arXiv subjects

Christos Galanopoulos

Publications and source records attributed to Christos Galanopoulos.

2 recordsLinked to original sources

arXiv2026

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

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.

q-bio.GN↗

arXiv2026

bioETH-PRS: Confidential Polygenic Risk Scoring without a Trusted Evaluator via Fully Homomorphic Encryption on a Programmable Blockchain

Polygenic risk scores (PRSs) aggregate genetic effect estimates to predict disease susceptibility, yet clinical deployment often exposes raw genotype data to third-party compute infrastructure. Prior homomorphic-encryption approaches, still require trust in a designated evaluator. We present bioETH-PRS, a protocol that replaces that evaluator role with immutable smart contracts on a blockchain supporting Fully Homomorphic Encryption (fhEVM). Using the integer-exact TFHE scheme, bioETH-PRS computes the PRS dot product entirely within the encrypted domain, keeping both genotype dosage vectors and GWAS weight vectors hidden from external parties throughout execution. We introduce a three-step fixed-point quantisation scheme for representing signed GWAS weights as unsigned 64-bit integers, achieving machine-epsilon reconstruction accuracy on validated fixtures. A four-contract architecture separates data custody, model publication, computation, and output release, and supports both a classic chunked path and a streaming path, with the latter reducing mock-measured gas by 37%. An on-chain noisy output oracle emits an encrypted noisy-score handle and a publicly decryptable ternary category, reducing raw score exposure and probing risk. Prototype evaluation on real GWAS fixtures confirms linear gas scaling and suggests that the approach may be cost-competitive in low-gas deployment environments.

q-bio.GN↗