Tools and techniques to make sensitive data discoverable (Use-cases, hands-on session of Beacon implementation)

Workshop details
  • Date: Thu, 15 September 2022
  • Time: 13:30 – 16:30 CEST
  • Format: Virtual
  • Babita Singh, Postdoc Bioinformatics, European Genome-phenome Archive (EGA), Barcelona (Spain)
  • Lauren Fromont, Scientific Project Manager, European Genome-phenome Archive (EGA), Barcelona (Spain)

Sensitive data bioinformatics


One of the main bottlenecks in human genomics research is the lack of secure and federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention with the expansion of genomics data in clinical application, such as for medical diagnostic or prognostic purposes in rare diseases or cancer. This workshop aims to provide knowledge and hands-on sessions about the discoverability of sensitive genomics and clinical data without jeopardizing the privacy or ownership of such datasets. European Genome-phenome Archive along with ELIXIR and GA4GH has been involved to develop tools and techniques to tackle this challenge. Beacon recently became an approved GA4GH standard for data sharing. Now, anyone handling sensitive human dataset can choose to ‘Beaconize’ their dataset and add it to Beacon network to make their data discoverable.

Target Audience
  • Researchers or clinicians working with human genomics dataset (mutations, variants, CNVs etc).
  • Researchers or clinicians working with molecular dataset of the patients, diagnostics markers, treatments etc.
  • Private entities hosting identifiable human data such as data biobanks, genome sequencing data providers, eg. 23andMe, research institutions or hospitals
Call for abstracts

Call is open to everyone working with human omics research and/or clinical dataset who would like to learn how to light a Beacon on their dataset. Participants will be selected on first come first serve basis with following weightage:

  • They have their own omics dataset (for example, VCF files with associated metadata) to light a Beacon
  • They have considerable technical background in shell scripting, python etc
  • Preference will be given to create a gender balanced, diverse team accommodating participants around the globe
13:30 – 14:00Session I – Sensitive data challenges. What makes data, a sensitive data? Introduction to long-term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data. Re-usuablity of datasets, FAIR data principles, public trust and policies on data governance.
Babita Singh
14:00 – 14:30Session II – Beacon use case: Secure sharing of clinical genomics data by connecting different hospitals of Catalunya. Bottlenecks of sensitive data sharing and data re-usability challenges, how does it impact in real-life scenarios? Patient’s journey, stories, use-cases and Introduction to Beacon pilot project launched to connect hospitals of Catalunya.
14.00-14.15h | Beacon – API Jordi Rambla
14.15-14.30h | Beacon – RI introduction Mauricio Moldes
14:30 – 16:30Session III – Demo Beacon Implementation (BYOD: Bring your own dataset). Participants will learn how to make their sensitive data discoverable without jeopardising the privacy of such dataset through demo/hands-on training on Beacon tool reference implementation (Documentation: http://docs.genomebeacons.org/).

We also recommend to bring your own genomics datasets, such as a VCF file with associated phenoclinic/metadata information (eg. patient’s metadata, age/sex/disease etc.)
Mauricio Moldes
Babita Singh
Arnau Soler
Aleix Canalda