Integrated Circuit HMM Processing for Genomic Analysis Bottlenecks
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Solution Overview
Problem
Current bioinformatics methods for analyzing genomic data are labor-intensive, prone to errors, and inefficient, particularly in handling the rapid growth of genomic data from Next Gen Sequencers, leading to increased costs and data analysis bottlenecks.
Innovation Solution
A hardware-accelerated platform using integrated circuits with hardwired digital logic circuits, such as FPGA or ASIC, optimized for performing secondary genetic analysis tasks like variant call operations, significantly improving processing speed and accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If software-based bioinformatics methods are used for genomic data analysis, then flexibility and adaptability are maintained, but processing speed and efficiency deteriorate
Solution Approach 1:
The patent replaces software-based computational processing with hardware-based processing using FPGAs and ASICs. This substitution transforms the mechanical system (software execution on general-purpose processors) into a dedicated hardware system that performs bioinformatics operations directly in circuit logic, thereby achieving both high speed and maintained adaptability through reconfigurable hardware architectures.
2Productivity
If more computational resources are allocated to handle increased sequencing throughput, then processing capacity is improved, but cost and power consumption increase
Solution Approach 1:
The patent changes the fundamental parameter of computational resource architecture from general-purpose software-based processing to specialized hardware-based processing. This parameter change enables processing capacity to scale with sequencing throughput while power consumption remains optimized, as hardware circuits perform operations in parallel with minimal energy per operation compared to software execution on CPUs.
3Ease of manufacture
If traditional computing platforms are used for bioinformatics analysis, then ease of implementation is maintained, but processing accuracy and sensitivity deteriorate
Solution Approach 1:
The patent segments the bioinformatics analysis pipeline into distinct functional modules (alignment, variant calling, filtering) that are implemented as separate hardware circuits on the FPGA/ASIC. This segmentation allows each module to be optimized for its specific function, improving overall accuracy while maintaining ease of implementation through modular design and standardized interfaces.
Data Source
AI summary
A system, method and apparatus for executing an HMM analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the HMM analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the HMM analysis.