Fabric Enterprise 6.2 | Pipeline 6.6 - Pre-Release Release Notes

Charlene Son-Rigby -

13 November 2019 - Target Release Date 

The Fabric Enterprise 6.2 release brings introduces several new features to both the web app, as well as the API. Some minor bug fixes and performance enhancements have been implemented as well. A significant change is an update of the Projects and Genomes pages to the modern Fabric Enterprise interface (and further deprecating the Opal Classic interface).  For high throughput hereditary cancer panels, case status can be automatically advanced based on the classified variants within the case to support rapid turn around of negative cases. 

Lastly, a complete update of all data sources has been made, as detailed below.

 

Fabric Enterprise Graphical User (Web App) Interface Updates

Fabric Enterprise 6.6

  • Update of Projects page to modern User Interface design 
  • Auto-status of cases now accounts for unclassified variants
  • Filter out intergenic variants: filter based on association with a gene symbol
  • Ability to add genomes for all report types (not just panels)
  • Minor updates to the Structural Variant (SV) Viewer 
  • “Modified by” and “Modified on” now displayed for filters sets & condition genes
  • Gene Sets now require name
  • Pipeline version of genome is now automatically checked before running Family cases
  • Retired gene panels are now excluded from filter options
  • Genome external ID is now displayed during case creation
  • Custom report labels are now properly listed in the clinical report Set Scoring Dialog
  • Gene-condition can now be auto-assigned during batch classification within panels.
  • Added ability to make notes on SV tab in Select screen
  • Additional, customizable report sections
  • “Latest Classification” field now sorts custom classification
  • Gene Filters are now listed by alphabetical order
  • Ability to reorder columns when interpreting variants

 

Fabric API Enhancements

API version 1.2.3

  • Ability to add Family ID as an attribute for genome uploads
  • Ability to update BAM file genome attribute 
  • Ability to launch Somatic cases
  • Corrected export of Structural Variant classifications

 

Fabric Secondary Pipeline Updates

  • Expanded metrics in QC Room 
  • Updated Sentieon libraries

 

Fabric Annotation Pipeline Updates

 

Fabric Pipeline 6.6 

Third-party tool Installations (GRCh37 and GRCh38)

  • VEP was updated to version 95 for both genome builds 

Data Source Updates (GRCh37)

  • ClinVar is now based on the 2019-08-01 release, including OMIM downloaded on 2019-08-20
  • HPO OBO: releases/2019-06-03
  • GO OBO: releases/2019-07-01
  • HGNC/HUGO gene names were updated 2019-08-16
  • VEP Cache was updated to version 95_37
  • CG_DB’s containing UMLS database was updated to 2019AA
  • GnomAD was updated to version 2.1.1
  • Genomenon was updated to version of 2019-09-27
  • Gene_viewer was updated on 2019-09-30
  • Repeat region db bases now on ensembl95_37
  • Regulatory regions db bases now on ensembl95_37

Data Source Updates (GRCh38)

  • ClinVar is now based on the 2019-08-01 release, including OMIM downloaded on 2019-08-20
  • HGNC/HUGO gene names was updated 2019-08-18
  • VEP Cache was updated to version 95_38
  • CG_DB’s containing UMLS database was updated to 2019AA
  • GnomAD was updated to version 2.1.1
  • Genomenon was updated to version of 2019-09-27
  • Gene_viewer was updated on 2019-09-30
  • Repeat region db bases now on ensembl95
  • Regulatory regions db bases now on ensembl95_38
  • Ensembl_lookup includes now RefSeq v96 and CCDS 

 

Full Data Source Manifest

Fabric Pipeline 6.6 

  • 1000 Genomes Phase 3 version 5 (2013-05-02) plus mitochondrial variants
  • CADD v1.0
  • CIVIC 2018-01-17 (b37 only)
  • ClinGen ISCA 2016-10-16 (b37 only)
  • ClinVar 2019-08-01
  • COSMIC v83 (b38), v82 (b37)
  • dbSNP 150
  • dbVar 2016-09-28 (b37 only)
  • DGV 2016-05-15 (b37 only)
  • Ensembl v95
  • EVS 6500 v.0.0.30 (2014-11-03)
  • ExAC 0.3
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO October 13, 2017
  • GeneSplicer February 19, 2003
  • Genomenon Mastermind 2019-09-27
  • GnomAD r2.1.1
  • GWAS 2018-01-23 (b38), 2014-05-21 (b37)
  • HGNC and Entrez gene synonyms (downloaded February 13, 2019)
  • Human Phenotype Ontology OBO (downloaded March 4, 2019)
  • LSDB 2014-04-30
  • MaxEntScan September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM 2019-08-20
  • 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 v96 (b38), v80/81 (b37)
  • SIFT (dbNSFP) v3.5 (b38), v2.9 (b37)
  • UMLS version 2017AA (May 8, 2017)
  • VAAST Variant Prioritizer v1.1
  • VEP v95
  • WEKA 3-6-10

 

Additional Updates:

  • Variants with the classification “pathogenic/likely pathogenic” are now marked with the color amber instead of red
  • Audit trail enhancements
  • Unselect prevalence in condition-gene dialog
  • Tooltip improvements for functional scores
  • Exon/Intron display in consequence dialog

  

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/s13059-016-0974-4)

 

Support Notes

1. Genomes annotated with different major pipeline versions (e.g. 6.2.X versus 6.5) cannot be used in the same clinical report, e.g. for family tests. 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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