Opal 4.17 Release Notes

Charlene Son-Rigby -

24 February 2016

We are excited to announce that Opal 4.17 is live! In this release, we have upgraded to Ensembl version 83. We also continue to augment our clinical product to further support high-throughput labs' requirements, including enhancing our ACMG Scoring and Classification module, released in January. Opal Clinical fully supports compliance with the 2015 ACMG Guidelines for interpretation of sequence variants, and accelerates evaluation of the evidence associated with each of the 28 criteria to classify variants.

ACMG Scoring is fully integrated into the standardized clinical interpretation workflows in Opal Clinical. Opal Clinical provides an end-to-end solution for clinical NGS testing, combining Omicia’s industry-leading Opal annotation platform with structured workflows, full support for clinical report generation, curated gene panels and LIS integration -- all within a secure, HIPAA-compliant environment. Contact sales@omicia.com if you’d like to try Opal Clinical.

 

Ensembl 83

Opal Clinical Enhancements

Project and Genome Search

Data Source & Algorithm Versions

 

Ensembl 83

Opal has been upgraded to use Ensembl 83 annotations.

This significant update includes:

  • Update of gene symbols and HGNC synonyms
  • More comprehensive mapping to RefSeq transcripts
  • Upgrade of VAAST 3 background database to Ensembl 83
  • Architecture for structural variant interpretation (coming in March)

 


Opal Clinical Enhancements

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

  • Template content for Recommendations can be included clinical report template for panel tests
  • Default filtering protocols can be set up for panel tests
  • Clinical report filters now enable searching by rsID
  • Family reports now include zygosity of all family members in the Add Variants page

Opal Clinical can also be configured to meet your lab's specific reporting workflow with custom report statuses. For information on configuring report statuses, please contact support@omicia.com.

 


Project and Genome Search

The Projects list view now has a text search box, which allows searching for projects and genomes based on Project Name, Project Description and Genome Label. 

 


Data Source & Algorithm Versions

 Opal Pipeline 5.1.1 - Released February 24, 2016

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinVar (downloaded February 2016)2
  • COSMIC v71
  • 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 February 10, 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 February release had an issue with a repeated submission id. In the ClinVar February XML file, SCV000023327 was associated with two condition variant records (RCV’s): RCV000003169 and RCV000202436. Due to the unique relationship Opal expects between RCV and SCV, this SCV was associated with RCV000003169 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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