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Scalable genomic data exchange and analytics with sBeacon

Nature Biotechnology volume 41, pages 1510–1512 (2023)Cite this article

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Developing accurate precision health interventions, such as polygenic risk scores, requires disease allele frequencies for different populations4. Currently, only 54 organizations have stood up a beacon (as of March 2023 (ref. 5)) and the data within these beacons will not be representative of genetically diverse cohorts. sBeacon reduces the barrier to entry for smaller or economically disadvantaged organizations to stand up a beacon (Supplementary Note 1). These individual sBeacons comply with the GA4GH specifications and can exchange information with the Beacon Network6, while being operated for as little as US $16 per month (Supplementary Note 2).

On the other end of the spectrum, sBeacon also supports mega-biobanks by scaling to 3 billion genomic locations and 40 million individuals (the average population per country in 2021 (ref. 7); Supplementary Note 3), supporting ELIXIR’s Genomic Data Infrastructure strategy (pillar 1: long-term scalability). By contrast, MongoDB — used by current beacon implementations (for example, Beacon Reference Implementation8 and Barcelona Supercomputing Centre Beacon9) — cannot scale beyond 100,000 samples (Supplementary Note 4). Querying millions of samples provides the statistical power to tackle difficult clinical tasks, such as interpreting variants of uncertain significance and training models for automatic variant prioritization in genomic pathology.

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Fig. 1: sBeacon application cases and comparison with existing implementations.

References

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Acknowledgements

The authors thank CSIRO for financial support and the Australian Genomics Health Alliances for their input to this work.

Author information

Author notes

  1. These authors contributed equally: Anuradha Wickramarachchi, Brendan Hosking, Yatish Jain.

Authors and Affiliations

  1. Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Westmead, New South Wales, Australia

    Anuradha Wickramarachchi, Brendan Hosking, Yatish Jain, Mitchell J. O’Brien, Laurence O. W. Wilson & Natalie A. Twine

  2. Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia

    Yatish Jain, Laurence O. W. Wilson, Natalie A. Twine & Denis C. Bauer

  3. Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Herston, Queensland, Australia

    John Grimes, Tracey Wright & Michael Lawley

  4. Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia

    Mark A. Burgess

  5. Centre for Cancer Research, University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia

    Victor San Kho Lin, Florian Reisinger & Oliver Hofmann

  6. Department of Biomedical Sciences, Macquarie University, Macquarie Park, New South Wales, Australia

    Denis C. Bauer

  7. Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia

    Denis C. Bauer

Authors
  1. Anuradha Wickramarachchi
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  14. Denis C. Bauer
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Contributions

A.W., B.H. and T.W. implemented sBeacon and conducted experiments with Y.J., M.J.O’B. and M.A.B.; J.G. and M.L. guided Ontoserver integration; V.S.K.L., F.R., O.H., L.O.W.W., N.A.T. and D.C.B. conceived and supervised the study. All authors contributed to the document.

Corresponding author

Correspondence to Denis C. Bauer.

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The authors declare no competing interests.

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Nature Biotechnology thanks Jordi Rambla and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplemental Notes including additional information and figures.

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Wickramarachchi, A., Hosking, B., Jain, Y. et al. Scalable genomic data exchange and analytics with sBeacon. Nat Biotechnol 41, 1510–1512 (2023). https://doi.org/10.1038/s41587-023-01972-9

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