Method to manage raw genomic data in a privacy preserving manner in a biobank

Inventors

Hubaux, Jean-Pierre • Ayday, Erman • RAISARO, Jean-Louis • Hengartner, Urs • MOLYNEAUX, Adam • XU, Zhenyu • CAMBLONG, Jurgi • HUTTER, Pierre

Assignees

Sophia Genetics SA

Abstract

A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads' positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank.The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.

Core Innovation

The document describes a privacy preserving biobank system and method for storing and retrieving aligned raw genomic reads in a manner that prevents revealing read locations to the biobank. A plurality of short reads aligned to a reference DNA sequence is used, where the biobank stores, for each short read, encrypted nucleotides, an encrypted cigar string, and an encrypted position in the reference DNA sequence encrypted with an order preserving encryption algorithm.

The medical unit requests a range of nucleotides of genomic data in an encrypted form comprising an encrypted lower bound and an encrypted upper bound. Upon the encrypted range request, the biobank retrieves all short reads including at least one nucleotide for the requested range and then masks nucleotides outside the range defined by the encrypted lower bound and the encrypted upper bound.

The document further describes preventing leakage to the medical unit and/or beyond the requested and consented scope by masking out-of-range and non-consented nucleotide positions at the biobank using masking vectors based on patient consent and access rights. Retrieval-time processing is described where a decrypted lower bound is adjusted and then re-encrypted using the order preserving encryption algorithm to produce an adjusted nucleotide position range, and the document reports evaluation results indicating that unauthorized or leaked genomic data, including leaked SNPs, becomes 0 when masking is applied.

Claims Coverage

The independent claim covers a privacy preserving requesting and retrieval method in which the biobank stores encrypted aligned short reads with order preserving encryption for reference positions, retrieves reads for an encrypted nucleotide range, and masks nucleotides outside the encrypted lower and upper bounds before providing masked short reads to the medical unit. The set of dependent claims further specifies additional inventive features for encryption of nucleotides, masking with masking vectors, masking/encryption delegation to a masking and key manager, adjustment of encrypted bounds at retrieval time, and modifying cigar string representation for masked nucleotides.

Overall, the claims focus on encrypting aligned read components (encrypted nucleotides, encrypted cigar string, and order-preserving encrypted reference positions), requesting an encrypted nucleotide range (encrypted lower bound and encrypted upper bound), retrieving candidate short reads, masking nucleotides outside the encrypted bounds (including masking via masking vectors and possible delegation to a masking and key manager), and modifying cigar string representation for masked nucleotides. Additional dependent features specify stream cipher encryption and XOR masking with a random masking string.

Stated Advantages

Documented Applications