Flex Cohort can be accessed in the individual project view under the Launch App menu.  


Data Source Release Versions

  • 1000 Genomes phase 3 version 5 (downloaded 5/2/2013)
  • ClinVar (downloaded 3/2015)
  • COSMIC v71
  • dbNSFP version 2.5
  • dbSNP release 142
  • ENSEMBL version 75
  • ExAC 0.3 release
  • Exome Variant Server version 6500
  • GWAS catalogue (downloaded 05/21/2014)
  • HGMD Public version 7.1
  • OMIM (downloaded 3/10/2015)
  • PharmGKB (downloaded 1/2010)
  • PhenCode / LSDB (downloaded 05/2013)
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