bioETH-Beacon: A Confidential On-Chain Genomic Beacon with Encrypted Counts, Filters, and Bounded Noise over a Fully Homomorphic EVM

Quantitative Biology > Genomics [Submitted on 18 Jun 2026] bioETH-Beacon: A Confidential On-Chain Genomic Beacon with Encrypted Counts, Filters, and Bounded Noise over a Fully Homomorphic EVM Christos Galanopoulos, Kimon Antonios Provatas, Ilias Georgakopoulos-Soares The Global Alliance for Genomics and Health (GA4GH) Beacon protocol lets researchers ask whether a genomic variant has been observed in a participating cohort and receive aggregate variant-level counts. As Beacon networks grow, two privacy risks remain: host institutions can see plaintext queries, and repeated rare-variant queries can support membership-inference attacks. We present bioETH-Beacon, a smart-contract prototype that runs the Beacon "aggregate count" query over encrypted data on a fully homomorphic Ethereum Virtual Machine (fhEVM). Hospitals upload encrypted marker-count entries, authorized researchers submit encrypted marker queries, and the contract returns an encrypted answer that is released, via an off-chain key-management service, only to the requester named in the contract's on-chain ACL. The design is organized as a 3x4 tier-by-query-family grid spanning genotype, sex, age, and phenotype queries, with tiers that trade stronger confidentiality for lower query cost. For genotype paths, the prototype can add bounded on-chain noise to mitigate probing attacks. Experiments on synthetic panels derived from a Polygenic Score (PGS) catalog show the expected scaling behavior and demonstrate that pre-aggregation can substantially reduce query gas when public marker presence is an acceptable trade-off. Overall, bioETH-Beacon provides a research prototype for confidential Beacon-style genomic querying without a trusted compute evaluator. Comments: 11 pages, 6 figures, 8 tables. Research prototype for privacy-preserving genomics using Fully Homomorphic Encryption (FHE) on blockchain (fhEVM) Subjects: Genomics (q-bio.GN); Cryptography and Security (cs.CR) MSC classes: 68U99, 92D20 ACM classes: K.6.5; J.3; H.2.7; H.2.8 Cite as: arXiv:2606.20315 [q-bio.GN]   (or arXiv:2606.20315v1 [q-bio.GN] for this version)   https://doi.org/10.48550/arXiv.2606.20315 Focus to learn more Submission history From: Kimon Antonios Provatas [view email] [v1] Thu, 18 Jun 2026 14:49:13 UTC (7,366 KB) Access Paper: HTML (experimental) view license Current browse context: q-bio.GN < prev   |   next > new | recent | 2026-06 Change to browse by: cs cs.CR q-bio References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)