Interactive Genome Browser for Clinical Genetic Data Analysis
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Solution Overview
Problem
Current technologies for detecting chromosomal DNA copy gains and losses, such as array CGH, while effective, lack a comprehensive platform for efficiently leveraging accumulated knowledge and experience in clinical settings, hindering rapid and accurate genetic analysis.
Innovation Solution
An interactive genome browser application that allows users to view, manipulate, and analyze large genetic data sets within a web browser, enabling alignment of patient data with community and private databases, facilitating quick ordering of additional genetic tests, and generating reports while ensuring patient confidentiality through anonymous data publication.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If array CGH technology is used to detect chromosomal DNA copy gains and losses, then detection capability is improved, but the ability to leverage accumulated knowledge and experience in clinical settings deteriorates
Solution Approach 1:
The patent creates a virtual copy of the physical microarray slide through a genome browser interface. The browser displays graphical representations of chromosomal data that can be viewed, manipulated, and analyzed without requiring the physical slide to be present. This allows clinicians to access and analyze genetic data remotely, leveraging accumulated knowledge through shared access to the same data representation across multiple users and locations.
Solution Approach 2:
The genome browser acts as an intermediary between the physical array CGH technology and the clinician's analysis process. It translates complex chromosomal data into visual representations and provides tools for comparison with reference genomes and previously analyzed cases. This intermediary layer enables efficient leveraging of accumulated knowledge by facilitating easy access to and comparison with historical data without requiring direct manipulation of physical slides.
2Measurement precision
If complex technologies like array CGH are used to detect sub-microscopic imbalances, then detection accuracy is improved, but operational complexity and time requirements worsen
Solution Approach 1:
The genome browser provides self-service capabilities by automatically performing data analysis, comparison with reference genomes, and generation of visual representations. Clinicians can upload raw data and the system automatically processes it, aligns it with reference sequences, and presents it in an interpretable format. This eliminates the need for manual analysis procedures and reduces operational complexity while maintaining high detection accuracy.
Solution Approach 2:
The patent replaces manual mechanical procedures with automated computational processes. Instead of physically manipulating slides and manually analyzing patterns, the system uses software-based genome browsing, automated data processing, and computational comparison algorithms. This substitution dramatically simplifies the operational process while preserving the high detection accuracy of array CGH technology.
3Measurement precision
If comprehensive genetic data analysis is performed, then diagnostic accuracy is improved, but time consumption and processing speed worsen
Solution Approach 1:
The system performs preliminary actions by pre-aligning and storing reference genome sequences and previously analyzed case data. When new data is uploaded, the system can immediately compare it against pre-prepared reference data without requiring time-consuming manual alignment or analysis setup. This preliminary preparation of reference materials and analysis frameworks significantly reduces processing time while maintaining comprehensive diagnostic accuracy.
Solution Approach 2:
The genome browser enables continuous analysis by allowing users to work with data indefinitely without time constraints. Once data is uploaded and initial processing is complete, users can continuously explore, compare, and analyze the data at their own pace. The system maintains data availability and allows iterative analysis, eliminating the need for rushed decisions and enabling thorough diagnostic accuracy without artificial time pressure.
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 solution enhances the speed and accuracy of genetic analysis by providing a collaborative platform for researchers and clinicians to share and compare data, improving diagnosis and treatment strategies for genetic disorders.
Implementation Method 1
fragments of the patient and control DNA compete to attach (or 'hybridize') to the DNA fragments in each dot of the microarray slide
Implementation Method 2
This DNA is then tagged with a fluorescent dye. A control sample from another person, meanwhile, is also prepared and tagged with a fluorescent dye of a different color
Data Source
AI summary
Disclosed is an interactive genome browser executing within a web browser application, configured to display patient genetic data and additional genetic data tracks which are aligned by base pair. Additional tracks may include public data, community data, private data, sequence gaps, and additional genetic tests or probes which are available. Tests or probes may be ordered by selecting them from a test or probe track. Data in a genetic information database may also be searched using the interactive genome browser. Analyzed patient data may be published and made available to a community of users, which may communicate with one another.