Nanopore Selective Sequencing for Pathogen Detection
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Solution Overview
Problem
Current sequencing technologies, such as Next-Generation Sequencing (NGS), face challenges in efficiently and cost-effectively identifying pathogens, detecting copy number variations, and analyzing DNA methylation due to their limitations in read length, complexity of protocols, and high costs, which hinder rapid diagnosis and increase sequencing costs.
Innovation Solution
The implementation of nanopore selective sequencing using Oxford Nanopore Technology (ONT) sequencers, which enables targeted sequencing through the Read-Until (RU) interface, allowing for the ejection of unwanted DNA/RNA reads during sequencing, reducing the need for complex library preparation and enabling longer read lengths, thereby improving diagnostic efficiency and reducing costs.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Length of moving object
If Next-Generation Sequencing (NGS) is used for pathogen identification and genetic analysis, then sequencing can be performed with established protocols, but the read length is limited (150 bp) and the protocol complexity is high
Solution Approach 1:
The patent extracts and removes the unwanted host DNA sequences from the sequencing workflow by implementing selective sequencing that ejects host reads during the sequencing process, allowing pathogen identification without complex library preparation steps for enrichment
Solution Approach 2:
The nanopore sequencing platform provides multi-functionality by enabling simultaneous detection of pathogen DNA, RNA modifications, and genetic variations using a single sequencing run, eliminating the need for separate protocols for different analyses
2Productivity
If selective sequencing is implemented to eject unwanted reads, then sequencing costs and time are reduced, but the system requires real-time computational analysis capability
Solution Approach 1:
The system performs preliminary computational analysis during the sequencing process itself, using real-time signal processing to identify and eject unwanted host reads before the sequencing run completes, thereby increasing productivity without requiring post-sequencing computational resources
Solution Approach 2:
The patent implements feedback control by continuously monitoring sequencing signals in real-time and dynamically adjusting the sequencing process through read ejection decisions, allowing the system to adapt to the specific composition of each sample and optimize productivity
3Measurement precision
If multiple separate libraries are prepared for different analyses (pathogen detection, CNV, methylation), then each analysis can be optimized, but the cost and time requirements increase significantly
Solution Approach 1:
The patent merges multiple sequencing applications into a single unified nanopore sequencing run, simultaneously detecting pathogen DNA, copy number variations, and DNA methylation patterns without requiring separate library preparations, thereby reducing turnaround time while maintaining analysis accuracy
Solution Approach 2:
The nanopore sequencing platform provides multi-functionality by enabling simultaneous detection of pathogen DNA, RNA modifications, and genetic variations using a single sequencing run, eliminating the need for separate protocols for different analyses
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach significantly reduces sequencing costs and time by allowing for longer read lengths, enabling simultaneous analysis of copy number variations and DNA methylation without the need for separate libraries, and improving pathogen detection efficiency, making it more economical and efficient than traditional methods.
Implementation Method 1
Nanopore sequencers measure the electrical signal fluctuations caused by a single DNA molecule moving across the pore
Implementation Method 2
the sequencer can invert the electrical field polarity applied across the designated pore for a period of time to eject the current read
Data Source
AI summary
The subject invention pertains to DNA/RNA sequencing by measuring the characteristic electrical signal when DNA/RNA moves across a pore that is only nanometers in diameter. The sequencer allows reads to be rejected during sequencing in real time through selective sequencing by computational methods, reducing human labor and cost requirements. Electrical signals are used directly to decide if the sequenced reads are from selected genomic regions or from different sources. Provided Artificial Intelligence (AI) models are established by training deep learning neural networks using collected nanopore sequencing signals. The method can be easily integrated into existing nanopore sequencing infrastructure, offering real-time parallel molecule classification with the flexibility to meet the requirements of a variety of selective sequencing applications such as detecting pathogens in clinical samples, targeted gene panel for cancer diagnosis, as well as drug resistant bacterial screening, and numerous other applications.