MSI Detection via Capillary Electrophoresis Migration Profiles
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Solution Overview
Problem
Current methods for identifying microsatellite instability (MSI) in tumors are hindered by the need for sequencing and are prone to stutter artefacts, making diagnosis difficult and time-consuming, and often require external equipment and sequencing devices, increasing costs and contamination risks.
Innovation Solution
A method using real-time PCR combined with capillary electrophoresis that determines MSI based on the migration profile of amplicons without resolving them to single molecule peaks, eliminating stutter artefacts and providing a closed system for analysis, thereby simplifying the diagnosis and reducing the need for external sequencing devices.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequencing methods are used to determine MSI, then measurement precision is improved, but device complexity and cost increase
Solution Approach 1:
The invention extracts only the essential information needed for MSI determination (migration profile patterns) from the complex sequencing process. By focusing on the migration behavior of amplicons rather than full sequence resolution, the method eliminates the need for sequencing devices while maintaining diagnostic accuracy.
Solution Approach 2:
The invention replaces expensive, complex sequencing equipment with simpler, more affordable capillary electrophoresis technology. The migration profile analysis provides sufficient information for MSI determination without requiring the high precision and cost of sequencing instruments.
2Measurement precision
If traditional CE methods with resolution to single molecule peaks are used, then measurement precision is improved, but stutter artefacts increase making diagnosis difficult
Solution Approach 1:
The invention extracts only the relevant migration profile characteristics needed for MSI determination while discarding the problematic detailed peak resolution that generates stutter artefacts. By analyzing overall migration patterns rather than individual peak positions, the method eliminates stutter interference.
Solution Approach 2:
Instead of resolving amplicons to single molecule peaks and then trying to distinguish true signals from stutter artefacts, the invention inverts the approach by analyzing the collective migration behavior of all amplicons. This reverses the problem-solving sequence and naturally eliminates stutter artefact interference.
3Measurement precision
If external sequencing devices and equipment are used, then measurement precision is improved, but contamination risk increases
Solution Approach 1:
The invention merges the PCR amplification and capillary electrophoresis analysis into an integrated closed system. By combining these steps in a single automated platform, the method eliminates intermediate sample handling steps that would expose samples to contamination risks while maintaining diagnostic precision.
Solution Approach 2:
The invention introduces an automated closed system as an intermediary between sample preparation and analysis. This intermediary platform performs all operations without manual intervention, preventing external contamination while preserving measurement accuracy.
4Measurement precision
If sequencing and detailed amplicon resolution are performed, then measurement precision is improved, but analysis time increases
Solution Approach 1:
The invention performs partial analysis by focusing only on the migration profile patterns essential for MSI determination, rather than complete amplicon sequencing. This partial approach provides sufficient diagnostic information much faster than full sequencing would require.
Solution Approach 2:
The invention skips the time-consuming steps of complete amplicon sequencing and detailed peak resolution. By rushing through to the essential migration pattern analysis, the method achieves rapid MSI determination without sacrificing diagnostic accuracy.
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 allows for faster, more accurate, and cost-effective determination of MSI without sequencing, reducing contamination risks and enabling easier handling and analysis of MSI profiles, facilitating earlier results and improved diagnostic capabilities.
Implementation Method 1
separating the labeled nucleic acids, in particular of the obtained amplicons, by capillary electrophoresis (CE)
Implementation Method 2
separating the labeled nucleic acids, in particular of the obtained amplicons, by capillary electrophoresis (CE)
Data Source
AI summary
The present invention is directed to a method for determining of at least one microsatellite instability (MSI) based on a shift in a capillary electrophoresis (CE) profile (CE profile shift), the CE profile shift being determined by a comparison between the capillary electrophoresis (CE) profile of a target sequence of at least one microsatellite (MSI target profile) and the capillary electrophoresis (CE) profile of its specific wild type sequence (MS wild type profile). Further, the invention encompass suitable primer for use in said method, a kit comprising all essential components for performing said method successfully, a complete closed device as a system, namely “MSI Modaplex Analysis System” and a method for diagnosis of MSI phenotypes associated with an inflammation, cancer, inflammation associated cancer and/or auto immune disease, wherein the diagnosis comprises the method for determining of at least one CE profile shift as mentioned above. Finally, the present invention is directed to the use of an improved MSI panel for the determination and preferably diagnosis of MSI tumors, said panel consist of the STR biomarker NR-21, NR-24, Mono27, D2S123, D5S346, D17S250, Bat-25 and Bat-26.