Integrated Circuit Genomic Pipeline for Faster Variant Analysis
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Solution Overview
Problem
Current bioinformatics methods for analyzing genomic data are labor-intensive, time-consuming, and prone to errors, particularly in constructing full-length genomic sequences and determining variants, which creates a bottleneck in data analysis and hinders the transition of genomic data from research to medical applications.
Innovation Solution
Implementing a hardware-based solution using an integrated circuit with hardwired digital logic circuits to perform bioinformatics tasks, such as sequence analysis pipelines, optimizing algorithms for faster and more accurate processing of genomic data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If software-based bioinformatics methods are used for analyzing genomic data, then flexibility and adaptability are maintained, but processing speed and productivity are insufficient
Solution Approach 1:
The patent replaces software-based processing with hardware-based processing using FPGAs and ASICs. This substitution of mechanical/computational systems accelerates genomic data analysis by performing mapping, alignment, and variant calling operations in parallel at hardware level, directly resolving the productivity bottleneck while maintaining analytical capabilities through configurable hardware architectures.
Solution Approach 2:
The patent divides the genomic data analysis pipeline into distinct hardware modules: data reception units, mapping engines, alignment engines, and variant calling units. Each module processes specific aspects of the analysis independently and in parallel, improving overall processing speed while reducing the complexity burden on any single component through functional decomposition.
2Loss of time
If manual or software-based sequence analysis is performed, then accuracy can be maintained through careful processing, but time consumption and labor intensity increase significantly
Solution Approach 1:
The patent replaces manual and software-based sequence analysis with automated hardware systems that perform mapping, alignment, and variant calling operations simultaneously. This eliminates time-consuming sequential processing while maintaining accuracy through dedicated hardware circuits designed for specific analytical tasks, reducing both analysis time and operational complexity.
Solution Approach 2:
The patent implements pre-configured hardware circuits and lookup tables for common genomic operations before data arrives. Mapping indices, alignment parameters, and variant calling thresholds are pre-loaded into the hardware system, enabling immediate processing without requiring time-consuming setup or configuration during actual analysis, thus reducing operational complexity and analysis time.
3Measurement precision
If hardware-based processing is implemented, then processing speed and accuracy are improved, but device complexity and manufacturing difficulty increase
Solution Approach 1:
The patent designs FPGA-based systems that can be reconfigured to perform multiple genomic analysis functions (mapping, alignment, variant calling) using the same hardware platform. This universal approach improves manufacturing ease compared to custom ASICs for each function, while maintaining high accuracy through hardware-level processing. The reconfigurable nature allows a single manufacturing process to serve multiple analytical needs.
Solution Approach 2:
The patent combines multiple analysis functions (mapping, alignment, variant calling) into an integrated hardware system rather than separate devices. This merging reduces the overall manufacturing complexity compared to producing multiple separate systems, while achieving improved accuracy through coordinated hardware processing of the complete analysis pipeline in a unified architecture.
Data Source
AI summary
A system, method and apparatus for executing a sequence analysis pipeline 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 connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are 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 sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.