Methylation Analysis Sample Identification via Bisulfite-Stable Nucleic Acid
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Solution Overview
Problem
Current methods for methylation analysis lack effective solutions for detecting sample interchange and cross-contamination, particularly during bisulfite treatment, which is crucial for accurate DNA methylation analysis in biological samples.
Innovation Solution
The use of identifiers, such as nucleic acids with specific sequences or lengths, that are applied to biological samples and can be detected or quantified even after bisulfite treatment, allowing for simultaneous detection of sample identity and methylation analysis, thereby addressing sample interchange, cross-contamination, and other errors in high-throughput methods.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If bisulfite treatment is performed for methylation analysis, then DNA methylation can be detected, but sample interchange and cross-contamination cannot be detected
Solution Approach 1:
An identifier nucleic acid is added to the biological sample before bisulfite treatment. This identifier serves as a tracking marker that remains intact through the bisulfite conversion process, enabling subsequent detection of sample identity and prevention of sample interchange or cross-contamination while maintaining methylation analysis capability
Solution Approach 2:
The identifier nucleic acid acts as an intermediary element between the biological sample and the detection system. It provides a detectable signal that confirms sample integrity without interfering with the methylation analysis, effectively mediating the conflict between accurate methylation detection and reliable sample identification
2Reliability
If identifiers are added to biological samples, then sample identity can be tracked, but the complexity of the analysis increases
Solution Approach 1:
The identifier nucleic acid serves multiple functions simultaneously: it tracks sample identity, detects sample interchange, prevents cross-contamination, and does not interfere with methylation analysis. This multi-functionality reduces the need for separate identification procedures, thereby minimizing added complexity
Solution Approach 2:
The identifier nucleic acid is designed with specific parameters (sequence composition, length) that allow it to remain stable during bisulfite treatment and subsequent analysis. By optimizing these parameters, the identifier provides reliable detection without requiring complex additional reagents or procedures
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
Enables accurate detection of sample interchange and cross-contamination, facilitates normalization and calibration, and ensures the correctness of methylation analysis by generating a unique identification pattern across samples, improving the reliability of high-throughput processes.
Implementation Method 1
wherein the applied at least one identifier is detected or quantified by hybridization with a detection nucleic acid
Implementation Method 2
contacting the DNA of each sample with bisulfite; subjecting each sample to a detection or quantification reaction specific for the binding site(s) of the one or more applied identifiers
Data Source
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AI summary
Aspects of the present invention relate to compositions and methods of identifying at least one biological sample in the field of methylation analysis. In particular aspects at least one biological sample is provided, at least one identifier is applied for each sample, the applied identifier(s) are detected or quantified, and the methylation analysis is performed. Additional aspects provide a methods for testing an experimental procedure. Additional aspects provide kits suitable for realizing the aspects of the invention.