Reference-Based Genomic Data Compression and Encryption
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Solution Overview
Problem
Current genomic data transmission and storage face challenges due to low accuracy, short read lengths, high costs, and security concerns, particularly in clinical settings, where next-generation sequencing technologies produce inefficient and insecure data that requires significant post-processing and storage resources.
Innovation Solution
A system and method for secure and compressed transmission of genomic data using reference-based compression, which generates edit calls and encrypts location information, allowing for efficient storage and transmission by storing only the differences between sequence reads and a reference genome, thereby reducing data size and ensuring security through HIPAA-compliant encryption.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If genomic data is transmitted and stored in full format, then data accuracy is maintained, but storage costs and transmission costs increase significantly
Solution Approach 1:
The patent segments genomic data into reference sequences and variations (SNPs, indels, structural variants). Instead of storing complete genomic sequences, only the variations from the reference are stored, dramatically reducing data size while maintaining accuracy. This is achieved through reference-based storage where genomic data is represented as a reference genome plus a set of variation calls.
Solution Approach 2:
The patent uses reference genomes as templates and stores only the differences (variations) rather than copying complete genomic sequences. This allows accurate reconstruction of individual genomes by combining the reference with stored variations, reducing storage requirements from hundreds of gigabytes to kilobytes or megabytes per sample.
2Quantity of substance
If genomic data is compressed using conventional methods, then storage space is reduced, but data security and scalability are compromised
Solution Approach 1:
The patent applies different processing and storage strategies to different types of genomic variations. SNPs are stored as simple nucleotide changes, indels as insertion/deletion events with position and length information, and structural variants as complex rearrangements. Each variation type is optimized for its specific characteristics, improving both compression efficiency and security.
Solution Approach 2:
The patent transforms genomic data from sequence space to variation space, changing the fundamental parameters of representation. Instead of storing base-by-base sequences, the system stores variations defined by position, type, and effect parameters relative to a reference genome, achieving superior compression while maintaining data integrity and security.
3Speed
If next-generation sequencing is used, then read length and speed are improved, but post-processing requirements and error rates increase
Solution Approach 1:
The patent performs reference-based compression and variation calling as part of the sequencing workflow itself, rather than as separate post-processing steps. By integrating the compression algorithm with the base-calling process, the system reduces the computational burden of post-processing while maintaining high sequencing speeds and accuracy.
Data Source
AI summary
An exemplary system, method and computer-accessible medium can be provided for generating an encrypted reference-based secure-compression of randomly located short sequence reads from a genome(s), which can, for example, including obtaining information related to the randomly located short sequence reads, obtaining second information related to a plurality of reference sequences for the genome(s), generating third information related to a set of edit calls containing location information based on the first and second information using a base-calling procedure and an alignment procedure, and generating the encrypted reference-based secure-compression of the first information based on the third information. The exemplary system, method and computer-accessible medium can facilitate the exemplary chemistry box to generate analog information to be locally and physically separated from informatics box interpreting digital data.