Opal 4.18 Release Notes

Jeanette McCarthy -

31 March 2016

Opal 4.18 is live! We are excited to announce support of Structural Variants in this release of Opal. We also continue to expand Opal Clinical with enhancements to scoring and classification, general citations and expanded custom report statuses.

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.


Structural Variants

Opal Clinical Enhancements

OMIM Disease Gene Set & Panel

VCF Annotation Enhancements

Data Source & Algorithm Versions


Structural Variants

Opal 4.18 allows interpretation of structural variants. Structural variants and SNV/indels can be analyzed in a unified and matched way, facilitating identification of overlapping and potential compound heterozygous mutations composed of a structural variant and an SNV/indel.

Structural variant classifications are automatically saved to your lab’s Previously Seen database. This database is built over time as variants are classified and can be immediately reused when the variant is seen again in another patient. Classified structural variants that overlap an SNV/indel are highlighted in theSNV/indel's Scoring History, and vice versa.

Structural variant analysis is available for both Opal Clinical and Opal Research users. Within Opal Clinical, family reports allow analysis of structural variants based on mode of inheritance. Structural variants and SNV/indels can be reported on within the same test.

Structural variant annotation sources include Database of Genomic Variants (DGV), dbVar from NCBI, and ClinGen Dosage Sensitivity Project ISCA annotations. Opal currently supports interpretation of Structural Variant data in VCF format.


Opal Clinical Enhancements

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

  • Scoring and Classification - The Variant Description and Notes have been moved to the Scoring tab to facilitate capturing notes and writing the variant description during the scoring process.
  • Scoring and Classification - Additional classes such as risk factor can be added to your workspace. Please contact support@omicia.com.

  • General citations can now be captured, in addition to co-segregation and functional study citations

  • Patient Information. Full Patient Information now available on the Interpret Variants page in the header. In addition, users can go directly to the Interpret Variants page after viewing or editing case information on Patient Information page

This version of 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.


OMIM Disease Gene Set & Panel

The OMIM Gene Set and OMIM Panel names have been changed to OMIM Disease Gene Set and OMIM Disease Gene Panel, respectively, to reflect the genes within these data sets. These data sets contain genes from OMIM variants that have not been reclassified as VUS or Benign, and genes from the OMIM MorbidMap that correspond to diseases with known molecular bases, with at least one catalogued mutation.


VCF Annotation Enhancements

Opal now displays coverage information from VCF files generated from SoftGenetics and Complete Genomics.


Data Source & Algorithm Versions

 Opal Pipeline 6.0 - Released March 31, 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 March 2016)2
  • COSMIC v71
  • DGV Database of Genomic Variants (download July 23, 2015)
  • dbVar 
  • 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 Public version 7.1
  • Human Phenotype Ontology3 build #110
  • Human Phenotype Ontology OBO 1699 (January 13, 2016)
  • MutationTaster (dbNSFP v2.9)
  • Omicia Score v2.0
  • OMIM (downloaded March 6, 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


2ClinVar Duplicate Submission ID issue. ClinVar's March release had an issue with a repeated submission id. In the ClinVar March XML file, SCV000207162 was associated with two condition variant records (RCV’s): RCV000183818 and RCV000157421. Due to the unique relationship Opal expects between RCV and SCV, this SCV was associated with RCV000183818 only.

3Sebastian 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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