Opal 4.26 Release Notes

Charlene Son-Rigby -

 

27 January 2017

 

The Opal 4.26 release provides data source updates as well as the recently amended version of the ACMG Incidental Findings gene panel. 

  

ACMG Incidental Findings - Panel & Gene Set

Data Source & Algorithm Versions

  

ACMG Incidental Findings - Panel & Gene Set

ACMG released an updated gene list for incidental findings (Kalia et al., Nov 2016). The ACMG Incidental Findings Panel and Gene Set in Opal have been updated to reflect the new 59 gene list. New genes: BMPR1A, SMAD4, ATP7B, OTC. Removed gene: MYLK. Opal's Public ACMG Panels and Gene Sets have been versioned so labs that are still using the original 56 gene panel in their SOP can continue to do so. The current version has a “-Nov 2016” in the name.

  


Data Source & Algorithm Versions

Opal Pipeline 6.0.9 - Released January 27, 2017

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded October 16, 2016)
  • ClinVar (downloaded January 10, 2017 - weekly release)1
  • COSMIC v79
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar September 28, 2016 Release
  • dbNSFP version 2.9
  • dbSNP release 149
  • ENSEMBL version 83
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO  November 29, 2016 
  • 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 November 29, 2016)
  • Human Phenotype Ontology2 build #110
  • Human Phenotype Ontology OBO 1699 (January 13, 2016)
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded January 9, 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 79 (November 7, 2016)
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • UMLS version 2015AB (November 12, 2015)
  • VAAST Variant Prioritizer v1.1

 

1Two ClinVar RCVs had non-standard clinical significance values in the downloaded XML file. The clinical significances in Opal's ClinVar database were edited to match the clinical significances from the associated SCVs (Submissions) This affects for the following RCVs:

  • RCV000047863.2 (original value: “NM_005591.3(MRE11):c.[497C>T];[168G>T]” changed to “not provided”)
  • RCV000047829.3 (original value: “NM_005371.5(METTL1):c.542T>C” changed to: “Pathogenic”)

 

2Sebastian 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

 

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