Fabric Enterprise / Opal 5.7 Release Notes

Charlene Son-Rigby -

10 July 2018

The Fabric Enterprise / Opal 5.7 release expands the Fabric Enterprise platform to include interpretation of structural variants. Opal Clinical™ users with existing SV workflows can now begin transitioning to our improved UI in Fabric Enterprise.

This release also includes the Lab Manager Dashboards in Fabric Enterprise. The Lab Manager Dashboards provides clinical labs with enhanced ability to manage their clinical workflows and signouts, enabling management of turnaround time for specific tests, and streamlined assignment of case interpretation and sign out to specific individuals. Please contact [email protected] to enable the dashboards in your workspace.

Fabric Enterprise / Opal 5.7 also upgrades the annotation pipeline with updates for ClinVar, OMIM and HGNC reference data.

  

Data Source & Algorithm Versions

Opal Pipeline 6.2.10 -  July 10, 2018

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • CIViC (downloaded January 17, 2018) 
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded October 16, 2016)
  • ClinVar (2018-06-05 weekly XML release)
  • COSMIC v82
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar September 28, 2016 Release
  • dbNSFP version 2.9
  • dbSNP release 150
  • ENSEMBL version 83
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO  October 13, 2017
  • GeneSplicer  February 19, 2003
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGNC and Entrez gene synonyms (downloaded May 24, 2018)
  • Human Phenotype Ontology1 build #133
  • Human Phenotype Ontology OBO October 5, 2017
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded June 3, 2018)
  • PhastCons - phastCons46way (October 8, 2012)
  • PhenCode / LSDB (download April 30, 2014)
  • PhyloP - phyloP46way (December 1, 2009)
  • PolyPhen-2 v2.2.2 (dbNSFP v2.9)
  • RefSeq release 80/81 
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • UMLS version 2017AA (May 8, 2017) 
  • VAAST Variant Prioritizer v1.1
  • VEP2 version v89

 

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

2McLaren et. al. 2016 (doi:10.1186/s13059-016-)

 

Support Notes

1. Clinical reports can no longer be created using samples annotated with Opal Pipeline version 6.0.14 or older (samples annotated prior to July 8, 2017). 

 

 

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