Opal 5.4 Release Notes

4 January 2018

The Opal 5.4 release significantly expands Fabric's somatic offering. Fabric's oncology capabilities now include variant calling, annotation from cancer-specific databases, clinical curation from multiple providers, support for 2017 AMP scoring guidelines, and the ability to quickly create physician-ready clinical reports. 

This release also upgrades the annotation pipeline with updates for ClinVar and OMIM.

Feature Enhancements

Somatic:

• Expanded clinical curation from multiple partners. Clinical curation can include SNPs, InDels, SVs, and CNVs

API:

• Clinical Report variant scoring audit log and scoring summary can now be exported via the API "Get Scored Variants" command.

 

Data Source & Algorithm Versions

Opal Pipeline 6.2.5 - 4 January 2018

• 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
• CADD v1.0
• ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded October 16, 2016)
• ClinVar (2017-11 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
• GWAS catalogue (downloaded May 21, 2014)
• HGNC and Entrez gene synonyms (downloaded August 9, 2017)
• 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 November 25, 2017)
• 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 v89

 

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

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).