Fabric Enterprise 5.10 | Pipeline 6.4.2 - Release Notes

Charlene Son-Rigby -

20 December 2018 - Europe Server; 9 January 2019 US Server

The Fabric Enterprise 5.10 release extends the Fabric Enterprise platform with a new integration with Genomenon's Mastermind literature search tool, to accelerate identification of pertinent literature for variant review and classification. In addition this release features enhancements to  Test SOPs.

This release also upgrades the annotation pipeline for ClinVar and OMIM.

 

Feature Enhancements in Fabric Enterprise

  • Genomenon Mastermind integration: Fabric Enterprise now provides an integration with Genomenon's Mastermind literature search tool. An icon is displayed in the variant table when there is literature indexed against a variant
  • SOP Enhancements: Parent zygosity and Classified Variant Database classifications can now be used in SOPs in Test Management
  • Patient age auto-calculation: Patient age is now automatically calculated upon case creation or entry of birth date.
  • Required password reset every 90 days: User passwords must be changed every 90 days. Passwords re-use is not allowed

  

Data Source & Algorithm Versions

Fabric Pipeline 6.4.2 - 20 December 2018 Europe Server; 9 January 2019 US Server

  • 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 (2018-11-26 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
  • Genomenon Mastermind  November 27, 2018
  • 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 August 23, 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 November 26, 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 v91

 

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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