SVAT

SVAT performs secure annotation and aggregation of genetic variant data using homomorphic encryption to preserve participant privacy and enable variant interpretation and allele frequency computation.

Key Features:

• Homomorphic Encryption: Employs homomorphic encryption to allow computation on ciphertext so genetic data remain encrypted during storage, transmission, and analysis.
• Vectorized Data Representation: Leverages a vectorized representation to enable efficient execution of annotation and aggregation operations within a unified framework on encrypted data.
• Secure Re-encryption Mechanism: Incorporates secure re-encryption to facilitate combination of disparate genotype datasets for federated analyses and to compute allele frequencies across aggregated datasets without exposing plaintext genotypes.
• Client-side Encryption and Encrypted Operations: Encrypts variant data at the client side before transfer and performs annotation and aggregation directly on encrypted inputs to prevent unauthorized plaintext access.

Scientific Applications:

• Variant interpretation and causal variant detection: Enables secure annotation, filtering, and aggregation to support identification and interpretation of causal genetic variants.
• Privacy-preserving allele frequency estimation: Allows computation of allele frequencies across combined genotype datasets in a federated manner without sharing raw genotypes.
• Research with data-sharing restrictions: Supports genomic studies where raw data sharing is restricted, including investigations involving indigenous populations or stigmatizing conditions.

Methodology:

Genetic variant data are encrypted at the client side and processed using homomorphic encryption with a vectorized data representation for annotation and aggregation; secure re-encryption enables combining disparate genotype datasets for federated aggregation and allele frequency computation, with all operations performed on encrypted data.