Fabric Enterprise 6.7.2 | Pipeline 6.6.5 - Release Notes

Charlene Son-Rigby -

On December 21, 2020, Fabric Genomics released to the US a minor update to Fabric Enterprise (EU will follow shortly after). The web app was updated from v6.6.3 to 6.7.2, customer-facing API remains at v1.2.4, the annotations pipeline updated from 6.6.4 to 6.6.5, and GEM updated from v00.8.0 to 00.9.0.

This release is a minor update, bringing several new small features, addressing several bugs, as well as updates to Clinvar, OMIM and Genomenon

A summary of key changes to each component are listed below:

Fabric Enterprise Web App & API Updates

  • Web App version 6.7.2, API version 1.2.4
  • Workspace switch turn on/off display of all Structural Variants GEM reports
  • GEM will now only classify variants listed as PASS or “.” in VCF filter failure field
  • In scoring module, ability to modify strength of all ACMG criteria (workspace setting, OFF by default)
  • In scoring module, criteria are re-organized according to Clingen recommendations
  • Enhanced ability to choose gene symbol synonyms for panels and gene filters

Known Issues:

  • Some b38 symbols cannot be added to gene filters and panels
  • SV Viewer: may show different genes affected then stated as overlapped
  • Filter option Inheritance Mode for structural variants only shows Denovo as an option
  • Intermittent VAAST failures

Bug fixes:

  • Structural variant scoring not editable after retraction of case
  • Lab Director and Projects Don't persist when adding someone to a workspace
  • Variant in existing approved case shows as "report deleted" in CVdb
  • Latest Classifications not always populating Clinical Reporter
  • Notes for SVs do not pass between the selection and interpretation tab
  • No scrolling with ROH viewer in projects
  • Variant Description option not showing up in ACMG scoring module

Annotation Pipeline changes (pipeline version 6.6.5)

  • Update to latest OMIM, Clinvar and Mastermind
  • Ensembl transcript versions now tracked (available via API in upcoming patch)

Third-party tool Installations (GRCh37 and GRCh38)

  • No third party tools were installed or updated.

Data Source Updates (GRCh37)

  • ClinVar is now based on the 2020-11-01 release (monthly release),
  • including OMIM downloaded on 2020-11-20
  • HGNC/HUGO gene names were updated 2020-11-16
  • Genomenon was updated to version of 2020-10-02

Data Source Updates (GRCh38)

  • ClinVar is now based on the 2020-11-01 release (monthly release), including OMIM downloaded on 2020-11-20
  • HGNC/HUGO gene names were updated 2020-11-16
  • Genomenon was updated to version of 2020-10-02

Bug fixes:

  • None

Known issues:

  • Splice site scores are shown for variants in UTR or intergenic regions

Fabric Enterprise Data Source Manifest

Fabric Pipeline 6.6.5

  • 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 2020-11-01
  • 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 2020-10-02
  • GnomAD r2.1.1
  • GWAS 2018-01-23 (b38), 2014-05-21 (b37)
  • HGNC and Entrez gene synonyms 2020-11-16
  • Human Phenotype Ontology OBO (downloaded March 4, 2019)1
  • LSDB 2014-04-30
  • MaxEntScan September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM 2020-11-20
  • 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 v952
  • WEKA 3-6-10
  •  

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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