Portable Biosurveillance Kit Using Local Reference Data
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Solution Overview
Problem
Current methods for sequencing and analyzing metagenomic samples require immobile laboratory equipment and internet connections, making it impractical to perform analysis in remote or inaccessible locations without risking sample damage and increasing operational costs.
Innovation Solution
A portable nucleic acid sequencing kit that allows for DNA extraction, preparation, and sequencing without internet or line power, using locally stored conserved-signature sequences and probabilistic data structures for efficient identification of target organisms in field environments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If metagenomic sample sequencing and analysis is performed using traditional laboratory equipment, then analysis accuracy and reference data access are improved, but equipment portability and field deployability deteriorate
Solution Approach 1:
The patent divides the metagenomic analysis system into modular components: portable sequencing device, local reference data storage, and field-deployable processing software. This segmentation allows the system to be transported and deployed in remote locations while maintaining analysis capabilities.
Solution Approach 2:
The patent transitions from centralized cloud-based reference data access to local distributed storage across multiple portable devices. This dimensional shift from network-dependent to locally-stored reference data enables field deployment without internet connectivity.
2Reliability
If metagenomic samples are transported from field environment to dedicated laboratory, then analysis infrastructure is improved, but sample integrity and operational efficiency deteriorate
Solution Approach 1:
The patent enables the field deployment location to perform sequencing and analysis independently using portable equipment and locally-stored reference data. This self-service capability eliminates the need to transport samples to centralized laboratories, keeping samples at their collection location throughout the analysis process.
3Quantity of substance
If vast libraries of reference data are accessed via internet connection, then reference data completeness is improved, but network dependency and operational flexibility deteriorate
Solution Approach 1:
The patent pre-loads comprehensive reference data libraries onto portable storage devices before field deployment. This preliminary action ensures that all necessary reference data is available locally without requiring internet connectivity during field operations, enabling complete operational independence.
4Ease of operation
If portable field-deployable sequencing components are used, then equipment portability is improved, but reference data access capability deteriorates
Solution Approach 1:
The patent employs advanced data compression techniques and optimized data structures to maximize the amount of reference data that can be stored on portable devices. By changing the parameters of data storage (compression ratios, data organization), the system accommodates large reference libraries on limited portable storage capacity.
Data Source
AI summary
Portable biosurveillance kits for sequencing and sample identification are provided, and techniques for configuring said kits are provided. A system for configuring a kit may receive data representing a first and second set of nucleic acid sequences, and may generate and store first and second indexes representing the respective sets. The system may then use the indexes to identify conserved-signature sequences that satisfy abundance criteria with respect to the first set and sparsity criteria with respect to the second set. The identified conserved-signature sequences may be stored on (or represented in storage on) a portable sequencing and sample-identification kit, which may compare the conserved-signature sequence to a sample sequence in order to identify the sample sequence.