Opal 4.4 Release Notes

Jeanette McCarthy -

8 December 2014

Omicia Opal 4.4 went live over the weekend. This release of Opal includes numerous functional and performance enhancements, extending our analysis capabilities for both clinical and research users.

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

Opal Annotation Engine 4.1 - New Annotations and Analyses

Opal Clinical Advanced Analysis

Data Source Release Versions

Opal Annotation Engine 4.1 - New Annotations and Analyses

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.

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 support@omicia.com. Any newly uploaded sequences are automatically annotated using 4.1.

ExAC and EVS6500 population frequencies

We have extended our population frequencies to include ExAC and EVS6500 in addition to 1000 Genomes, enabling you to analyze variants with respect to multiple minor allele frequency reference datasets. ExAC and EVS6500 are available in both Opal Research and Opal Clinical.

Regions of Homozygosity Analysis

Visual analysis highlighting large regions of homozygosity, as well as a table outlining runs of homozygosity >5MB, enabling you to identify and analyze large deletions, uniparental disomy, etc.

Updated Opal Clinical Grade

Opal’s Clinical Grade is a measure of a variant file’s overall quality. It’s important to confirm the quality of your sequence data before starting to interpret NGS data. We have refined the methodology and updated the reference dataset for Clinical Grade calculations. Now, we calculate the Clinical Grade using coding variants, while providing metrics for all variant data. Samples that do not fit the definition of an exome or genome (“Other”) are also scored. The Clinical Grade is now presented in Opal Clinical.

VAAST Variant Prioritization (VVP) Score - Beta

A new deleteriousness score that applies the VAAST algorithm to individual variants. VVP incorporates allele frequency, amino acid substitution severity and phylogenetic conservation into a single score that is normalized within a gene, intronic or intergenic region. VVP is unique in that it takes frequency into consideration when calculating a variant deleteriousness score. VVP is currently available in Variant Miner.  

Opal Clinical

This release also includes numerous additional enhancements to Opal Clinical:

  • Enhanced gene summary, accessed by clicking on a gene symbol, includes:
    • Graphical gene viewer so you can interactively analyze transcript information and annotations in multiple tracks on a gene
    • Inclusion of links to NCBI, Ensembl, UCSB and other external sites in addition to a Gene Summary
  • Clinical report template management for exome and family tests, accessible from the Clinical Reporter main page
  • Simplified test setup process so you are not required to go through the Edit Patient Information page during setup
  • Addition of quality and coverage as sortable columns, and the rsID in the Interpret variant modal
  • Inclusion of variants from Variant Miner in clinical reports
  • Gene symbol filter


New VAAST Workflows

We have added two new VAAST workflows, supporting Duos and focused Case-Controls. VAAST is Omicia’s unique genome analysis algorithm that ranks genes candidates based on their likelihood to cause disease. VAAST was co-developed with the University of Utah. We have implemented VAAST in easy-to-use workflows, making a powerful, expert algorithm accessible to non-bioinformaticians. Access these new workflows in any Project list view from the Launch App dropdown menu.

  • Case-Control: In addition to our VAAST cohort analysis, we are introducing a focused case-control workflow. This allows you to include control individuals in your analysis. If  you have control samples that were sequenced using the same process, this can significantly increase the power of your studies.
  • Duo: Complementing our family analysis workflows for Trios and Quads, we have developed a Duo workflow to support situations where you only have genomic data for the proband and one unaffected parent.

VAAST Report Enhancements

We have made several upgrades to the VAAST report, including enabling filtering by VAAST rank instead of gene score, displaying a VAAST rank column and using p-value for the VAAST Manhattan plot. In addition, the complete set of deleteriousness scores for each variant is available by clicking on the Omicia Score, as well as transcript information by clicking on the Effect.

Improved Filtering and Reporting in FLEX

We have enhanced Flex with additional filtering options including removing polymorphic gene sets, filtering by disease gene sets, and removing genes with many variants within a sample or cohort. In addition, the complete set of deleteriousness scores for each variant is available by clicking on the Omicia Score, as well as transcript information by clicking on the Effect.

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
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