Opal 4.13 Release Notes

Charlene Son-Rigby -

3 September 2015

We are proud to announce that Opal 4.13 is live! In this release, we continue to augment our clinical product with expanded lab workflow support including a new Lab Director role. We also introduce a new Panel Trio test, for targeted panels with family information. 

We have also made some exciting improvements to handling of indels. Indel annotations are often missed or mis-associated due to different representations of indels, and inconsistencies in indel alignment across annotation sources as well as input vcfs. In this release, we have standardized indels across annotation sources with uniform alignment, and by reducing all indels to their minimal form. This was a significant bioinformatics undertaking, and we expect it will significantly improve the accuracy of indel interpretation.

Opal Clinical provides an end-to-end solution for clinical NGS testing, 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 - Lab Director Role, Clinical Report Assignment and Internal Notes

Opal Clinical - Panel Trio

Omicia API

Annotation Pipeline

Data Source Release Versions

 

Opal Clinical - Lab Director Role, Clinical Report Assignment and Internal Notes

Opal Clinical now supports a specific Lab Director role, who can approve Clinical Reports.  

In addition, lab members can be assigned responsibility for specific clinical reports, enabling labs to better manage workflow and utilization. To assign a workspace member to a report, click the Actions dropdown menu for a report, and select “Assign”.

Finally, Internal Notes captured during variant interpretation are now versioned with author and time stamp.

 


Opal Clinical - Panel Trio

Opal Clinical provides a comprehensive set of standard workflows for analysis of panels, exomes and families. In this release, we deliver a Panel Trio workflow for labs running targeted panels, who also want to include family information in the interpretation. This complements the Trio workflow, which is for analyzing whole exome or genome data, and utilizes VAAST and Phevor algorithmic ranking.

The Panel Trio report can be launched from the +New Report dropdown menu in Clinical Reporter.

 


Omicia API

The Omicia Opal API has been significantly expanded to support upload of quality control metrics as well as creation and editing of panels.

Higher-throughput labs will benefit from using the Omicia API to integrate with existing lab systems and automate processes including:

  • Uploading genomes
  • Setting up clinical tests including upload of patient information
  • Uploading quality control data from sequencing and/or alignment
  • Sanger confirmation of variants
  • Export of final report results
  • Creation and editing of panels

 

If you are interested in using the Omicia API in your lab, please contact support@omicia.com.

 


Annotation Pipeline

Indel Realignment

Indel annotations are often missed or mis-associated due to different representations of indels, and inconsistencies in indel alignment to 5' or 3' across annotation sources as well as input vcfs. In this release, we have standardized indels across annotation sources with uniform 5' alignment, and by reducing all indels to their minimal form (doi:10.1093/bioinformatics/btv112). This was a significant bioinformatics undertaking, and we expect it will significantly improve the accuracy of indel interpretation.

hg19 and Mitochondrial Variants

The hg19 reference from UCSC used an older mitochondrial reference from GRCh36, NC_001807 (chrM). Omicia's Opal annotation pipeline uses the GRCh37 reference, C_012920. We recommend that you use the GRCh37 reference for alignment and variant calling.

Verification of Reference Calls in VCF

Opal's annotation pipeline now verifies that reference calls in uploaded vcfs match the reference base expected at the specifed positions.

 


Data Source Release Versions

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • ClinVar (downloaded August 2015)
  • COSMIC v71
  • dbNSFP version 2.9
  • dbSNP release 144
  • ENSEMBL version 75
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • GWAS catalogue (downloaded May 21, 2014)
  • HGMD Public version 7.1
  • HPO build #89 
  • OMIM (downloaded August 5, 2015)
  • PhenCode / LSDB (download April 30, 2014)

 

 

 

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