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
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Publication Number
US-10013575-B2
Publication Date
2018-07-03
Expiration Date
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 invention relates to privacy preserving storage and retrieval of genomic data in a biobank, where a plurality of short reads are aligned to a reference deoxyribonucleic acid (DNA) sequence. For each short read, the biobank stores encrypted nucleotides, an encrypted cigar string, and an encrypted position in the reference DNA sequence. The encrypted position is encrypted with an order preserving encryption algorithm, enabling the system to restrict retrieval to a requested range of nucleotides without exposing unencrypted positional information.
A medical unit (MU) requests nucleotides in a requested range defined by a lower bound and an upper bound by encrypting the lower bound and the upper bound with the order preserving encryption algorithm and sending the encrypted bounds to the biobank. The biobank retrieves all short reads that include at least one nucleotide for the requested range and masks nucleotides of the retrieved short reads outside the range defined by the encrypted lower and upper bounds.
The masking mechanism is enabled by a masking and key manager (MK) that derives masking vectors from requested encrypted nucleotide ranges and patient consent/access rights. Masking is performed so that nucleotides outside the authorized nucleotide range and non-consented SNP/positions are masked without decrypting the encrypted short-read content.
Claims Coverage
The document provides one independent claim, covering a privacy preserving range-request method by a medical unit (MU) for retrieving masked aligned short reads from a biobank. The independent claim includes four inventive elements: encrypted range request using order preserving encryption, storage of encrypted nucleotides and encrypted cigar strings with encrypted reference positions, range-based retrieval, and biobank-side masking of out-of-range nucleotides.
Privacy preserving range request for aligned short reads
A method to request by a medical unit (MU) a range of nucleotides of genomic data in a privacy preserving manner stored in a biobank, wherein the genomic data comprises a plurality of short reads aligned to a reference deoxyribonucleic acid (DNA) sequence.
Encrypted short read components with order preserving encrypted positions
The biobank stores for each short read encrypted nucleotides, an encrypted cigar string, and an encrypted position in the reference DNA sequence, the encrypted position being encrypted with an order preserving encryption algorithm.
Encrypted lower and upper bounds and retrieval of relevant short reads
Encrypting by the medical unit the lower and upper bound with the order preserving encryption algorithm, sending the encrypted lower bound and upper bounds to the biobank, retrieving by the biobank all short reads which include at least one nucleotide for the requested range of nucleotides.
Masking out-of-range nucleotides and providing masked results
Masking by the biobank nucleotides of the retrieved short reads outside the range defined by the encrypted lower and upper bounds and providing the masked retrieved short reads to the medical unit (MU).
Overall, the independent claim is directed to restricting genomic short-read retrieval to a requested nucleotide range using order preserving encryption on encrypted bounds, while keeping short-read content encrypted and producing masked short reads that conceal nucleotides outside the requested range.
Stated Advantages
Provides genomic data restricted to a requested nucleotide range in privacy-preserving form.
Documented Applications
Privacy preserving requesting and retrieval of aligned raw genomic data (SAM/BAM short reads) by a medical unit (MU) from a biobank in response to a requested nucleotide range.
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