Development Roadmap

This section links to material on the changes and new functionality planned or underway for BRCA Exchange development.

This page is updated quarterly. To get the most recent roadmap, please see our Waffleboard.

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Big Picture

• Here are notes from a brainstorming meeting on upcoming development priorities.

• The UCSC and ETH Zurch BRCA Exchange teams held a joint meeting in Santa Cruz on Aug 21-23, 2017. Here are some planning notes, the meeting agenda, and meeting report with slides.

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Portal Development

• Mobile app (Faisal)

• Restructure the help pages. Here is a prototype page for background information targeted to a BRCA testing patient. Here is an outline of questions to ask of stakeholders such as patient advocates (Amy). And here is a recent draft.

• Reporting on Beacons of all variants. This code was developed by Audrey, and has not yet been integrated into the pipeline. There are throughput issues with all-against-all Beacon searches. These wireframes propose an alternative approach, whereby Beacon data is fetched or refreshed per-variant, as demanded by users.

• Literature search: currently refining the method for production (Audrey, Chloe).

• BRCA Exchange / MuPIT integration (Melissa)

• Implement BRCA Exchange News (see the wireframes). (Charlie)

• Expand the suite of unit tests (Collin)

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Collecting and presenting variant-level evidence

Splicing and prediction of truncation

• Team Splicing is gathering the ingredients for computing the splicing prior, including predicting truncating variants (Tyler, Melissa M, Luis). These documents describe respectively the method and the data, and this document shows wireframes for splicing data visualization. Finally, this document lists pseudocode for calculating the priors.

Gathering and presenting allele frequency data

• Adding subpopulation data from ExAC:

  • The BRCA Exchange output data now includes allele counts, allele numbers, homozygous counts and allele frequencies for the seven ExAC subpopulations: AFR, AMR, EAS, FIN, NFE, OTH, SAS.

  • Prototype allele frequency graphs are under development (Joe)

• Incorporating data from gnomAD: Awaiting the release of "gnomAD minus TCGA" (Sam)

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Collecting case-level evidence

• See the draft specification of forms of evidence by analysis type.

Analysis Types

• Co-occurrence

  • See the draft specification for the data needed for co-occurrence (Melissa).

• Summary family history

  • See the UCSC IRB exemption for the ENIGMA pilot

Data collection issues

• Parsing text data from images of reports

  • OCR methods (Chloe).
  • We have some scans of blank test order forms here

• Managing redundancy: one-way cryptographic hashes (Johnnie)