Iterative Real-Time Sequencing for Species Detection in Complex Samples
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Solution Overview
Problem
Existing real-time sequencing technologies struggle to accurately detect and quantify biological species of interest in complex samples due to interference from matrix species and the need for efficient quality control during nucleic acid extraction and sequencing processes.
Innovation Solution
A method involving the addition of a control species with a known genome to the sample, followed by real-time sequencing, iterative sequence assignment, and threshold comparisons to detect and quantify the species of interest, using a real-time sequencer like nanopore sequencers to generate sequences in real-time for rapid analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If real-time sequencing is used to rapidly detect biological species, then detection speed is improved, but measurement precision deteriorates due to interference from matrix species
Solution Approach 1:
A control species is introduced as an intermediary element into the sample. This control species serves as a reference marker that allows differentiation between matrix species and the species of interest. By comparing sequence reads against the known control species genome, the system can accurately identify and quantify the species of interest even in complex mixtures, thereby maintaining measurement precision while enabling rapid real-time detection.
2Measurement precision
If the quantity of control species is increased to improve quantification accuracy, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The method utilizes changes in sequence read quantities as a parameter to monitor and quantify the species of interest. By tracking the cumulative number of sequence reads assigned to the species of interest against a threshold value, the system can determine presence/absence and estimate concentration without requiring complex additional instrumentation. The control species concentration serves as a reference parameter that simplifies the quantification calculation.
3Reliability
If iterative sequencing is performed to improve detection reliability, then measurement precision is improved, but loss of time increases
Solution Approach 1:
The sequencing process is made dynamic and adaptive rather than static. The system continuously monitors the cumulative sequence reads during real-time sequencing and dynamically adjusts the sequencing duration based on whether the threshold is reached. This allows the process to terminate early when sufficient evidence is obtained, maintaining high detection reliability while minimizing unnecessary sequencing time for clear positive or negative cases.
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
Enables rapid and accurate detection and quantification of biological species of interest by minimizing interference from matrix species, ensuring the quality of extraction and sequencing processes, and providing flexible sequencing control.
Implementation Method 1
Nanopore sequencing of DNA is based on the passage of a molecule comprising an oligonucleotide strand through a nanopore, which forms a channel. When the molecule passes through the channel, a potential difference can be measured on either side of the channel that is dependent on the nature of each base forming the strand.
Data Source
AI summary
A metagenomic analysis of a sample for the purpose of detecting the presence of a species of interest in the sample is carried out iteratively. During each iteration, sequences corresponding to each species of interest are identified and counted. The iterations stop when the presence of a species of interest is confirmed or when a maximum number of iterations have been carried out. The detection of a species of interest can be followed by a more precise characterization of the genome of said species of interest. The characterization implements supplementary iterations.