Fabric Enterprise / Opal 5.8 Release Notes

Charlene Son-Rigby -

6 September 2018

The Fabric Enterprise / Opal 5.8 release extends the Fabric Enterprise platform with GnomAD allele frequency annotations, a significant upgrade to the Secondary pipeline and other feature enhancements.

This release also upgrades the annotation pipeline with the addition of GnomAD reference data.

 

Feature Enhancements in Fabric Enterprise

  • GnomAD: GnomAD data is now available in the Allele Frequency column of the variant table. GnomAD frequency data can also be used in filters and SOP steps, and is presented with other allele frequency data in the variant scoring module. Subpopulation data is also available. GnomAD continues to be supported through link outs in the Opal interface
  • Structural Variant Evidence: Structural Variant interpretation in the Select Variants page includes annotations for Genes Affected and Evidence Overlap with ClinGen, DBVar and DGV. 
  • Evidence icons: Evidence column icons indicate level of match with color coding
  • Allelic Balance filter: The Allelic Balance filter supports custom ranges instead of only preset ranges. Custom ranges allow for more flexible analysis. Note that homozygous variants will always be filtered in unless the Zygosity filter is used
  • Flexible Schema: Custom columns for annotations beyond two columns are now supported. Please contact support@fabricgenomics.com if you would like to utilize this capability
 

Feature Enhancements in Fabric Enterprise and Opal

  • Secondary Pipeline: The Secondary pipeline has been significantly upgraded, including a new upload client. Uploads are organized by sequencer run to easily integrate with upstream data production. QC metrics are available in the Opal Secondary Dashboard. Secondary analysis for SNVs and indels is supported
  • Automatic Log off: Users are now automatically logged out after 1 hour of inactivity, for enhanced security 

 

API Enhancements

  • Ability to pull approved reports by approved_before and approved_after date/time stamps  
  • Ability to exclude retired tests in queries of tests by test code

 

Data Source & Algorithm Versions

Fabric Pipeline 6.4.0 - September 6, 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
  • GnomAD r2.0.2
  • 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. Genomes annotated with different major pipeline versions (e.g. 6.2.X versus 6.4.0) cannot be used in the same clinical report. Genomes should be re-annotated with the same pipeline version.

2. 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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