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Opal 4.19 Release Notes

Jeanette McCarthy -

4 May 2016

We are excited to announce that Opal 4.19 is live! In this release, we have expanded Opal Clinical's family test workflows to support larger families and multiple affected individuals. We have also delivered enhancements to scoring and classification and to the Previously Seen classified variant database.

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.

 

Flexible Family and Solo Clinical Reports

Opal Clinical Enhancements

HGMD & Other Annotation Enhancements

Data Source & Algorithm Versions

 

Flexible Family, Duo and Solo Clinical Reports

The newest version of Opal Clinical provides more flexible support for family tests, accommodating up to five family members and multiple affected individuals. The Flexible Family test has replaced the Duo test in Opal Clinical.

For example with a trio, you can analyze recessive, de novo, x-linked as well as dominant modes of inheritance, regardless of whether you specify upfront that a parent is affected.

Nuclear family as well as other relationships can be defined. 

We have also improved the Solo and Family workflows:

  • Variant review starts on the Variant Selection page.

  • Variants of interest can be identified and added to the Variant Interpretation page.

  • In-depth review of variants, as well as scoring and classification, takes place on the Variant Interpretation page.

  • After variants have been added to the Variant Interpretation page for a test, the test will automatically open to the Variant Interpretation page, streamlining the review process.

  • Additional variants can always be added to Variant Interpretation by returning to the Variant Selection page. 

 

Opal Clinical Enhancements

Opal Clinical has been enhanced to further support high-volume labs' requirements. Updates include: 

  • Scoring and Classification - Variant classifications can be changed prior to report approval. Variant classifications in in-progress reports can still be used as starting points for scoring in new reports

  • Previously Seen classified variant database - Previous Sanger confirmation results are now stored and displayed when the variant is seen in a new patient.

  • Clinical Reports page filters - On the Clinical Reports page, filters including Report Status and Assigned To are sticky, streamlining updating and interpreting a set of clinical reports

  • Pipeline and VAAST versions - Annotation pipeline and VAAST versions are now provided in the Clinical Report header for reference.

 

Opal Clinical also provides expanded support for custom report statuses to meet your lab's specific reporting workflow requirements.  For information on configuring report statuses, please contact support@omicia.com.

 

HGMD & Other Annotation Enhancements

Opal 4.19 include the following enhancements:

  • HGMD Professional annotations

  • HGVS for variants on a non-canonical transcript are now shown in Variant tables

  • Mitochondrial variant frequencies from Thousand Genomes are now included

  • Multi-allelic variants that have been split and are represented as separate lines in the VCF with genotype notation of 1/. or ./1 are now annotated as heterozygous variants

  • Additional biotypes and genes are now annotated. See Appendix 6

 

Data Source & Algorithm Versions

 Opal Pipeline 6.0.1 - Released May 4, 2016

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded March 20, 2016)
  • ClinVar (downloaded April 2016)
  • COSMIC v71
  • DGV Database of Genomic Variants (download July 23, 2015)
  • dbVar February 2016 Release
  • dbNSFP version 2.9
  • dbSNP release 146
  • ENSEMBL version 83
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO February 12, 2016 
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGMD Professional 2016.1
  • Human Phenotype Ontology1 build #110
  • Human Phenotype Ontology OBO 1699 (January 13, 2016)
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded April 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

 

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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