Genomic Alignment Data Compression and Encryption
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Solution Overview
Problem
Next-generation sequencing technologies generate vast amounts of genomic data, leading to storage challenges and privacy concerns, with existing compression and encryption methods being inefficient and insecure, particularly in handling large datasets and ensuring secure data access.
Innovation Solution
A method that encodes genomic data alignment information by transposing read-based data into position-based data, compressing it using reference-based encoding, and encrypting it with an order-preserving and symmetric encryption scheme, enabling secure and efficient storage and retrieval while maintaining privacy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If standard compression formats (BAM, CRAM) are used to store genomic alignment data, then storage space is reduced, but data privacy and security are compromised
Solution Approach 1:
The patent implements nested encryption by applying multiple encryption layers: first encrypting the compressed genomic data with a symmetric encryption scheme (e.g., AES), then encrypting the resulting ciphertext with an asymmetric encryption scheme (e.g., RSA). This nested structure allows the data to maintain compression efficiency while achieving strong privacy protection through layered security.
Solution Approach 2:
The patent segments the encryption process into distinct stages: compression stage (where data is compressed to reduce storage space), first encryption stage (symmetric encryption for efficiency), and second encryption stage (asymmetric encryption for security). This segmentation allows each component to optimize for its specific function while working together to solve both storage and privacy requirements.
2Object-affected harmful factors
If encryption is applied to genomic data before compression, then privacy is protected, but storage efficiency and retrieval performance deteriorate
Solution Approach 1:
The patent applies compression to the genomic data before encryption, which is the optimal sequence for achieving both storage efficiency and security. By compressing first, the data size is reduced, making the subsequent encryption operation faster and more efficient. This preliminary compression action ensures that encryption operates on smaller data volumes, improving overall storage efficiency and retrieval performance while maintaining privacy protection.
3Measurement precision
If full genomic data is decrypted and processed, then analysis accuracy is improved, but computational overhead and security risks increase
Solution Approach 1:
The patent enables selective decryption where only the specific portions of encrypted genomic data that are needed for analysis are decrypted and processed, rather than decrypting the entire dataset. This extraction approach allows researchers to access only the necessary genomic information (e.g., specific gene regions or variants) while keeping the rest of the data encrypted, thereby reducing computational overhead and minimizing security risks while maintaining analysis accuracy for the queried regions.
Data Source
AI summary
A genomic data decoder may jointly compress and encrypt genomic data alignment information while preserving the privacy of sensitive genomic data elements at retrieval stage. Genomic data alignment information organized as a read-based alignment data stream may be transposed into a position-based alignment data stream. The position-based alignment information may been coded into a reference-based alignment data stream. The reference-based alignment data stream may be encrypted with a combination of order-preserving encryption of the genomic position information and symmetric encryption of the reference-based alignment differential data. Differential encoding and entropy coding schemes may further compress the reference-based alignment data stream. The resulting compressed and encrypted stream may be indexed and stored in a biobank storage unit. A genomic data decoder may efficiently retrieve, decrypt and decode a specific subset of the resulting compressed and encrypted stream without leaking information on the other genomic data subsets in the resulting stream.