Integrated Circuit Genomic Processing for Fast Variant Calling

Solution Overview

Problem

Current bioinformatics systems face challenges in efficiently processing large volumes of genomic data from Next Gen Sequencers, requiring substantial computational resources and incurring high costs, while existing software tools 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 secondary and tertiary processing protocols like mapping, alignment, sorting, and variant calling, optimizing these processes for faster and more accurate analysis on genetic sequence data.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Ease of operation

If software tools are used for genomic data 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 transforms the mechanical system from software execution on general-purpose processors to dedicated hardware circuits that perform genomic data processing operations in parallel, achieving both high processing speed and maintained flexibility through reconfigurable logic.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The patent introduces an intermediary hardware layer (FPGA/ASIC) between the data input and output systems. This intermediary contains dedicated processing pipelines for mapping, alignment, sorting, and variant calling operations, enabling fast parallel processing while maintaining the flexibility to process different genomic data types through reconfigurable logic elements.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Adaptability or versatility

If software tools are used for genomic data processing, then adaptability to different protocols is improved, but processing accuracy and reliability deteriorate

Engineering Contradiction:

Improveadaptability to protocolsVSAvoidprocessing accuracy

Core Design Contradiction:

Adaptability or versatilityVSReliability

Solution Approach 1:

The patent replaces software-based processing with hardware-based processing using FPGAs and ASICs. This substitution transforms the mechanical system from software execution on general-purpose processors to dedicated hardware circuits that perform genomic data processing operations in parallel, achieving both high processing speed and maintained flexibility through reconfigurable logic.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The patent introduces an intermediary hardware layer (FPGA/ASIC) between the data input and output systems. This intermediary contains dedicated processing pipelines for mapping, alignment, sorting, and variant calling operations, enabling fast parallel processing while maintaining the flexibility to process different genomic data types through reconfigurable logic elements.

Inventive Principle:

Principle #24Intermediary (Mediator)

3Productivity

If hardware-accelerated platforms are used, then processing speed and accuracy are improved, but device complexity increases

Engineering Contradiction:

Improveprocessing speedVSAvoidsystem complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent segments the genomic data processing system into distinct functional modules implemented in hardware: mapping modules, alignment modules, sorting modules, and variant calling modules. Each module is implemented as separate hardware logic that can operate in parallel processing pipelines, achieving high throughput while organizing complexity into manageable, independent units.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent implements universal hardware processing elements that can perform multiple genomic data processing functions. The FPGA-based architecture uses reconfigurable logic blocks that can be programmed to execute different processing algorithms and protocols, allowing a single hardware platform to handle various genomic analysis tasks without requiring separate dedicated hardware for each function.

Inventive Principle:

Principle #6Universality (Multi-functionality)

Data Source

PatentUS11842796B2Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Publication Date: 2023.12.12 EDICO GENOME CORP

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.