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. 2019 Mar;37(3):220-224.
doi: 10.1038/s41587-019-0046-x.

Federated discovery and sharing of genomic data using Beacons

Marc Fiume  1 , Miroslav Cupak  2 , Stephen Keenan  3   4 , Jordi Rambla  5 , Sabela de la Torre  5 , Stephanie O M Dyke  6 , Anthony J Brookes  7 , Knox Carey  8 , David Lloyd  9 , Peter Goodhand  3   10 , Maximilian Haeussler  11 , Michael Baudis  12   13 , Heinz Stockinger  13 , Lena Dolman  3   10 , Ilkka Lappalainen  4   14 , Juha Törnroos  14 , Mikael Linden  14 , J Dylan Spalding  4 , Saif Ur-Rehman  4 , Angela Page  3   15 , Paul Flicek  4   16 , Stephen Sherry  17 , David Haussler  11 , Susheel Varma  9 , Gary Saunders  9 , Serena Scollen  9
Affiliations

Federated discovery and sharing of genomic data using Beacons

Marc Fiume et al. Nat Biotechnol. 2019 Mar.

Erratum in

  • Publisher Correction: Federated discovery and sharing of genomic data using Beacons.
    Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Fiume M, et al. Nat Biotechnol. 2019 Apr;37(4):480. doi: 10.1038/s41587-019-0094-2. Nat Biotechnol. 2019. PMID: 30894680 Free PMC article.
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Beacon Network system architecture.
The user interacts with the Beacon Network system by asking for information about the existence of a particular genetic mutation. The Beacon Network federates the query across many Beacon instances serving various types of data, such as a variant database, VCF files or patient records. The Beacon Network collects the responses from Beacons and presents aggregated information to the user. BIPMed (http://bipmed.org), the Brazilian Initiative on Precision Medicine, is a population sequencing effort while MSSNG (http://mss.ng) collects sequence information from subjects with autism and their families.
See this image and copyright information in PMC

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References

    1. Global Alliance for Genomics and Health. Science. 2016;352:1278–1280. doi: 10.1126/science.aaf6162. - DOI - PubMed
    1. Knoppers BM. HUGO J. 2014;8:3. doi: 10.1186/s11568-014-0003-1. - DOI - PMC - PubMed
    1. 1000 Genomes Project Consortium. et al. Nature. 2015;526:68–74. doi: 10.1038/nature15393. - DOI - PMC - PubMed
    1. Adzhubei IA, et al. Nat. Methods. 2010;7:248–249. doi: 10.1038/nmeth0410-248. - DOI - PMC - PubMed
    1. Stenson PD, et al. Hum. Genet. 2014;133:1–9. doi: 10.1007/s00439-013-1358-4. - DOI - PMC - PubMed

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