Beacon⁺ - Genome Beacon concept with quantitative and metadata elements

This project aims to extend the GA4GH Beacon concept for metadata-rich queries, structural variation data and quantitative reporting. It is developed by the SIB Technology Group together with group of Michael Baudis at the University of Zurich.

• Quantitative reporting => because somatic mutations in cancer, especially structural variations, occur at a very high rate and should be evaluated with regard of their prevalence in a given context
• Metadata-rich queries => because metadata/clinical information is required to determine and query these contexts
• Structural variations => because structural genome variations, e.g. copy number imbalances (CNV and somatic CNA) or translocation events, contribute to genome variability and in the case of CNA are highly abundant in cancer

An implementation of the Beacon⁺ concept based on the arrayMap dataset can be found at beacon.arraymap.org.

Table of Contents

• BeaconPlus Concept
• BeaconPlus Query Parameters
• BeaconPlus Return Parameters
• Beacon feature proposal at GA4GH Vancouver 2016-10-17

Links

• Accessing arrayMap attribute and value lists
• Comparison of arrayMap and GA4GH metadata schemas (first mapping tests)
• GA4GH Beacon concept description
• Beacon Network
• arrayMap Beacon test implementation, developed by the SIB Technology Group