30 April 2015
We are excited to announce that Opal 4.9 is now live. This is a substantial release, which includes general availability of Phevor to integrate phenotype data directly into disease gene analysis, significant enhancements to Clinical Reporter, and the incorporation of Beacon, the Global Alliance for Genomics and Health's protocol for sharing de-identified variant level data to improve disease gene identification and patient diagnosis.
Opal Clinical provides an end-to-end solution for clinical NGS, combining Omicia’s industry-leading Opal annotation platform with structured interpretation workflows, full support for clinical report generation, curated gene panels and LIS integration -- all within a secure, HIPAA-compliant environment. Contact firstname.lastname@example.org if you’d like to try Opal Clinical.
ExAC - Issue with Non-reduced Representation Alleles and Low Quality Calls
Phevor is Generally Available
Phevor provides a novel algorithmic approach that directly integrates phenotype and gene function information with genomic data. Phevor works with VAAST to bring the most likely and relevant variant candidates to the top of the consideration list, maximizing disease gene discovery for single affected individuals or small nuclear families. Phevor can be launched from the Launch App menu in the Projects view, as well as in Clinical Reporter for Family Trio reports. Phevor was co-developed by Mark Yandell's lab at University of Utah and Omicia.
Opal Clinical Enhancements
We have added a substantial number of enhancements to Opal Clinical, in addition to integrating Phevor:
- Filters. Interactive filtering features have been significantly expanded. Now, you can filter by allele frequency, coverage, quality, chromosome, position, effect, predicted class and more
- Interpret Variants table. The Interpret Variants table has a streamlined look-and-feel, allowing clear presentation of more data to speed the process of variant identification. Changes include replacing the Interpret button with a small clickable icon
- Gene Summary. The gene summary and gene viewer are now also available in the Interpret Variants modal
- Panel Builder. Panel Builder has been simplified and focused on gene curation. Variant curation now takes place in Clinical Reporter with the Previously Seen classification database. Contact email@example.com if you want to import an existing database of classified variants
The Global Alliance for Genomics and Health (GA4GH) launched the Beacon project to facilitate sharing of de-identified variant level data to improve disease gene identification and patient diagnosis. When a variant has not been observed in any of the reference populations, a beacon icon will appear in the allele frequency field in Variant Miner. Beacon will also soon be available in Opal Clinical. A number of reference sites including NCBI, Sanger, the Institute of Systems Biology and UCSC have launched public Beacon web services. Clicking on the beacon icon in Opal will send a query to each of the Beacon reference sites asking whether they have any genomes. The only information exchanged is the chromosome, position and variant. More information on Beacon is available at the GA4GH Beacon project site.
Default Workspace Settings
Default workspace settings can now be updated in user settings. Click on your email address in the navigation bar to access user settings.
ExAC - Issue with Non-reduced Representation Alleles
5/18/15 ExAC frequency annotations for Opal pipeline versions 4.1.0 to 4.1.4 (January 29 release to today) reflect ExAC’s use of padded or non-reduced representation alleles, which include extra bases on either the 5’ or 3’ end of an allele, for many multi-allelic sites. Consequently, user provided alleles or variants that are unpadded representations that correspond to alleles represented in a non-reduced representation or padded by Exac, may be impacted, with ExAC frequencies incorrectly being missed. We are currently incorporating code provided by Daniel MacArthur’s lab, which converts ExAC’s annotations to reduced representation alleles to ensure that variants are matched correctly. ExAC frequency annotations in Opal do not currently filter out low quality calls from ExAC's annotations, as is done on ExAC's website. This will result in a mismatch in allele frequency data seen in Opal versus the ExAC website, when variants within the ExAC reference data set have low quality calls. Opal's ExAC frequency data is being updated to filter out low-quality calls as well. Both of these issue will be addressed in the 4.1.5 release, targeted for end of May.
Data Source Release Versions
- 1000 Genomes phase 3 version 5 (downloaded 5/2/2013)
- ClinVar (downloaded 4/2015)
- COSMIC v71
- dbNSFP version 2.5
- dbSNP release 142
- ENSEMBL version 75
- ExAC 0.3 release
- Exome Variant Server 6500 v0.0.30
- GWAS catalogue (downloaded 05/21/2014)
- HGMD Public version 7.1
- OMIM (downloaded 4/7/2015)
- PharmGKB (downloaded 1/2010)
- PhenCode / LSDB (downloaded 05/2013)