Pathogen Transmission Metric Generation via Phylogeny Tree Analysis
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Solution Overview
Problem
Current next-generation sequencing (NGS) techniques face challenges in efficiently identifying and tracking transmission pathways of genetically related infections, requiring tedious reviews of patient trajectories and pathogen matching within care systems.
Innovation Solution
A computer-implemented method and system that generates a transmission metric by analyzing genomic sequence data, proximity tags, and temporal information to create a phylogeny tree, linking clinical correlates and probable transmission vectors, using probabilistic correlations and weighting algorithms to identify related pathogens and predict transmission paths.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional NGS techniques are used for pathogen identification, then genetically related and unrelated infections can be identified and distinguished, but transmission pathways require a tedious review of each patient trajectory through the care system
Solution Approach 1:
The patent introduces an intermediary computational system that processes genomic sequence data and correlates it with patient trajectory data. This intermediary system automatically matches pathogens to transmission pathways without requiring manual review, thereby maintaining identification accuracy while dramatically reducing analysis time. The system acts as a mediator between raw sequencing data and transmission pathway conclusions.
Solution Approach 2:
The patent replaces the mechanical/manual process of reviewing patient trajectories with an automated computational system. The system uses algorithms to process genomic sequence data, compare it against databases, and automatically determine transmission pathways. This substitution of manual mechanical review with automated computational analysis resolves the contradiction by maintaining precision while eliminating time loss.
2Reliability
If manual review of patient trajectories is performed to match pathogens, then transmission pathways can be identified, but the process is tedious and time-consuming
Solution Approach 1:
The patent implements a dynamic automated system that can process multiple patient trajectories simultaneously. The computational system adapts to varying data inputs and can adjust its analysis parameters dynamically. This dynamic approach maintains the reliability of transmission pathway identification while significantly increasing productivity by processing many cases in parallel rather than sequentially through manual review.
Solution Approach 2:
The system performs preliminary computational processing of genomic sequence data and patient trajectory information before final transmission pathway determination. By pre-processing and organizing data computationally, the system ensures reliable identification while improving overall productivity. The preliminary automated sorting and matching of data reduces the burden on subsequent analysis steps.
3Measurement precision
If genomic sequence data is analyzed to identify related pathogens, then accurate transmission metrics can be determined, but complex computational processing is required
Solution Approach 1:
The patent divides the complex computational task into distinct segments or modules. The system separately handles genomic sequence processing, patient trajectory analysis, data correlation, and transmission metric calculation. This segmentation maintains measurement precision by allowing each module to specialize in specific tasks while reducing overall system complexity through modular design. Each segment can be independently optimized and maintained.
Data Source
AI summary
Provided herein are computer implemented methods, systems and processes for determining a transmission metric or transmission path for related pathogens. Also provided herein is a non-transitory computer-readable storage medium with an executable program stored thereon, which program is configured to instruct a microprocessor to generate a transmission path for related pathogens.