28 September 2016
We are excited to announce that Opal 4.23 is live! In this release, we introduce the STAT Whole Genome Service, which provides priority processing for urgent clinical whole genome cases. We have also delivered custom scoring rubrics which extend our ACMG Classification Module. In addition, we have enhanced our somatic reporting capabilities and significantly updated Opal's API Documentation.
Opal Clinical provides an end-to-end solution for clinical NGS testing, combining Omicia’s industry-leading Opal annotation platform with structured workflows, integrated ACMG-guided classification, full support for clinical report generation and LIS integration -- all within a secure, HIPAA-compliant environment. Opal Clinical has been extended to support somatic cancer testing, enabling labs to use one interpretation platform for hereditary and somatic NGS testing. Contact firstname.lastname@example.org if you’d like to try Opal Clinical.
Data Source & Algorithm Versions
STAT Whole Genome Service
In Opal 4.23, we introduce priority processing for urgent clinical whole genome cases. Opal's STAT service allows genomes to be designated as STAT cases on upload. STAT whole genomes are processed and annotated first and at highest speed, supporting rapid turnaround for NICU and other critical clinical cases.
Please contact email@example.com if your lab is interested in using the STAT Whole Genome Service.
Customizable Scoring Rubrics
Opal now supports customized scoring rubrics. In January 2016, Omicia introduced the ACMG Scoring & Classification Module, which implements the ACMG 2015 Guidelines in an intuitive, streamlined and standard workflow. With Opal 4.23, labs can use a customized scoring rubric that implements a lab’s desired scoring and classification protocol while leveraging Opal’s intuitive classification workflow and Classified Variant Database.
Custom scoring rubrics enable labs to apply standardized scoring to other types of tests beyond rare, Mendelian disease including carrier testing, somatic and wellness.
Please contact firstname.lastname@example.org if your lab would like to use a customized scoring rubric.
Curation Module Enhancements
The Curation Module was introduced in August, and enables review of current and previous variant classifications as well as ACMG scoring criteria. In addition, administrators can retire outdated classifications as needed.
Opal 4.23 delivers enhancements to the Curation Module interface to the Classified Variant Database, adding new data columns and filters to simplify finding variants of interest and improve user experience.
Enhanced API Documentation
The documentation for the Opal API has a new look and feel, as well as expanded content and examples: https://api.omicia.com.
Higher-throughput labs will benefit from using the Omicia API to integrate with existing lab systems and automate processes including:
- Uploading genomes
- Setting up clinical tests including upload of patient and phenotype information
- Uploading quality control data from sequencing and/or alignment
- Sanger confirmation of variants
- Export of final report results
- Creation and editing of panels
If you are interested in using the Omicia API in your lab, please contact email@example.com.
Data Source & Algorithm Versions
Opal Pipeline 6.0.6 - Released September 28, 2016
- 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
- CADD v1.0
- ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded June 28, 20161)
- ClinVar (downloaded September 12, 2016 - weekly release)
- COSMIC v78
- DGV Database of Genomic Variants (download May 15, 2016)
- dbVar May 26, 2016 Release
- dbNSFP version 2.9
- dbSNP release 147
- ENSEMBL version 83
- ExAC 0.3 release
- Exome Variant Server 6500 v0.0.30
- Gene Ontology OBO February 12, 2016
- GeneSplicer February 19, 2003
- GERP++ 2010 release
- Genome Reference Consortium Human Genome Build v37
- GWAS catalogue (downloaded May 21, 2014)
- HGMD Professional 2016.2
- HGNC and Entrez gene synonyms (downloaded September 20, 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 September 17, 2016)
- PhastCons - phastCons46way (October 8, 2012)
- PhenCode / LSDB (download April 30, 2014)
- PolyPhen-2 v2.2.2 (dbNSFP v2.9)
- SIFT (dbNSFP v2.9)
- SiPhy v0.5
- UMLS version 2015AB (November 12, 2015)
- VAAST Variant Prioritizer v1.1
- phyloP - phyloP46way (December 1, 2009)
1The ClinGen update file contained a duplicate line for the SOX5 gene, with no gene_id. This was removed from the data set
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