Differential Filtering of Genetic Data for Copy Number Aberration Identification
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Solution Overview
Problem
Current methods for analyzing and displaying genetic data from nucleic acid probe arrays are inadequate in simplifying and visualizing large quantities of genetic information in a user-friendly manner, particularly in identifying biologically relevant genetic events and distinguishing between disease-related copy number aberrations and normal variations.
Innovation Solution
The development of software systems and methods that allow users to define specific genetic regions of interest, apply differential filtering, and visualize genetic data in an interactive and color-coded format, enabling the identification of genetic events and distinguishing between disease-related copy number aberrations and normal variations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If comprehensive genetic data from probe arrays is analyzed, then the quantity of genetic information increases, but the ease of operation and visualization deteriorates
Solution Approach 1:
The patent segments the genome into chromosomal regions and divides the analysis into manageable components such as copy number aberrations, single nucleotide polymorphisms, and indels. The software interface presents this segmented information through organized displays with filters and search functions, making the overwhelming quantity of genetic data accessible and navigable for users.
Solution Approach 2:
The patent introduces computational algorithms and software tools as intermediaries between the raw genetic data and the user. These intermediaries process, filter, and interpret the complex genetic information, transforming it into meaningful results that can be easily visualized and interpreted without requiring users to manually process the raw data.
2Measurement precision
If differential filtering is applied to genetic data, then the identification precision of biologically relevant events improves, but the device complexity increases
Solution Approach 1:
The patent implements dynamic filtering capabilities where the software can adaptively adjust analysis parameters based on user-defined criteria and biological context. The system dynamically selects and applies appropriate algorithms for copy number aberration detection, SNP analysis, and indel identification, optimizing precision for each specific analytical task while managing complexity through automated decision-making.
Solution Approach 2:
The patent utilizes parameter changes in filtering thresholds and analysis criteria to optimize the identification of biologically relevant genetic events. The system allows users to adjust parameters such as copy number thresholds, significance levels, and region-specific filters to precisely control the analysis sensitivity and specificity for different biological questions.
3Measurement precision
If copy number aberration analysis is performed, then the measurement precision of genetic variations improves, but the loss of time for data processing increases
Solution Approach 1:
The patent performs preliminary computational tasks during the data processing pipeline, including pre-alignment of genetic markers, pre-calculation of copy number ratios, and pre-identification of potential aberrations. These preliminary actions prepare the data in advance for more complex analysis, reducing the time required for final interpretation while maintaining high measurement precision through systematic processing steps.
Solution Approach 2:
The patent implements efficient algorithms that can rapidly process large datasets by skipping unnecessary computational steps for regions or data types that do not require detailed analysis. The system prioritizes processing based on user-defined regions of interest and can rapidly identify and report copy number aberrations without exhaustively analyzing every genetic marker, thus reducing processing time while maintaining precision for relevant findings.
Data Source
AI summary
Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.