Tool: Omicia Opal™ Research - Variant Annotation and Disease-Gene Prioritization
gravatar for Moses M. Feaster
6.6 years ago by
United States
Moses M. Feaster30 wrote:

Omicia's Opal Research is an SaaS platform that integrates a comprehensive, automated genome annotation engine with the VAAST variant prioritization tool to rank gene variants on the severity of their impact on protein function and likelihood to cause disease.

Omicia Opal Research genome interpretation and variant prioritization platform

Variant Annotation and Disease Gene Mutation Discovery

Access all gene variant-related information, including medical references and predictive scores, with the Variant Miner genome browser.

Automated Annotation - Attach evidence to all gene variants with known medical relevance, drawing annotations from comprehensive gene databases including  OMIM, ClinVar, HGMD Lite, Locus-Specific Databases, GWAS, and PharmGKB.

Integrated Pathogenicity Disease Scoring - Each variant is assessed on the severity of its impact on protein function using multiple algorithms including the Omicia Variant Score, which aggregates several widely-used variant scoring algorithms as a single output.

Cross-Genome Comparison - Find shared or unique variants and mutated genes between multiple genomes

Interactive Filtering - Sort, select, or remove variants from your gene lists by criteria such as:

  -----    Predicted disease-causing potential (as determined by Omicia Score and/or SIFT)

  -----    Evidence of associated disease or biological function

  -----    Type and impact of protein structural change (determined by PolyPhen)

  -----    Frequency of variant occurrence in a specific population

  -----    Genome region (intron or intergenic), gene type (coding vs non-coding), or chromosome/base pair position


Disease Gene Prioritization

Omicia's Vaast: Variant Annotation, Analysis And Search Tool algorithm is integrated into the user-friendly Opal interface.  VAAST analyzes each gene variant based on impact on protein function, conservation and frequency to prioritize causative genes.  VAAST also reduces false positives from sequencing, alignment, and variant-calling errors

Causative Ranking - Rank genes instead of filtering to ensure critical targets are not prematurely removed, a superior approach to filtering methodologies.

Automated Workflows - for individual, family (duo, trio, quad), or cohort genome analyses


Additional Features

Quality Assurance - The Omicia Clinical Grade is a compilation of commonly used quality control criteria to determine the quality of your genome variant file before performing interpretation analysis

Version Control - Keep track of your “variant discovery process” with saved previous and current states of your filter reports

Collaboration - Share genomes, gene sets, and projects with collaborators inside your organization, or with external partners.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Moses M. Feaster30

It has a nice interface.

ADD REPLYlink written 6.6 years ago by Zev.Kronenberg11k

Thanks Zev!

Have you used Opal yourself? We'd love your feedback on the UI, the utility of the annotation pipeline, VAAST integration, etc. It may help you "suffer through your annotation-based projects" a bit less!

I know you're an user of the stand-alone command line VAAST tool, and we think its integration into the Opal interface will allow for faster and more standardized causative variant discovery in human rare disease studies. It's also good for researchers who work with clinicians who need an interface for reporting.

We're offering our current stand-alone VAAST users who are studying human rare disease a free trial of Opal Pro, which comes with integrated VAAST. Anyone can contact me at mfeaster[at]omicia[dot]com and we'll get them set up.

ADD REPLYlink modified 20 months ago by Ram32k • written 6.6 years ago by Moses M. Feaster30

Looks like you need the Pro version to get the VAAST annotations and prioritization. $99/Sample seems a little steep even for the clinical market.

ADD REPLYlink written 6.6 years ago by DG7.2k

Hi Dan,

The free version gives researchers access to the Opal genome browser and variant annotation. Users can upload full genomes or exomes, and get:

  • sequence quality assessment with the Omicia Clinical Score
  • automated annotation from 40 databases (including phyloP, CADD, SIFT, MutationTaster) with links to published evidence
  • predicted pathogenicity scoring with 18 scores, including phyloP, CADD, SIFT, MutationTaster, and our own Omicia Score
  • interactive filtering to discover causative variants

We encourage anyone to try our free version, and upgrade to the Pro version for

  • pre-configured workflows for single, duo, trio quad analyses with VAAST prioritization and other advanced analytical tools
  • curated gene sets that show variants belonging to genes with known association to disease, pharmacological agents, or signalling pathways
  • comparing genomes, which allows users to do things like identify shared or unique variants to find the few that have significance to the phenotype being studied.

Do you have a genome or exome that you would like to annotate? Even if you don't upgrade to Pro, I think you'll find Opal's variant annotation and scoring useful for your orphan disease studies. We'd love your feedback on our platform.

ADD REPLYlink modified 20 months ago by Ram32k • written 6.6 years ago by Moses M. Feaster30

I received an e-mail earlier about testing the platform and responded that I would like to evaluate it. It does look interesting.

ADD REPLYlink written 6.6 years ago by DG7.2k
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