What is the Beacon Project doing to mitigate the possibility and likelihood of reidentification through Beacons?

Any publica data resource containing “human derived” data has a potential for re-identification attacks, that is the identification of individuals contributing data to the resource.

Since its inception, the Beacon Project has been actively working with experts in GA4GH’s membership to address potential privacy concerns.

What is a Beacon?

A Beacon is an online web service that allows users to query an institution’s databases, to determine whether they contain a genetic variant of interest. The query is structured as a yes/no question of the form: “Do you have any genomes with an ‘X’ at position Y on chromosome Z?”

Range Queries and Structural Variants

FAQ - Precise Variants

Precise variants are such with annotated sequences of 0….n length, and bases of [ATCGN] for the referenceBases and alternateBases attributes (N for “not specified”).

What do institutions commit to when they join the Beacon Network?

When an institution “lights” a Beacon, it demonstrates its willingness and ability to share data.

How is sharing data through Beacon different from traditional medical practice?

In current medical practice, doctors commonly share basic, de-identified information about patients’ conditions and genetic variations in the hopes of matching a second case that could be therapeutically transformative. This practice is a long-standing tradition in the medical community but it is neither standardized nor optimized. The Beacon Project turns that informal transaction into a more efficient and effective search that can be a key initial step for learning from valuable genomic information.

Beacons & the importance of global genomic data sharing

Beacons present an easy-to-implement strategy for determining whether an institution has genomic data in its data set that would be useful to share.

Local Jekyll based website generation

In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.

Genome Coordinate use for Beacon Queries

Website - Directories and Files

The Progenetix Jekyll template modifies the standard Jekyll file structure.

Website - Header for Web Pages

The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.

Website - Add and Edit Pages

New pages are added to the website inside one of the “collections” directories in the / directory. This can either be done by adding files locally or on Github (if hosted there).

Beacon Installation and Deployment

Example Queries

This page gives examples for query strings against Beacon implementations. This documentation is expected to be expanded over time, with adjustments for the expanding protocol options.