Opal 4.21 Release Notes

Charlene Son-Rigby -

1 August 2016

We are excited to announce that Opal 4.21 is live! This release delivers expanded support for high-volume labs with batch assignment of Clinical Reports. Opal Clinical's tools have also been extended with additional splice site analysis algorithms as well as additional filtering tools for family member zygosity and HGMD annotations.

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.

In our July 8 release, Opal Clinical was extended to include automated variant classification, allowing high-volume testing labs to automatically use previously classified variant data in new clinical reports, accelerating interpretation and improving standardization. In addition, Opal Clinical has been extended to support somatic cancer testing, enabling labs to use one interpretation platform for hereditary and somatic NGS testing. Contact sales@omicia.com if you’d like to try Opal Clinical.

 

Batch Assignment of Clinical Reports

New Clinical Reporter Filtering and Analysis Tools

Automatically Launch Phevor with Opal API

Data Source & Algorithm Versions

 

Batch Assignment of Clinical Reports

Clinical Reports can now be assigned in batch by workspace administrators. Batch assignment accelerates administration and allows for more efficient management of the clinical reporting workflow. For workspace administrators, an additional Manage Assignment button is available on the Clinical Reports page.

 


New Clinical Reporter Filtering and Analysis Tools

Opal Clinical's tools have also been extended with additional splice site analysis algorithms as well as additional filtering tools for family member zygosity and HGMD annotations. 

  • Two new splice site prediction algorithms have been integrated, MaxEntScan and GeneSplicer. These scores, in additional to NNSplice, are accessible in the Variant Interpretation table by clicking on the hyperlink in the Effect column. 
  • Filtering of variants based on presence of HGMD evidence is now available.
  • For family tests, Opal now provides a single filter combining Heterozygous and None genotypes for family members.
  • Accession ID and Test Code now allow wildcard searches on the Clinical Reports page.

 


Automatically Launch Phevor with Opal API

The Opal API now allows Phevor, Omicia's advanced algorithm that ranks genes based on association to disease, to be run automatically when Clinical Reports are launched and HPO terms are included in the API request. 

Contact support@omicia.com to get started with the Opal API. 

 


Data Source & Algorithm Versions

Opal Pipeline 6.0.4 - Released August 1, 2016

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded June 28, 20161)
  • ClinVar (downloaded July 7, 2016 - weekly release)
  • COSMIC v77
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar May 26, 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 2016.2
  • HGNC and Entrez gene synonyms (downloaded June 27, 2016)
  • Human Phenotype Ontology2 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 July 11, 2016)
  • PhastCons - phastCons46way (October 8, 2012)
  • PhenCode / LSDB (download April 30, 2014)
  • 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

 

1The ClinGen update file contained a duplicate line for the SOX5 gene, with no gene_id. This was removed from the data set

2Sebastian 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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