Privacy-Preserving Genomic Data Management via Order-Preserving Encryption
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current genomic privacy solutions fail to address the secure storage, retrieval, and processing of aligned, raw genomic data, particularly in clinical trials, where patient privacy is at risk due to leakage of genetic information.
Innovation Solution
A privacy-preserving system using order-preserving encryption for short read positions and stream cipher encryption for content, masking unauthorized data at the biobank to prevent information leakage to medical units, ensuring secure retrieval and processing of SAM files without revealing sensitive information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If raw genomic data is stored in SAM files at a biobank for medical research, then the ability to perform genetic analysis and clinical trials is improved, but patient privacy is compromised due to potential leakage of genetic information
Solution Approach 1:
The SAM file data structure is segmented into multiple fields (QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL, and optional fields). Encryption is selectively applied to privacy-sensitive fields (POS, MAPQ, RNEXT, PNEXT, SEQ, QUAL) while leaving non-sensitive fields in plaintext, enabling balanced privacy protection and data usability
Solution Approach 2:
Different encryption approaches are applied to different fields based on their privacy sensitivity. Position and quality fields use order-preserving encryption to maintain analytical utility, while sequence fields use semantic encryption for stronger privacy protection. This local differentiation resolves the contradiction between privacy and research capability
2Object-affected harmful factors
If all short reads are encrypted to protect patient privacy, then privacy protection is improved, but the ability to perform accurate genetic variant calling deteriorates due to loss of ordering information
Solution Approach 1:
Order-preserving encryption is applied to position fields (POS, MAPQ, RNEXT, PNEXT) before storage, preserving the numerical ordering relationships necessary for variant calling algorithms to function accurately. This preliminary encryption approach maintains both privacy and analytical precision
Solution Approach 2:
The encryption method transforms position parameters using order-preserving encryption functions that maintain the relative ordering relationships. This parameter transformation allows encrypted data to retain its functional properties for genetic analysis while protecting privacy
3Object-affected harmful factors
If position information is encrypted using semantic encryption, then privacy protection is improved, but the ability to retrieve specific genomic regions deteriorates due to loss of order information
Solution Approach 1:
Order-preserving encryption transforms position parameters while maintaining their numerical ordering relationships. This parameter transformation enables both strong privacy protection and efficient retrieval operations on encrypted position data
Data Source
Figure 1~4
Figure 5(a)~5(c)
Figure 6~7a
AI summary
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.