Opal 4.24 Release Notes

Charlene Son-Rigby -

 

31 October 2016

 

We are excited to announce that Opal 4.24 is live! 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.

 

ACMG Classification Enhancements

Filter Enhancements

Usability Enhancements

Data Source & Algorithm Versions

  

ACMG Classification Enhancements

Omicia’s Scoring Module allows classification of variants accurately and quickly. This release includes several enhancements. Several of the 28 ACMG criteria can be answered automatically, accelerating and streamlining classification. This capability is particularly valuable for those running high-throughput panel tests.

To expedited interpretation and ensure quality, the workflow to evaluate criteria with different strength assessments have now been aligned with Yes / No criteria. In addition, Notes and Caveats of criterion from the ACMG 2015 Guidelines paper are now accessible during the scoring process.

If you are interested in enabling the Omicia Classification auto-answering capability for existing Workspaces, please contact support@omicia.com. This feature is enabled by default for any newly defined workspaces.

 


Filter Enhancements

Filtering criteria across all reports are now organized in more intuitive subgroupings. New filtering subgroups introduced include: Gene filters, Quality, Evidence, Allele Frequency, Impact Scores, Variant Effect. Within gene filters, clinical user can now specify if they want to look for variants that match to any gene filter (“or” logic), or look for variants that match to all gene filters (“and” logic).

 


Usability Enhancements

In this release, the “Inheritance Mode” column is renamed to “VAAST Inheritance Mode” in order to clarify that it is based on the VAAST algorithm rules. In the ROH viewer, the chromosomes are now oriented in the standard format with the short arm at the top.

 


Data Source & Algorithm Versions

Opal Pipeline 6.0.7 - Released October 31, 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 October 18, 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  February 12, 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 September 20, 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 October 17, 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)
  • 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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