PRIVACY-ENHANCING TECHNOLOGIES FOR MEDICAL TESTS USING GENOMIC DATA

• US 20160224735A1
• Filed: 01/12/2016
• Published: 08/04/2016
• Est. Priority Date: 09/14/2012
• Status: Active Grant

• Current Assignee: Ecole polytechnique fãdãrale de lausanne epfl (Schweizerische Eidgenossenschaft)
• Original Assignee: Ecole polytechnique fãdãrale de lausanne epfl (Schweizerische Eidgenossenschaft)
• Inventors: Ayday, Erman, Hubaux, Jean Pierre, Telenti, Amalio, MCLAREN, Paul Jack, Humbert, Mathias, Raisaro, Jean Louis, Fellay, Jacques, Rougemont, Jacques
• Granted Patent: US 9,536,047 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G06F 21/6245 Protecting personal data, e.g. for financial or medical purposes
• CPC Class Codes: G06Q 2220/10 Usage protection of distributed data files
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16B 50/40 Encryption of genetic data
• CPC Class Codes: G16H 10/60 for patient-specific data, e.g. for electronic patient records
• CPC Class Codes: H04L 2209/76 Proxy, i.e. using intermediary entity to perform cryptographic operations
• CPC Class Codes: H04L 2209/88 Medical equipments
• CPC Class Codes: H04L 9/008 involving homomorphic encryption
• CPC Class Codes: H04L 9/0866 involving user or device identifiers, e.g. serial number, physical or biometrical information, DNA, hand-signature or measurable physical characteristics
• CPC Class Codes: H04L 9/0894 Escrow, recovery or storing of secret information, e.g. secret key escrow or cryptographic key storage
• CPC Class Codes: H04L 9/14 using a plurality of keys or algorithms

Abstract

In this invention, we propose privacy-enhancing technologies for medical tests and personalized medicine methods, which utilize patients'"'"' genomic data.

Assuming the whole genome sequencing is done by a certified institution, we propose to store patients'"'"' genomic data encrypted by a patient'"'"'s public keys at a Storage and Processing Unit (SPU). A part of the corresponding private key is also stored on the SPU. At the time of the test by a Medical Unit (MU), the patient provides the second part of the private key to the MU. A test with its associated markers is determined by the MU and sent to the SPU. The test is carried out on the encrypted values thanks to homomorphic operation and returned back to the MU. The latter uses the second part of the private key to access the result.

Claims

1. A method to process genomic data comprising the steps of:

associating, by a Certified Institution, a patient identification with a given patient;

generating, by the Certified Institution, a pair of asymmetric keys related to said patient comprising a private and a public key;

analyzing, by the Certified Institution, an output of a Deoxyribonucleic Acid (DNA) sequencer and preparing an aligned genomic data for said patient comprising approved variants, such as Single Nucleotide Polymorphisms (SNPs) or structural variants (SVs), each approved variant representing a position in the genome and a value representing a nucleotide that varies between individuals;

extracting, by the Certified Institution, real and potential variants from said approved variants, said real and potential variants having each a position, said real variants being a subset of the approved variants and being different for each human being, said potential variants being the remaining part of the approved variants;

encrypting the value of each real variant and of at least some selected potential variants with the public key of the patient;

sending the encrypted values with their respective positions and the patient identification to a Storage and Processing Unit.

2. The method of claim 1, further comprising:

selecting, by the Certified Institution, all or part of the potential variants;

analyzing, by the Certified Institution, the correlation between the selected potential variants and a privacy sensitivity of the real variants;

selecting, by the Certified Institution, a number of other potential variants, said number being determined according to the previous analysis and a level of privacy required.

3. The method of claim 1, further comprising:

dividing, by the Certified Institution, the private key into at least a first and a second part;

storing, by the Certified Institution, the second part of the private key in a medical unit or in a patient device;

transmitting, by the Certified Institution, the first part of the private key to the Storage and Processing Unit.

4. The method of claim 1, further comprising the steps of:

generating, by the Certified Institution, a dummy variant comprising a dummy position and a dummy value, said dummy position being outside of the overall variant positions of a sequence;

encrypting, by the Certified Institution, the positions of the real variants with a symmetric key of the patient;

encrypting, by the Certified Institution, the dummy value with the public key of the patient;

encrypting, by the Certified Institution, the position of the dummy variant with the symmetric key of the patient;

sending, by the Certified Institution, to said Storage and Processing Unit, together with the encrypted variants, the dummy variant as well as the encrypted positions and the encrypted dummy position.

5. The method of claim 4, further comprising the steps of:

storing, by the Certified Institution, the position of the dummy variant into a patient device;

determining by the Certified Institution a set of positions which are common between the marker'"'"'s position and the real variant'"'"'s positions;

receiving by the Certified Institution from the medical unit an encrypted set of positions with the symmetric key of said patient, and for the marker'"'"'s positions not present in the variant'"'"'s position, dummy positions;

sending by the Certified Institution to the Storage and Processing Unit the encrypted marker'"'"'s positions as well as the patient identification.

6. A method to process genomic data, said method comprising the steps of:

receiving by a Storage and Processing Unit encrypted values of real variants, such as Single Nucleotide Polymorphisms (SNP) or structured variants (SVs), for a patient, each real variant representing a position in the genome and a value representing a nucleotide that varies between individuals;

storing in the Storage and Processing Unit the encrypted values with their respective positions into the Storage and Processing Unit, as well as an identification of the patient;

receiving a first part of a private key of the patient;

receiving by the Storage and Processing Unit from a medical unit genetic markers related to a personalized clinical test, the respective contributions of the related genetic markers and the patient identification of the patient;

retrieving by the Storage and Processing Unit the encrypted values for said patient matching the position of the genetic markers;

executing by the Storage and Processing Unit a genetic test by using the retrieved encrypted values, and the contribution of those markers thanks to homomorphic operations;

partially decrypting by the Storage and Processing Unit the result of the genetic test using said first part of the private key;

sending by the Storage and Processing Unit the partly decrypted result to a medical unit.

7. The method of claim 6, further comprising receiving by the Storage and Processing Unit encrypted values of at least some potential variants of said patient, said real and potential variants having each a position, said real variants being different for each human being, said potential variants being the remaining part of the approved variants.

8. The method of claim 6, further comprising the steps of retrieving by the Storage and Processing Unit, together with the encrypted variants, dummy variants encrypted with the public key of the patient, as well as positions of the real variant and of the dummy variants encrypted with a symmetric key of the patient.

9. The method of claim 6, further comprising receiving by the Storage and Processing Unit the allele associated with said genetic markers related to the personalized clinical test, and the corresponding probabilities.

10. A method to process genomic data of a patient, comprising the steps of:

selecting by a medical unit, a personalized clinical test to be carried out and genetic markers related to said test, each marker having a position and a contribution;

determining by the medical unit the contribution of each marker according to the personalized clinical test selected;

transmitting by the medical unit the genetic markers with their respective contribution to a Storage and Processing Unit as well as an identification of the patient;

receiving by the medical unit from said Storage and Processing Unit partly decrypted results;

using in the medical unit a second part of a private key of said patient to obtain a result of the performed personalized clinical test.

11. The method of claim 10, further comprising the steps of transmitting by the medical unit to the Storage and Processing Unit, the allele associated with said genetic markers related to the personalized clinical test, and the corresponding probabilities.