Microsatellite Marker Panel for Low-Cost CMMRD MSI Detection
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Solution Overview
Problem
Current methods for detecting microsatellite instability (MSI) in samples, particularly in non-neoplastic tissues of Constitutional Mismatch Repair Deficiency (CMMRD) patients, are limited by low sensitivity and specificity, and require high-cost, high-capacity sequencing platforms, making them inefficient for timely diagnosis and genetic counseling.
Innovation Solution
Development of a novel panel of MSI markers, optimized for single-round multiplex PCR, which can differentiate between CMMRD and control samples with 100% sensitivity and specificity, and can be used in low-cost, scalable assays, including analysis in blood samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If high-capacity sequencing platforms are used for MSI detection, then measurement precision is improved, but device complexity and cost increase
Solution Approach 1:
The invention segments the complex sequencing task into a focused PCR-based assay targeting only 5 specific mononucleotide repeat markers. This segmentation allows MSI detection to be performed on standard PCR machines rather than requiring complex high-capacity sequencing platforms, thereby reducing device complexity while maintaining diagnostic precision through targeted analysis of the most informative markers
Solution Approach 2:
The invention extracts the essential diagnostic information by selecting and analyzing only 5 specific mononucleotide repeat markers that provide the highest discriminatory power for CMMRD detection. This extraction approach eliminates the need for comprehensive sequencing of the entire genome or even all microsatellite regions, enabling accurate MSI detection using simpler, lower-cost PCR-based methods rather than complex sequencing platforms
2Measurement precision
If comprehensive sequencing is performed to ensure diagnostic accuracy, then measurement precision is improved, but loss of time increases
Solution Approach 1:
The invention performs preliminary action by pre-selecting and optimizing a panel of 5 mononucleotide repeat markers that have been validated to provide maximum discriminatory power for CMMRD detection. This preliminary selection of the most informative markers allows the diagnostic assay to achieve high accuracy without requiring time-consuming comprehensive sequencing, as the pre-validated marker panel captures the essential diagnostic information in a rapid PCR-based format
Solution Approach 2:
The invention skips the time-consuming steps of library preparation, sequencing, and complex bioinformatics analysis by rushing directly to the core diagnostic need through a streamlined PCR amplification and fragment analysis workflow. This approach achieves comparable or superior diagnostic accuracy by focusing resources on the most critical measurement (marker length variation) rather than performing exhaustive sequencing
3Measurement precision
If multiple microsatellite markers are analyzed to improve detection accuracy, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The invention applies local quality by assigning different functional roles to different marker types within the assay panel. Specifically, it uses 5 mononucleotide repeat markers that are particularly sensitive to MMR deficiency, rather than uniformly analyzing all types of microsatellite markers. This localized optimization of marker selection enhances detection accuracy for CMMRD while keeping the panel size manageable and the assay complexity low
Solution Approach 2:
The invention achieves universality by designing a PCR-based assay that can detect MSI across all types of MMR deficiency (MLH1, MSH2, MSH6, PMS2) using a single standardized panel of 5 mononucleotide markers. This multi-functional marker panel universally detects the microsatellite instability phenotype regardless of which specific MMR gene is defective, eliminating the need for separate assays for different MMR genes and thereby reducing overall assay complexity
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
The novel markers achieve 100% sensitivity and specificity in differentiating CMMRD from control samples, enabling accurate MSI detection in both solid and fluid samples, such as blood, and can distinguish between microsatellite stable and unstable cancers, reducing the need for expensive sequencing platforms.
Implementation Method 1
uses PCR to amplify 5 mononucleotide repeat microsatellite markers
Implementation Method 2
analysis of fluorescently tagged amplicons using capillary electrophoresis to identify microsatellite indels
Data Source
AI summary
The invention provides novel methods for evaluating levels of microsatellite instability in a sample and evaluating the biological significance of sequence variations identified in a sample during sequencing. The invention further relates to the use of novel microsatellite instability markers for evaluating levels of microsatellite instability in a sample and evaluating the biological significance of sequence variations identified in a sample during sequencing. Corresponding kits are also provided.