Opal 4.3 Release Notes

Jeanette McCarthy -

14 October 2014


Variant Miner

In this release, we have upgraded and expanded the Gene Viewer and Summary in Variant Miner. We have added a beta version of Enlighten Gene, which provides a list of conditions associated with this gene, strength of association and prioritized list of PubMed abstracts, generated through natural language processing. And, the location of a variant is now highlighted in the gene viewer when you click on the variant in the Protein Changing Variants tab.

Evidence has also been changed so when a piece of evidence matches the allele it is outlined in red, if it matches position it is outlined in orange, and if it overlaps, it has a very subtle outline.

Opal Clinical

Now, you can automatically build a variant reference database as variants are classified, to expedite interpretation in  new patient samples. Classifications are automatically captured during clinical interpretation. If a variant has been seen before at your institution, the previous classification information will be shown in the Interpret Variant modal, Seen Before tab. The patients' Accession IDs, associated condition as well as description are provided. You can also integrate your proprietary reference database. Please contact support@omicia.com for more information on this option.

You now have the option to include COSMIC evidence in your interpretation results when a clinical test is set up. Select this for cancer tests.

Expanded filtering options now exist in Clinical Reporter. Additional filters for zygosity, VAAST inheritance mode (Trios), Predicted Class, and ClinVar/OMIM evidence are now available.

Help mouseovers for how scores and predicted class are calculated are also provided. In addition, mousing over the proband zygosity provides number of ref and alt reads.

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