DISEASE-ORIENTED GENOMIC ANONYMIZATION

• US 20190333607A1
• Filed: 06/19/2017
• Published: 10/31/2019
• Est. Priority Date: 06/29/2016
• Status: Active Application

• Current Assignee: Koninklijke Philips N.V.
• Original Assignee: Koninklijke Philips N.V.
• Inventors: Pletea, Daniel, Hulsen, Tim, van der Linden, Wilhelmus Petrus Maria, van Liesdonk, Peter
• Application Number:
  US16/310,065
• Publication Number:
  US 20190333607A1
• Time in Patent Office: Days
• CPC Class Codes: G06F 21/6254 by anonymising data, e.g. decorrelating personal data from the owner's identification
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/40 Encryption of genetic data

Abstract

A method, a system and a computer program product for anonymization of genetic data from at least one individual wherein the genetic data are grouped into a subset of genetic data being directly related to a disease and one or more subsets of genetic data being distantly related to the disease based upon the genome pathways network, and wherein the subsets of genetic data being distantly related to the disease are anonymized.

Claims

1. A method for anonymization of genetic data from at least one individual, said method comprising the steps of:

providing genetic data from at least one individual;

choosing a disease to be studied;

determining at least one subset of the genetic data, said subset of genetic data being directly related to the disease to be studied;

assorting the remaining genetic data which are not directly related to the disease to be studied into multiple subsets grouped into more than one layer based on the proximity of these subsets to the genetic data which are directly related to the disease to be studied, wherein the proximity is preferably established based on a genome pathway network that corresponds to the genetic data;

anonymizing the more than one layer containing the subsets of genetic data not directly related to the disease to be studied.

2. The method according to claim 1, wherein the method further comprises analyzing the genetic data with respect to the disease to be studied.

3. The method according to claim 1, wherein the genetic data are selected from the group consisting of nucleotide sequences, Amplified Fragment Length Polymorphisms, Randomly Amplified Polymorphic DNA, Restriction Fragment Length Polymorphisms, Single Nucleotide Polymorphisms, Short Tandem Repeats and Variable Number Tandem Repeats, RNA, amino acid sequences, polypeptides, proteins and copy number data.

4. The method according to claim 1, wherein the number of layers is 2, 3, 4, 5, 6, 7, 8, 9, or 10.

5. The method according to claim 1, wherein the anonymizing is performed by using at least one technique selected from the group consisting of statistical anonymization, encryption and secure multiparty anonymization and computation.

6. The method according to claim 5, wherein statistical anonymization is selected from the group consisting of k-anonymity, l-diversity, t-closeness and δ

-presence.

7. The method according to claim 5, wherein the encryption is selected from the group consisting of homomorphic encryption, searchable encryption and non-malleable encryption.

8. The method according to claim 1, wherein the different layers are anonymized by different techniques, preferably depending on the distance of the layers'"'"' subsets of genetic data to the subset of genetic data being directly related to the disease to be studied.

9. The method according to claim 1, wherein the subset of genetic data being directly related to the disease to be studied is selected from at least one database defining genes encoding polypeptides that were identified to be directly related to the disease to be studied.

10. The method according to claim 1, wherein genetic data of the first layer'"'"'s subsets of genetic data are selected from the group of genes encoding polypeptides which are not directly related to the disease to be studied, but known to directly interact with one of the genes and/or polypeptides encoded by one of the genes of the genetic data which are directly related to the disease to be studied.

11. The method according to claim 10, wherein at least one of the first layer'"'"'s subsets of genetic data is included into the subset of genetic data being determined to be directly related to the disease to be studied.

12. The method according to claim 11, wherein a subset of genetic data being in straight line to a given subset of genetic data is assorted into the layer next closer to the genetic data being directly related to the disease to be studied.

15. Use of the method according to claim 1, the computer program product according to claim 13 and/or the system according to claim 14 in one selected from the group consisting of genomics, genetics, bioinformatics research, transcriptomics, proteomics and systems biology or diagnosis.

13. A computer program product for anonymizing genetic data, the computer program product comprising instructions which when carried out on a computer cause the computer to perform at least one step of a method for anonymizing genetic data of at least one individual, the method comprising the steps of:

providing genetic data from at least one individual;

choosing a disease to be studied;

determining at least one subset of the genetic data, said subset of genetic data being directly related to the disease to be studied;

assorting the remaining genetic data which are not directly related to the disease to be studied into multiple subsets grouped into more than one layer based on the proximity of these subsets to the genetic data which are directly related to the disease to be studied, wherein the proximity is preferably established based on a genome pathway network that corresponds to the genetic data;

anonymizing the more than one layer containing the subsets of genetic data not directly related to the disease to be studied.

14. A system for anonymizing genetic data, said system comprising:

a data interface configured to receive genetic data of at least one individual;

a user input interface configured to receive user input commands form a user input device for choosing a disease to be studied;

a processor configured for

determining subset(s) of genetic data from the genetic data of the at least one individual being directly related to the disease to be studied;

assorting the subsets of the genetic data that are not directly related to the disease to be studied into different layers based on the subsets'"'"' distance to the genetic data being directly related to the disease to be studied, wherein the distance is preferably established based on a genome pathway network that corresponds to the genetic data; and

anonymizing the layers that are not directly related to the disease to be studied or the genetic data present in the layers that are not directly related to the disease to be studied.