Opal 4.10 Release Notes

Charlene Son-Rigby -

28 May 2015

  We are proud to announce Opal 4.10. This release continues our investment in clinical interpretation, with expanded workflows for single exomes and a new quad workflow. We have also introduced a new condition-gene association feature that integrates public and internally curated information on condition-gene associations, with the goal of accelerating interpretation.

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, curated gene panels and LIS integration -- all within a secure, HIPAA-compliant environment. Contact sales@omicia.com if you’d like to try Opal Clinical.

Opal Clinical - Expanded Solo and Quad Workflows

Condition-Gene Association

Panel Builder - Curating Panels from Genes in Existing Panels

Allelic Balance

Data Source Release Versions


Opal Clinical - Expanded Solo and Quad Workflows

The interpretation workflows for a single exome or genome have been expanded to include VAAST and Phevor, to rank variants and disease gene candidates.  Phevor provides a novel algorithmic approach that directly integrates phenotype and gene function information with genomic data. Phevor works with VAAST to bring the most likely and relevant variant candidates to the top of the consideration list, maximizing disease gene discovery for single affected individuals or small nuclear families.   We have also released a quad workflow supporting cases with an affected or unaffected sibling. Note that with an affected sibling, the De Novo report provides only candidates that are present in both siblings.


Condition-Gene Association

Condition-Gene Associations link genes to specific conditions, and can capture additional information such as mode of inheritance and age of onset. Within Clinical Reporter, Condition-Gene Associations are accessed in the Interpret Variants Modal. Disease-Gene Associations from ClinVar and OMIM are provided, as well as associations from Omicia's NLP Phenotype Mapper. Associations can be cloned and edited and new ones created, for use within a workspace. Workspace Condition-Gene Associations can also be managed from the Home Page.  


Panel Builder - Curating Panels from Genes in Existing Panels

Panel Builder has been enhanced so genes already curated in existing panels can be added to new panels.  


Allelic Balance

For heterozygous variants, coverage has been color coded to highlight allelic balance:

  • Black: variant fraction 45 – 55%
  • Orange: variant fraction 30-44% or 56-70%
  • Red: variant fraction <30% or >70%

These thresholds are based on analysis of allele balance and false positives (Pirooznia et al., 2014). There is also a Require filter available to filter out variants with reads in the red or orange bands. These features available in both Clinical Reporter and Variant Miner.  


Data Source Release Versions

  • 1000 Genomes phase 3 version 5 (downloaded 5/2/2013)
  • ClinVar (downloaded 5/2015)
  • COSMIC v71
  • dbNSFP version 2.5
  • dbSNP release 142 v2
  • ENSEMBL version 75
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • GWAS catalogue (downloaded 05/21/2014)
  • HGMD Public version 7.1
  • HPO build #85 (5/1/2015)
  • OMIM (downloaded 5/4/2015)
  • PhenCode / LSDB (downloaded 05/2013)
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