Fabric Enterprise 5.9 | Pipeline 6.4.1 - Release Notes

Charlene Son-Rigby -

23 October 2018

The Fabric Enterprise 5.9 release extends the Fabric Enterprise platform with Structural Variant and other feature enhancements.

This release also upgrades the annotation pipeline for VEP, ClinVar, OMIM and gene symbols.

 

Feature Enhancements in Fabric Enterprise

  • Structural Variant Enhancements: The Flag and Dismissing variant features are now enabled for Structural Variants. Bulk classification is also now supported for SVs. Column display is now configurable in the SV tab
  • Variant Description: The Variant Description field is now accessible within the scoring module throughout the scoring process, at the bottom of the window
  • Columns in Variant Tables: Custom scores and Classification (Condition) columns can now be sorted within variant tables. VVP is now displayed as a default column
  • Clinical Grade: Clinical Grade metrics are now available, accessed under Case Info
  • Custom Statuses: Case Custom statuses can now be used for filtering in the Case Queue 

  

API Enhancements

  • Ability to exclude retired tests when retrieving tests by test code

 

Data Source & Algorithm Versions

Fabric Pipeline 6.4.1 - October 23, 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 (2018-09-06 monthly 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 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 September 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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