DNA Methylation Analysis in Heterogeneous Tissue Samples
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for determining DNA methylation levels in biological samples are inaccurate, leading to difficulties in diagnosing and grading diseases, particularly in heterogeneous tissue samples where only a subpopulation of cells contributes to the disease state.
Innovation Solution
A method that quantifies the DNA methylation level of specific CpG positions within a subpopulation of cells within a tissue sample by determining the cell content and measuring the total DNA methylation level, allowing for precise analysis of disease-specific methylation patterns.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current methods are used to determine DNA methylation levels in heterogeneous tissue samples, then the analysis covers all cells in the sample, but the measurement precision deteriorates because only a subpopulation of cells contributes to the disease state
Solution Approach 1:
The method segments the heterogeneous cell population by identifying and isolating a specific subpopulation of cells that contribute to the disease state, using cell-type-specific markers to distinguish these cells from other cell types in the tissue sample. This segmentation allows for precise methylation analysis of only the relevant disease-contributing cells.
Solution Approach 2:
The method applies local quality by determining DNA methylation levels specifically within the identified subpopulation of disease-contributing cells, rather than averaging across all cell types. This localized measurement approach ensures that the methylation data reflects only the relevant pathological cells, improving diagnostic precision.
2Reliability
If total DNA methylation level is measured without cell content determination, then the analysis is simpler, but the reliability deteriorates due to inability to differentiate disease-specific methylation patterns
Solution Approach 1:
The method performs preliminary action by first determining the cell content and identifying the specific subpopulation of disease-contributing cells before measuring DNA methylation levels. This preliminary cell characterization step ensures that subsequent methylation measurements are performed on the correct cell population, thereby improving diagnostic reliability.
Solution Approach 2:
The method uses cell-type-specific markers as intermediaries to connect the heterogeneous cell population to the disease state. These markers serve as mediators that enable the identification and isolation of the relevant subpopulation, allowing for reliable differentiation of disease-specific methylation patterns from those of other cell types.
3Measurement precision
If DNA methylation analysis is performed on heterogeneous samples without cell content determination, then the processing time is shorter, but the differentiation capability deteriorates for samples with small number of altered cells
Solution Approach 1:
The method changes the parameter of cell population selection by using cell-type-specific markers to identify and focus analysis on the specific subpopulation of disease-contributing cells. This parameter change enables precise differentiation of disease-specific methylation patterns even when the altered cells represent a small fraction of the total sample.
Data Source
AI summary
Aspects of the present invention relate to the determination of the DNA methylation level at one or more CpG position within cells of a defined type in a tissue sample. This methylation level is deduced from the total DNA methylation level of all cells of the sample and from the content of said cells of interest. In aspects of the invention, the cell content is determined by means of histopatholoy, staining methods, antibodies, expression analysis or DNA methylation analysis.