Integrated Circuit Bioinformatics Pipeline for Fast Genomic Analysis

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Solution Overview

Problem

Current bioinformatics systems face challenges in efficiently processing large volumes of genomic data from Next Gen Sequencers, requiring significant computational resources and incurring high costs, while existing software-based methods are labor-intensive and prone to errors.

Innovation Solution

A hardware-accelerated platform using integrated circuits, such as FPGAs or ASICs, is employed to perform bioinformatics protocols like mapping, alignment, sorting, and variant calling, optimizing these processes for faster and more accurate execution on genetic sequence data.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Ease of operation

If software-based methods are used for bioinformatics processing, then flexibility and ease of implementation are improved, but processing speed and accuracy deteriorate

Engineering Contradiction:

Improveease of implementationVSAvoidprocessing speed

Core Design Contradiction:

Ease of operationVSProductivity

Solution Approach 1:

The patent replaces software-based processing with hardware-based processing using FPGAs and ASICs. This substitution of mechanical/system type fundamentally changes the processing architecture from software execution on general-purpose processors to dedicated hardware circuits, thereby achieving both improved processing speed and maintained flexibility through reconfigurable FPGA technology.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Adaptability or versatility

If software-based methods are used for bioinformatics processing, then adaptability is improved, but processing accuracy deteriorates

Engineering Contradiction:

ImproveadaptabilityVSAvoidprocessing accuracy

Core Design Contradiction:

Adaptability or versatilityVSMeasurement precision

Solution Approach 1:

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Productivity

If hardware-accelerated platforms are used for bioinformatics processing, then processing speed is improved, but device complexity increases

Engineering Contradiction:

Improveprocessing speedVSAvoidsystem complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent divides the bioinformatics processing system into distinct hardware modules including mapping modules, alignment modules, sorting modules, and variant calling modules. Each module is implemented as a separate functional unit on the FPGA or ASIC, allowing parallel processing while maintaining manageable complexity through modular design. This segmentation enables high-speed processing through parallel execution of multiple processing stages.

Inventive Principle:

Principle #1Segmentation

4Measurement precision

If hardware-accelerated platforms are used for bioinformatics processing, then processing accuracy is improved, but manufacturing cost increases

Engineering Contradiction:

Improveprocessing accuracyVSAvoidmanufacturing cost

Core Design Contradiction:

Measurement precisionVSEase of manufacture

Solution Approach 1:

The patent designs the hardware platform to perform multiple bioinformatics functions including mapping, alignment, sorting, and variant calling within a single integrated system. The FPGA architecture allows reconfiguration to handle different sequencing platforms and analysis workflows, making the expensive hardware investment applicable to multiple applications and reducing the effective cost per analysis through multi-functionality.

Inventive Principle:

Principle #6Universality (Multi-functionality)

Data Source

PatentUS20240185958A1Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

Publication Date: 2024.06.06 ILLUMINA INC

AI summary

A system, method and apparatus for executing a bioinformatics 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 bioinformatics 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 bioinformatics analysis.