Known Issues

KNOWN ISSUES in beta test BRCA Exchange Last Updated: Nov 8, 2016

The BRCA Exchange beta site (brcaexchange.cloudapp.net) is available for a second beta test period. Once again, this is an opportunity to identify and address issues before we update the public site.

To report new issues, please email [email protected].

We have identified the following issues:

Variant data:

One ENIGMA variant (c.671-245_671-244insAGG) appears in the Removed Variants list, despite the fact that no ENIGMA variants have been removed. This is really because the genomic coordinates of the variant have changed (we had previously been displaying an incorrect genomic coordinate). Because we represent variants internally by genomic coordinates, when the coordinates of a variant have changed relative to a previous release, we count the old coordinates as removed and the new coordinates as added. We are looking for ways to better account for the same variant being represented with different coordinates.

A number of structural variants (eg c.5641_5644delAAAT) appear to have incorrect coordinate translations, and is off by one base. We’re aware of this issue, which affects some but not all structural variants, and are looking into it.

User Interface:

Searches that should return no search results are returning false positive search results instead. We are looking into this.

The Release Notes page shows that there were 11923 variants in Version 1. The Version 1 data, currently up on brcaexchange.org, shows 13500 variants. The same set of variants is present in both cases. The difference in the number of variants reflects that some variants that previously should have been merged were not merged, due to a bug in the pipeline that has subsequently been fixed.

In the latest release, we have addressed the following issues that were open in the previous beta test release.

Performance:

Database queries of the variant data had become slow. This was causing the variant page to refresh slowly, and to respond to queries slowly. This has been fixed.

When the user clicks Show Lollipop Chart, it was taking a minute for the variants to appear on the chart. During this minute, the chart displayed “0 Variants”. This was a side-effect of Issue (a), and has been fixed. Variant data

The number of LOVD variants removed since the last release was unexpectedly large. Additionally, LOVD did not appear to have any missense variants, only structural variants. This turned out to be a side effect of a bug in the CrossMap tool, and has been fixed.

User interface:

Autocomplete was not working. This has been fixed.

While one can select subsets of variants, such as those that were deleted or those that have new classifications, it’s not apparent how to get back to the full set of variants (which one can do by clicking on the Variants link). This has been fixed with the addition of the Clear Release Filter button.

The release notes are currently unformatted. They will be formatted in a future release. They are now formatted.