Encoded Particle Mixture for Multiplex Genomic Hybridization
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Solution Overview
Problem
Current methods for evaluating genomic content, such as Comparative Genomic Hybridization (CGH), face challenges in efficiently detecting differences in genomic copy numbers and gene expression profiles across multiple samples, often requiring complex labeling and hybridization processes that can be cumbersome and prone to errors.
Innovation Solution
The method employs a mixture of encoded particles with nucleic acid hybridization probes for multiple genomic loci, allowing for the simultaneous evaluation of multiple samples using a single detectable label, either by keeping samples separate or combining them, and utilizing indirect labels to correct for variations through ratiometric assays.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If multiple samples are evaluated using traditional CGH methods with separate labeling and hybridization processes, then detection accuracy can be maintained, but the process becomes cumbersome and error-prone
Solution Approach 1:
The patent combines multiple samples and reference DNA into a single hybridization mixture, eliminating the need for separate labeling and hybridization processes for each sample. This merging approach simplifies the workflow while maintaining detection accuracy through ratiometric analysis of fluorescence signals from differentially labeled samples.
Solution Approach 2:
The patent employs a universal detection system using a single fluorescent label that can detect multiple differentially labeled samples simultaneously. The ratiometric assay framework allows the same detection mechanism to evaluate multiple samples with different genomic content, making the system multi-functional and broadly applicable.
2Productivity
If multiple samples are analyzed in parallel using traditional methods, then throughput increases, but labeling complexity and potential for errors increase
Solution Approach 1:
The patent merges multiple samples into a single hybridization reaction mixture, allowing parallel analysis of multiple genomic loci simultaneously. This approach increases throughput by evaluating multiple samples and reference DNA together rather than separately, while the ratiometric detection simplifies the overall process complexity.
Solution Approach 2:
The patent uses ratiometric detection that measures the ratio of fluorescence signals from differentially labeled samples. This parameter transformation converts absolute signal intensities into relative copy number ratios, simplifying the detection process and reducing sensitivity to labeling variations while maintaining high throughput capability.
3Manufacturing precision
If a single detectable label is used for multiple samples, then the assay simplifies and uniformity improves, but detection precision must be maintained across different samples
Solution Approach 1:
The patent incorporates reference DNA with known copy numbers as an internal control in each hybridization mixture. The ratiometric detection compares the fluorescence signal from the reference DNA to the test samples, providing feedback that corrects for variations in labeling efficiency and hybridization conditions. This feedback mechanism maintains measurement precision while using a single detectable label for all samples.
Solution Approach 2:
The patent transforms detection from absolute fluorescence intensity to relative copy number ratios through ratiometric analysis. By dividing the signal from test samples by the signal from reference DNA with known copy numbers, the system converts raw detection data into normalized copy number ratios, maintaining measurement precision across different samples while using a single label.
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 enables robust, efficient, and accurate evaluation of genomic content by facilitating parallel analysis of multiple samples with enhanced uniformity and error correction, improving the detection of copy number variations and gene expression profiles.
Implementation Method 1
contacting the sample to a portion of the particle mixture under hybridization conditions; and evaluating hybridization of the sample to particles in the respective portion of the mixture
Data Source
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AI summary
Disclosed herein pertains to a method of evaluating genomic DNA comprising the steps of: a) providing a genomic DNA sample; b) providing a particle mixture, the mixture comprises particles from different particle sets, wherein each particle set contains numerous encoded particles and a nucleic acid hybridisation probe for particular genomic locus, such that the mixture collectively includes probes for a plurality of different genomic loci; c) contacting the sample to a portion of the particle mixture under hybridisation conditions; and d) evaluating hybridisation of the sample to particles in respective portion of the mixture by monitoring a detectable label, wherein signals from the monitoring are indicative of the number of copies of each interrogated genomic locus. The invention further pertains to a particle mixture comprising particles from different particles sets thereof.