DNA Methylation Normalization Using Endogenous Controls
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Solution Overview
Problem
Current methods for determining DNA methylation levels in specific genomic regions rely on external standards and repetitive sequences, which are not precise and do not account for differential methylation patterns, limiting their diagnostic potential for tumor detection.
Innovation Solution
A method that quantitatively determines the presence of specific DNA segments and differentially methylated CpG dinucleotides within these segments, excluding repetitive sequences, to normalize DNA methylation levels, enabling the detection of hyper- and hypomethylation patterns in gene sections for tumor diagnosis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If external standards and repetitive sequences are used for methylation analysis, then the analysis can be performed, but the precision and accuracy of methylation level determination deteriorates
Solution Approach 1:
The patent extracts and eliminates the use of external standards and repetitive sequences from the methylation analysis process. Instead, it focuses on analyzing endogenous control regions within the target DNA itself, removing the sources of imprecision and improving both measurement precision and diagnostic reliability.
Solution Approach 2:
The method enables the DNA sample to serve itself by using endogenous control regions within the target DNA as internal references for normalization. This self-contained approach eliminates dependency on external standards and improves the reliability of methylation level determination.
2Adaptability or versatility
If transposon sequences are used for normalization, then genome-wide methylation changes can be detected, but the ability to detect hypermethylated regions deteriorates
Solution Approach 1:
Instead of using transposon sequences to normalize methylation data, the patent inverts the approach by using endogenous control regions within the target DNA itself as the normalization reference. This reversal enables accurate detection of both hypomethylated and hypermethylated regions while maintaining genome-wide applicability.
Solution Approach 2:
The patent introduces endogenous control regions as an intermediary element that mediates between the target DNA and the normalization process. These control regions serve as internal references that accurately reflect the methylation status of the target regions, enabling precise detection of differential methylation patterns.
3Quantity of substance
If repetitive DNA segments are included in analysis, then more genomic regions can be examined, but the accuracy of specific gene segment methylation determination deteriorates
Solution Approach 1:
The patent segments the DNA analysis into specific gene regions of interest with their associated endogenous control regions, rather than analyzing repetitive DNA segments. This segmentation allows examination of specific functional genes while using their internal control regions for accurate normalization, maintaining both quantity and precision.
Solution Approach 2:
The method applies local quality control by using endogenous control regions specific to each target gene segment being analyzed. Each gene region has its own internal reference that accounts for local variations in DNA extraction, amplification, and processing, thereby maintaining high precision for specific gene segment methylation determination.
Data Source
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AI summary
Method for determining the normalized degree of DNA methylation of one or more DNA segments, excluding repetitive sequences, in a sample of genomic DNA for the diagnosis of a bladder tumor.