ArticleAmerican journal of human genetics2015
Privacy Risks from Genomic Data-Sharing Beacons.
Article in American journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 2 of them syntheses that pooled it.
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Who cites it
95 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A systematic literature review of individuals' perspectives on privacy and genetic information in the United States.PloS one · 2018Pooled it
- Rapid evaluation of phenotypes, SNPs and results through the dbGaP CHARGE Summary Results site.Nature genetics · 2016Pooled it
- Privacy and Security Throughout the Health Data Life Cycle: From Primary Care to Research Networks.Annual review of biomedical data science · 2026Review
- Enhancing semantic interoperability in precision medicine: converting OMOP CDM to Beacon v2 in the Spanish IMPaCT-Data project.BMC medical informatics and decision making · 2026Article
- WiNGS-API: a federated genome/phenome data sharing platform enabling gene discovery and variant classification for rare diseases.Genome medicine · 2026Article
- Autism data sharing: Benefits, challenges, and recommendations.PLOS digital health · 2026Review
- A multi-branch ensemble learning framework for detection of non-small cell lung cancer via T-cell receptor sequencing.BMC cancer · 2026Article
- The Portuguese Beacon: sharing genomic variant data safely.Database : the journal of biological databases and curation · 2026Article
- CITADEL: a post-quantum secure blockchain framework for privacy-preserving electronic health records with temporally-partitioned federated learning.Frontiers in artificial intelligence · 2026Article
- A reinforcement learning-based approach for dynamic privacy protection in genomic data sharing beacons.Genome biology · 2025Article
- Toward owner governance in genomic data privacy with Governome.Cell reports methods · 2025Article
- Beacon Reconstruction Attack: Reconstruction of genomes in genomic data-sharing beacons using summary statistics.Bioinformatics (Oxford, England) · 2025Article
- Ethical Frameworks for Data-Driven Environmental Health Studies in the AI Era.Environment & health (Washington, D.C.) · 2025Article
- Learning-augmented sketching offers improved performance for privacy preserving and secure GWAS.iScience · 2025Article
- Proxy panels enable privacy-aware outsourcing of genotype imputation.Genome research · 2025Article
- A decade of research on genetic privacy: the findings of the GetPreCiSe Center at Vanderbilt University.Frontiers in genetics · 2025Review
- Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS.bioRxiv : the preprint server for biology · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Privacy-Enhancing Technologies in Biomedical Data Science.Annual review of biomedical data science · 2024Review
- FedGMMAT: Federated generalized linear mixed model association tests.PLoS computational biology · 2024Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The human genetics community needs robust protocols that enable secure sharing of genomic data from participants in genetic research. Beacons are web servers that answer allele-presence queries--such as "Do you have a genome that has a specific nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on chromosome 1)?"--with either "yes" or "no." Here, we show that individuals in a beacon are susceptible to re-identification even if the only data shared include presence or absence information about alleles in a beacon. Specifically, we propose a likelihood-ratio test of whether a given individual is present in a given genetic beacon. Our test is not dependent on allele frequencies and is the most powerful test for a specified false-positive rate. Through simulations, we showed that in a beacon with 1,000 individuals, re-identification is possible with just 5,000 queries. Relatives can also be identified in the beacon. Re-identification is possible even in the presence of sequencing errors and variant-calling differences. In a beacon constructed with 65 European individuals from the 1000 Genomes Project, we demonstrated that it is possible to detect membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were able to detect the presence of an individual genome from the Personal Genome Project in an existing beacon. Our results show that beacons can disclose membership and implied phenotypic information about participants and do not protect privacy a priori. We discuss risk mitigation through policies and standards such as not allowing anonymous pings of genetic beacons and requiring minimum beacon sizes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.