Fabric Enterprise 6.0 | Pipeline 6.4.3 - Release Notes

10 April 2019 

With the Fabric Enterprise 6.0 release, we are excited to announce the availability of 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’d like to try ACE.

Fabric Enterprise 6.0 also includes the following enhancements:

• Test Definition: Panels can now be defined using BED files
• Scoring module: ClinVar Classification History is now grouped by matches allele, codon, position or overlap
• Gene Knowledge Base: GnomAD browser link is available within modal
• Case Info modal: Genome ID is now displayed
• Clinical Report: Report template fields are now auto-populated if only one option is available
• VCF: CN tag is now supported, in addition to CNV

This release also upgrades the annotation pipeline for ClinVar, OMIM, HPO and HGNC and Entrez gene synonyms.

Data Source & Algorithm Versions

Fabric Pipeline 6.4.3 - 10 April 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 6.4.0) 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).