Versioning 1.1 and other new features

Melissa Cline and Mary Goldman

November 3, 2016

Versioning 1.1

Major features

• Fixes the performance issues that appeared in Versioning 1.0
• Reinstates autocomplete
• Addresses a pipeline bug (in a 3rd party tool) that had been “transforming” all missense variants in LOVD, exLOVD, BIC and 1000 Genomes into structural variants.
• Total variant count decreased from 22,000 to 16735

Timeline

• Released to beta on Tuesday 11/1
• Expected release to production on Tuesday 11/8.

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Versioning 1.1 on beta

Versioning 1.0 on beta

Beta test banner

Versioning 1.0 on beta

Updated Variant Count

Versioning 1 Features

New variants

Pre-existing variants with new classifications

Pre-existing variants with other updates

Deleted variants

Release recap

Links to variant sets

Change notes

Download link

Variant set indicator

Reset button

Known issues

1. While the three founder variants have been reviewed by ENIGMA and are in the Expert Reviewed portal, they are not yet searchable by all the BIC Nomenclature synonyms.
2. When the coordinates of a variant are updated (such as due to a bug fix), the variant appears as deleted (by the old coordinates) and added (by the new coordinates) rather than changed.
1. In consequence, one ENIGMA variant appears in the “deleted” set.
3. Our genomic coordinates are off by 1 relative to ClinVar for some structural variants.
4. On the Release Notes page, the number of variants added in Release 1 is not the same as the number of variants that currently appear in the public portal.

Plans for Versioning 2.0

• Implements features to show changes per-variant, as detailed here.
• Indicates when a variant has previous versions
• Allows search access to deleted variants, highlighted and labeled as such.
• BRCA Exchange News indicates variant updates
• Development roadmap
• Prototype release on beta on or around Nov 15.
• Community members will have 2-3 weeks to play with the prototype and provide feedback
• User feedback to be addressed in a subsequent beta release, targeted for early December.
• Release to production one week later.

Subsequent development plans

• Initial revision of the All Public Data portal
• Initial prototyping of an interface for case-level data
• Survey of GA4GH Beacons to identify which Beacons have data on each of the BRCA Exchange variants.
• Potential collaboration with MuPIT, a tool for assessing missense variants in the context of three-dimensional protein structure.
• A potential source of funding for some work we plan to do, plus a modest amount of additional work
• Would fund integration of additional data of value for variant curation
• Sean’s priors for all missense variants?
• Would offer interesting new functionality

MuPIT

• Interactive display of 3D protein structure from Protein Data Bank
• Location of mutation or variant rendered with spacefill balls
• Protein structure color-coded by categorical or numeric data

MuPIT for BRCA Exchange

• Shown: BRCA1 BRCT repeats (protein structure) interacting with BACH1 peptide (wires)
• Structure color-coded by BRCA1 variants
• Red: pathogenic
• Blue: benign
• Purple: VUS
• A single VUS of interest is shown with purple spheres
• Display would be brought up via a hyperlink on a BRCA Exchange protein nomenclature term.

Coming soon?