30 July 2015
Opal 4.12 is now live! In this release, we continue to broaden our clinical family workflows with duos, flexibly supporting inclusion of a parent or another family member in a clinical interpretation. We have introduced a pre-test report to allow clinical labs to easily provide detailed gene coverage information to physicians prior to ordering a test, as well as a number of other enhancements.
We are also discontinuing our free annotation service as of 31 July 2015.
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 email@example.com if you’d like to try Opal Clinical.
Opal Clinical - Duo Workflows
Opal Clinical now provides standard workflows for analysis of a duo, a proband and a relative. The duo workflow flexibly supports inclusion of a parent or another family member, affected or unaffected. VAAST and Phevor ranking are incorporated into the workflow, as well as analysis of family data based on modes of inheritance and other filters. The duo report can be launched from the +New Report dropdown menu in Clinical Reporter.
Discontinuation of Free Annotation Service
As previously announced, we are discontinuing our free annotation service as of 31 July 2015. Going forward, your account will charged when genomes are uploaded, or when clinical reports are generated, depending on your agreement. Uploaded samples automatically have access to advanced capabilities in Opal, including VAAST, Phevor, Flex and collaboration features. This change allows us to simplify and streamline the user interface, so samples do not need to be Upgraded to Pro after upload.
If you have previously loaded free samples that you want to retain for use in Opal, please contact firstname.lastname@example.org before 15 August 2015.
Opal Clinical - Pre-Test Report
We have introduced a pre-test report to allow clinical labs to easily provide detailed gene coverage information to physicians prior to ordering a test for a patient. Now, Opal can store information on low coverage of genes in an assay, and generate a pre-test report for a panel that covers all genes in the assay, or for an in silico panel that covers a subset of the assay.
Opal Clinical - Additional Enhancements
The following enhancements have been added to Opal Clinical:
- Quality Control data. Minimum and Maximum thresholds for quality control data can now be defined. Data falling outside of these thresholds is visually highlighted so a QC data approver can more easily identify issues when evaluating the quality of a sample.
- VAAST scoring of alternate transcripts. VAAST scores all transcripts, so a variant that may be intronic on the canonical transcript may be scored more highly by VAAST due to effect on an alternate transcript. These variants are now shown in clinical reports, with the Effect column displaying an asterisk. If you click on the hyperlink in the effect column, the transcript scored by VAAST is highlighted in yellow.
- Panel Report Default Filters. Default filters for Panel reports only filter No Calls and low quality VCF data (variants with information in the PASS field in the VCF). If you want to filter out introns, nonsynonymous variants or other data include these settings in your Filtering Protocol, or apply a dynamic filter in Clinical Reporter using the filter options to the left of the Interpret Variant table.
- Low quality VCF data in family reports. Low quality VCF data (variants with information in the PASS field in the VCF) is now included in family reports. The default filters do not show the data. You can display this data using the Exclude filter options to the left of the Interpret Variant table. Uncheck the VCF Filters. The zygosity column for quality VCF data will be highlighted in orange.
NNsplice Scores Indels
NNsplice has been updated to predict splice site impact for indels.
Opal Research - Interpretation Priority
Omicia is focused on developing methodologies to accelerate identification of causative variants. The new Interpretation Priority within Opal Variant Miner provides a visual prioritization of variants based on three data elements: ClinVar, Allele Frequency and Effect. Variants can be sorted based on the Interpretation Priority. The Interpretation Priority is an improvement on the Predicted Class, as it provides more granularity while still providing a unified score for prioritization. Annotation reports with Opal 4.2 or greater will display Interpretation Priority instead of the Predicted Class. More information is available here.
Opal Research - VAAST Cohort Report Export
The VAAST Cohort and Case-Control Reports now allow export of the VAAST ranking and annotations to CSV.
Data Source Release Versions
- 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
- ClinVar (downloaded July 9, 2015)
- COSMIC v71
- dbNSFP version 2.9
- dbSNP release 144
- ENSEMBL version 75
- ExAC 0.3 release
- Exome Variant Server 6500 v0.0.30
- GWAS catalogue (downloaded May 21, 2014)
- HGMD Public version 7.1
- HPO build #87
- OMIM (downloaded July 6, 2015)
- PhenCode / LSDB (downloaded May 2013)