Repeated Cell Extraction for Genetic Characterization
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Solution Overview
Problem
Current methods for genetic characterization and gene expression analysis of rare cells in fluid samples, such as circulating tumor cells, are hindered by cross-contamination with other cells, leading to inaccurate results due to high background noise from contaminating leukocytes, which requires excessive overexpression of tumor-associated markers for reliable detection.
Innovation Solution
A method involving repeated selective extraction of predetermined cells using immunobeads or similar techniques, followed by subtraction of gene expression profiles and copy number counts from subsequent extractions lacking the cells of interest, to isolate the true signal of the predetermined cells by leveraging the random and excessive presence of contaminating cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If selective extraction of predetermined cells is performed using immunobeads, then the concentration of predetermined cells is improved, but cross-contamination with other cells cannot be eliminated below a certain limit
Solution Approach 1:
The invention extracts the disturbing component (contaminating cells) from the system by performing repeated selective extractions. Each extraction removes a portion of contaminating cells while retaining most predetermined cells, progressively purifying the sample without losing target cells
Solution Approach 2:
The invention applies partial action by performing multiple extractions with the same sample. Instead of one complete extraction that would remove all cells, several partial extractions are performed, each removing a fraction of contaminants while preserving most predetermined cells, achieving cumulative purification
2Reliability
If repeated washing steps are performed to reduce unspecific binding, then the purity of predetermined cells is improved, but specific binding is reduced leading to loss of sensitivity
Solution Approach 1:
The invention performs multiple partial extractions instead of one complete extraction followed by washing. Each extraction is performed partially, removing only a fraction of bound cells, which reduces unspecific binding accumulation without requiring intensive washing that would displace specifically bound cells
3Adaptability or versatility
If tumor-associated markers are used for detection, then the specificity of predetermined cell identification is improved, but the signal-to-noise ratio deteriorates due to high background expression
Solution Approach 1:
The invention extracts the background noise (contaminating cells with high marker expression) from the system through repeated selective extractions. By removing contaminating cells progressively, the background signal is reduced, improving the signal-to-noise ratio while maintaining marker specificity
Solution Approach 2:
The invention converts the harmful effect of high background expression into a benefit. The high expression of tumor-associated markers in contaminating cells, which originally caused high background noise, now serves as a marker for selectively identifying and removing contaminating cells through repeated extractions, ultimately improving detection 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 significantly reduces variations and improves accuracy by generating a pure signal for predetermined cells, allowing for precise gene expression analysis and quantification, even in samples with high contaminating cell ratios, thereby enhancing the signal-to-noise ratio and enabling reliable detection of tumor-associated markers.
Implementation Method 1
selective extraction of said cells with immunobeads comprising antibodies against said cells
Data Source
AI summary
In the present invention, a method for the qualitative genetic characterization and/or gene expression characterization of predetermined cells in a fluid sample containing such cells is provided. The inventive method for the qualitative genetic and/or gene expression characterization of predetermined cells in a fluid sample containing such cells, comprises: a) selectively extracting at least a part of the predetermined cells from the sample forming a cell suspension cs0; and b) repeating the extraction step a) n times with the same sample of step a), with n≥1, forming at least one cell suspension csn; c) determining a gene expression profile gepn and/or a first copy number count cnc0 of at least one DNA and/or RNA with at least a part of the cell suspension cs0; d) determining at least one further gene expression profile gepn and/or a further copy number count cncn of at least one DNA and/or RNA with at least a part of at least one further cell suspension csn; e) calculating the predetermined cells' gene expression profile gep(P) of at least one predetermined DNA and/or RNA by subtracting gepn from gep, and/or the predetermined cells' copy number count cnc(P) of at least one predetermined DNA and/or RNA by subtracting cncn from cnc0; and f) evaluating the qualitative genetic and/or gene expression characteristics of the predetermined cells from gep(P) and/or cnc(P).