Fabric Enterprise 6.1 | Pipeline 6.5 - Release Notes

Jeanette McCarthy -

26 June 2019 

With the Fabric Enterprise 6.1 release, we are excited to announce our new Structural Variant Viewer, a significant upgrade to our existing Structural Variant interpretation and classification features.  The Structural Variant (SV) Viewer enables rapid evaluation of SV overlap with previously annotated variants, SNPs and indels and other evidence, in a visual track format.

Fabric also recently released Fabric Hereditary Panels with ACE (AI Classification Engine). ACE incorporates an extensively validated, automated ACMG-compliant classification engine, enabling clinical laboratories to dramatically accelerate turnaround times and scale test volume. Fabric Hereditary Panels with ACE is now available for inherited cancer risk, newborn screening, and ACMG Incidental Findings testing. Contact sales@fabricgenomics.com if you are interested in ACE.

Fabric Enterprise 6.1 also includes the following enhancements:


  • Fabric Secondary: CNV calling is now available. Set up requires a panel of normals data provided by customer. Sentieon DNAscope algorithm has also been incorporated for improved small variant calling
  • Custom Columns: Filtering is now enabled and data model supports 6 decimals and 9 digits left of the decimal
  • Variant Selection: Scoring history is now accessible from Variant Selection page by clicking on Latest Classification
  • Gene Drawer: ClinVar and OMIM are now displayed if no Curated Conditions exist
  • Case Workflow and Assignment: Admins and project members only are included in the Assign dropdown
  • Scoring module: Citations curated in Condition-Gene association are now also presented during variant classification
  • Condition Gene: Additional inheritance modes now available: Multiple, Imprinted, Digenic, Mosaic
  • Case Info modal: Genome Label and Case ID are now displayed
  • Workspace Administration: Clinical roles can be assigned in the workspace admin page
  • API: Classified Variant Database endpoints are now available



This release also includes a major version upgrade of the pipeline from 6.4 to 6.5. Clinical cases for family tests need all genomes to be annotated with the same major pipeline version. If a clinical case needs to be created with genomes annotated with Fabric Pipeline 6.5 and genomes previously uploaded that were annotated with 6.4 or prior, the older genomes must be re-annotated. Please contact support@fabricgenomics.com if you require assistance.


Data Source & Algorithm Versions

Fabric Pipeline 6.5 - 26 June 2019

  • 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 (2019-02-25 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 February 13, 2019)
  • Human Phenotype Ontology1 (downloaded March 4, 2019)
  • Human Phenotype Ontology OBO (downloaded March 4, 2019)
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded March 2, 2019)
  • 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/s13059-016-0974-4)


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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