Opal 4.25 Release Notes

Charlene Son-Rigby -

 

12 December 2016

 

Opal 4.25 will be live 12 December 2016! In this release, we have delivered significant enhancements to ACMG Classification with automatically answered ACMG criteria and workflow improvements to enable faster turnaround time and ensure quality. We have also reorganized filters into more intuitive subgroups.

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.

 

Clinical Reports - Batch Report Approval

Filter and Filtering Protocol Enhancements

Regions of Homozygosity Analysis

Viewing all Variants in Approved Solo & Family Reports

Data Source & Algorithm Versions

  

Clinical Reports  - Batch Report Approval

To speed the report approval process and turnaround time, Lab Directors can now approve multiple clinical reports at once. Multiple reports can be selected on the Clinical Reports queue page, and the new Manage Reports button allows both report approval for users with lab director responsibilities, and assigning multiple reports to workspace users. 

 


Filter and Filtering Protocol Enhancements

In the previous release, we organized the variant filter criteria into more intuitive subgroupings. In Opal 4.25, we have replaced the slider bars with numerical input for the allele frequency, impact score and quality score filter criteria. Users can now specify if they want to look for variants that match to any filter (“or” logic), or look for variants that match to all filters (“and” logic) within these subgroups.

We have also upgraded Filtering Protocols so any filter criteria can be included in a Filtering Protocol. 

 


Regions of Homozygosity Analysis

Analyzing regions of homozygosity (ROH) can be important in diagnostic odyssey cases, especially with consanguinous parents or in cases of uniparental disomy. Opal’s ROH viewer has been enhanced so smaller ROH can be identified and analyzed, and family member ROH can be visualized. In addition, there is a new Location filter for variants in ROH in Select Variants and Interpret Variants.

 


Viewing all Variants in Approved Solo & Family Reports

In this release, we have enhanced Solo and Family reports so the Select Variants page is now viewable as read only. Previously only the Interpret Variants page was accessible in approved report. This will allow all variants can be viewed in approved reports.

 


Data Source & Algorithm Versions

Opal Pipeline 6.0.8 - Released December 12, 2016

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded October 16, 2016)
  • ClinVar (downloaded November 22, 2016 - weekly release)
  • COSMIC v78
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar September 28, 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  November 29, 2016 
  • GeneSplicer  February 19, 2003
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGMD Professional 2016.3 (released October 5, 2016)
  • HGNC and Entrez gene synonyms (downloaded November 29, 2016)
  • Human Phenotype Ontology1 build #110
  • Human Phenotype Ontology OBO 1699 (January 13, 2016)
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded November 27, 2016)
  • PhastCons - phastCons46way (October 8, 2012)
  • PhenCode / LSDB (download April 30, 2014)
  • PhyloP - phyloP46way (December 1, 2009)
  • PolyPhen-2 v2.2.2 (dbNSFP v2.9)
  • RefSeq release 79 (November 7, 2016)
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • UMLS version 2015AB (November 12, 2015)
  • VAAST Variant Prioritizer v1.1

 

1Sebastian 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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