Opal 4.22 Release Notes

Charlene Son-Rigby -

31 August 2016

Opal 4.22 is live! In this release, we provide a direct curation interface to the Classified Variant Database, and deliver improved error handling for VCF data. 

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. 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.

 

Classified Variant Database

Improved Error Handling for VCFs

Data Source & Algorithm Versions

 

Classified Variant Database

Opal builds the Classified Variant Database automatically as variants are classified and reports are signed out by your lab. Data on previously classified variants is seamlessly accessible when variants are seen again in a new patient. Existing classifications as well as variant descriptions can be easily applied to new reports, and this can be automated for high-volume panels. The Classified Variant Database accelerates interpretation and improves standardization.

Opal 4.22 provides a direct interface to the Classified Variant Database, enabling review of current and previous variant classifications as well as ACMG scoring criteria. In addition, administrators can retire outdated classifications as needed. The Classified Variant Database is accessible from the Opal Home Page.

 


Improved Error Handling for VCFs

Opal Clinical's VCF upload feature follows VCF format standards. Documentation is provided in Appendix 1. We recognize that some files may not fully adhere to the VCF standard, and a lab may still desire to use these files for validation or related purposes. We have introduced improved error handling in this release. Now, Opal will not fail files with errors, such as erroneous reference bases. Instead, Opal will indicate that the file had errors in the Variant Report and the Clinical Report. Opal will also highlight all variants with issues in the variant table. This detailed information enables labs to identify and resolve VCF issues, and enables them to continue with some aspects of their validation work.

 


Data Source & Algorithm Versions

Opal Pipeline 6.0.5 - Released August 31, 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 August 8, 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 August 8, 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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