Federated discovery and sharing of genomic data using Beacons

To the Editor — The Beacon Project (https://github.com/ga4gh-beacon/) is a Global Alliance for Genomics & Health (GA4GH)1 initiative that enables genomic and clinical data sharing across federated networks. The project is working toward developing regulatory, ethics and security guidance to ensure proportionate safeguards for distribution of data according to the GA4GH-developed “Framework for Responsible Sharing of Genomic and Health-Related Data”2. Here we describe the Beacon protocol and how it can be used as a model for the federated discovery and sharing of genomic data.

[1]  Xiaoqian Jiang,et al.  Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks , 2017, J. Am. Medical Informatics Assoc..

[2]  Rachel G Liao,et al.  A federated ecosystem for sharing genomic, clinical data , 2016, Science.

[3]  Bartha M Knoppers,et al.  Registered access: a ‘Triple-A' approach , 2016, European Journal of Human Genetics.

[4]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[5]  Sue Healey,et al.  ENIGMA—Evidence‐based network for the interpretation of germline mutant alleles: An international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes , 2012, Human mutation.

[6]  Bartha M Knoppers,et al.  Sharing health-related data: a privacy test? , 2016, npj Genomic Medicine.

[7]  Euan A Ashley,et al.  The precision medicine initiative: a new national effort. , 2015, JAMA.

[8]  Yaniv Erlich,et al.  Routes for breaching and protecting genetic privacy , 2013, Nature Reviews Genetics.

[9]  K. Sirotkin,et al.  The NCBI dbGaP database of genotypes and phenotypes , 2007, Nature Genetics.

[10]  Bartha Maria Knoppers,et al.  Framework for responsible sharing of genomic and health-related data , 2014, The HUGO Journal.

[11]  Orion J. Buske,et al.  The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery , 2015, Human mutation.

[12]  Jordi Rambla De Argila,et al.  Consent Codes: Upholding Standard Data Use Conditions , 2016, PLoS genetics.

[13]  S. Nelson,et al.  Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays , 2008, PLoS genetics.

[14]  C. Bustamante,et al.  Privacy Risks from Genomic Data-Sharing Beacons , 2015, American journal of human genetics.

[15]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[16]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[17]  Chris Mungall,et al.  The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles , 2015, Human mutation.

[18]  Gary D Bader,et al.  International network of cancer genome projects , 2010, Nature.

[19]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[20]  K. Yamamoto,et al.  GLOBAL ALLIANCE FOR GENOMICS AND HEALTH , 2015 .

[21]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[22]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[23]  P. Stenson,et al.  The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine , 2013, Human Genetics.

[24]  M. Peplow The 100 000 Genomes Project , 2016, British Medical Journal.

[25]  Michael Brudno,et al.  PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases , 2015, Human mutation.