OTU Detection System Using Probe Pairs and Signal Deconvolution
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Solution Overview
Problem
Current methods for characterizing microbiomes face challenges due to the high variability of microbial genomes and the complexity of detecting and quantifying operational taxonomic units (OTUs) in samples, particularly when dealing with highly conserved polynucleotides and multiple environmental sources, leading to difficulties in designing effective probes and analyzing hybridization data.
Innovation Solution
A system comprising probe pairs for each OTU, including perfect match and mismatch probes, along with negative and positive control probes, and computer-executable logic for deconvoluting signal intensities to calculate probability estimates, while penalizing for potential cross-hybridization, enabling the detection and quantification of OTUs with high confidence levels.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If hybridization or binding reaction is used to detect multiple targets, then detection capability is improved, but analysis complexity and difficulty increase
Solution Approach 1:
The system segments the complex detection problem into manageable components by using probe pairs (perfect match and mismatch probes) for each OTU, allowing individual analysis of each target while maintaining overall system capability to detect thousands of OTUs simultaneously
Solution Approach 2:
The patent introduces computer-executable logic and statistical algorithms as intermediaries to automatically analyze hybridization data, deconvolute signal intensities, and calculate probability estimates, thereby reducing manual analysis complexity while preserving detection capability
2Quantity of substance
If many similar targets are detected in a single assay, then detection capacity is improved, but accuracy and cross-hybridization issues worsen
Solution Approach 1:
The system applies local quality by using OTU-specific probe pairs with tailored sequences for each operational taxonomic unit, allowing each probe to be optimized for its specific target while maintaining the ability to detect many similar targets through the use of mismatch probes that account for local sequence variations
Solution Approach 2:
The patent implements feedback mechanisms through statistical algorithms that analyze hybridization signals, calculate probability estimates for each OTU presence, and penalize probabilities based on potential cross-hybridization, thereby continuously refining detection accuracy as more targets are detected
3Area of stationary object
If highly conserved polynucleotides are used for detection, then universality is improved, but specificity and discrimination between similar species worsen
Solution Approach 1:
The system employs dynamics by using probe pairs that can adapt to different conservation levels - perfect match probes target highly conserved regions for broad coverage, while mismatch probes account for variable regions, allowing the system to dynamically adjust between universality and specificity based on the target organism
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
The system allows for the accurate detection and quantification of a large number of OTUs in a single assay, even when they comprise a small fraction of the total nucleic acids, with high sensitivity and specificity, effectively addressing the challenges of microbiome characterization.
Implementation Method 1
hybridization or another binding reaction is used as part of the identification step
Data Source
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AI summary
Disclosed are methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes for detecting, identifying and quantitating a plurality of biomolecules or rnicrorganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes. The disclosure further provides methods of selecting an oligonucleotide probe specific for a node on a clustering tree, and methods of selecting organism-specific or OTU-specific oligonucleotide probes for use in accurately detecting a plurality of organisms in a sample with high confidence. Further, the disclosure provides methods and systems to detect the presence of a rare OTU in a sample.