Cloud-Based BRCA Exchange Variant Analysis Environment Using GA4GH Standards in Camber

By integrating BRCA Exchange variant data with GA4GH standards, this GA4GH Implementation Forum (GIF) project creates open, platform-agnostic workflows and tools that can be used by anyone for scalable variant annotation, machine learning, and seamless data exchange. Camber — a cloud-native platform that provides intuitive, low or no-code “science engines” for running simulations, analysing large datasets, and Artificial Intelligence training — serves as the lead implementation showcasing these capabilities.

Background

The BRCA Exchange is a global resource for curated information on BRCA1 and BRCA2 gene variants associated with breast and ovarian cancer. To enable scalable, reproducible, and standards-based genomic analyses, this GA4GH Implementation Forum (GIF) project integrates BRCA Exchange variant data with GA4GH standards using Camber, a cloud-based scientific computing environment that provides low or no-code interfaces, high-performance infrastructure, and built-in support for Artificial Intelligence (AI), simulation, and large-scale data workflows. 

The project aims to adapt and extend community-driven standards to support interoperable workflows, variant annotation, and metadata description. By implementing GA4GH APIs like GKS, the Tool Registry Service (TRS), and the Data Repository Service (DRS), the project facilitates interactive access to genomic data, supports harmonised machine learning applications, and contributes to community-wide standardisation. The Camber platform allows researchers to query, analyse, and visualise data at scale, improving the clinical interpretation of variants and enabling collaborative genomics research.

Ongoing work

  • Integration of BRCA Exchange variant data and existing annotation pipelines using the Variant Representation Specification of GA4GH’s Genomic Knowledge Standards Work Stream
  • Development of interactive tools for querying tabular variant data in the cloud
  • Implementation of containerised, reproducible environments for variant analysis workflows
  • Evaluation and refinement of metadata models to enable interoperability and machine actionability
  • Support for dynamic data access via the DRS API
  • Expansion to include additional variant datasets and workflows
  • Contributions to GA4GH standards refinement based on implementation findings
  • Implementation of TRS-compliant workflow descriptors and comprehensive user documentation

How to participate

We welcome community input, collaboration, and discussion to improve and extend this work. If you are interested in variant annotation, GA4GH standards, machine learning, or cloud-based genomics workflows, please join the conversation. You can express interest in participating in this project here.

Visit our GitHub repository to view open issues, provide feedback, or propose new ideas:
 https://github.com/CamberCloud-Inc/variant-analysis/issues

Have questions?

Do you have questions about this GIF project, or are you looking to get involved? Email gif-cloud-brca-info@ga4gh.org to learn more.

References

GA4GH GKS standards: https://github.com/ga4gh/vrs-python

Camber Cloud: https://cambercloud.com

ERDERA: https://erdera.org/

GKS portal issue on variant data format: https://github.com/ga4gh/gks-portal/issues/8

GA4GH Variant Annotation specification