Genomic DNA Analysis via Global Pattern Recognition
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Solution Overview
Problem
Existing DNA-based profiling methods are time-consuming, require large amounts of DNA material, and are not scalable for clinical use, limiting their adoption in diagnostics and analysis, particularly for identifying relevant target DNA sequences in various applications.
Innovation Solution
The development of systems and methods for rapid genomic DNA analysis using Global Pattern Recognition (GPR) techniques, which analyze genomic DNA input to identify statistically significant copy number variations and fold changes in DNA sequences, enabling efficient and accurate diagnosis and evaluation of pathological conditions, such as cancer, using micro-titer plates and PCR-based methods.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional DNA profiling methods such as karyotyping and FISH are used, then DNA analysis can be performed, but the process is time consuming and technically demanding
Solution Approach 1:
The patent replaces traditional mechanical and manual DNA profiling methods (karyotyping, FISH) with automated real-time quantitative PCR systems. The QPCR instrumentation and automated data analysis algorithms eliminate manual chromosome spreading, staining, and visual inspection, thereby reducing analysis time while maintaining or improving measurement precision through standardized automated protocols and computational analysis.
2Measurement precision
If DNA microarray hybridization technologies such as CGH and ROMA are used, then genomic analysis can be performed, but large amounts of input DNA material and specialized equipment are required
Solution Approach 1:
The patent changes the fundamental parameters of DNA analysis by using real-time quantitative PCR instead of hybridization-based microarray methods. QPCR requires significantly less input DNA (can work with nanogram quantities) because it amplifies specific targets exponentially during the reaction, whereas microarray hybridization requires microgram quantities of DNA for sufficient signal detection. This parameter change in detection methodology directly reduces the quantity of substance needed.
3Quantity of substance
If conventional computational methods are used for QPCR analysis, then DNA quantification can be performed, but analytical limitations prevent reliable data for robust sets of target DNA sequences
Solution Approach 1:
The patent implements iterative feedback algorithms that continuously refine the analysis of multiple target DNA sequences. The computational method uses statistical models that incorporate feedback from control samples and replicate measurements to adjust normalization factors and significance thresholds. This feedback mechanism enables reliable detection of copy number variations across robust sets of target sequences by dynamically adapting the analysis parameters based on the observed data distribution and quality metrics.
4Measurement precision
If traditional DNA profiling methods are used, then analysis can be performed, but the methods are not scalable for clinical use
Solution Approach 1:
The patent segments the DNA analysis process into discrete, automated modules: sample preparation, real-time QPCR amplification of multiple targets, automated data collection, and computational analysis. This segmentation allows each step to be optimized and performed in parallel for multiple samples, enabling clinical-scale throughput while maintaining measurement precision through standardized protocols and automated quality control at each stage.
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
These methods provide rapid, accurate, and scalable DNA analysis, reducing the need for large DNA samples and enabling the identification of relevant DNA sequences for specific applications, enhancing diagnostic capabilities and clinical usability.
Implementation Method 1
DNA amplification and/or detection is performed on the samples. The DNA amplification/detection methods used in various embodiments may include PCR-based methods (i.e. QPCR)
Data Source
AI summary
Systems and methods for performing rapid genomic DNA analysis of samples, such as control samples and experimental samples. In one aspect, the system makes use of genomic DNA input, rather than gene expression input such as mRNA and/or cDNA associated with mRNA. The systems and methods perform statistical analyses on data generated from the samples to determine which DNA sequences in an identified set of DNA sequences have a basis of variation in an experimental sample when compared to a control sample, and additionally provide a quantitative measure of this variation. The quantitative measure may be based on metrics such as copy number and/or fold-change. The systems and methods employ this statistical framework in DNA-based evaluation settings, including the evaluation/diagnosis of a pathological condition such as cancer or transgenic analysis of transgenic plants and animals. The systems and methods also provide means to select and refine the selection of DNA sequences, such as genes, known to undergo copy change for a particular pathological condition. This leads to the creation of stock gene sets catered to individual application areas and/or clinical uses, which may be used with the systems and methods described in this application for the purpose of, for example, a clinical kit for rapid DNA-based evaluation.