Microarray Alignment via Substrate Shape Autofocus
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Solution Overview
Problem
Current microarray analysis methods struggle with accurate alignment, especially when dealing with DNA chips lacking positive control or containing small amounts of DNA, leading to potential contamination and increased costs, as well as difficulties in data acquisition due to weak fluorescence from house-keeping genes.
Innovation Solution
A microarray analysis method and device that utilize an irregularly shaped substrate, where probes are irradiated with excitation light to obtain fluorescence data, and reflected or scattered light is used to acquire alignment image data, allowing for the detection of reference points and correction of shear deformation in fluorescence image data to determine probe positions accurately.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If positive control is arranged on the DNA chip to enable alignment processing, then alignment accuracy is improved, but the number of probe DNAs that can be arranged is reduced and manufacturing cost increases
Solution Approach 1:
The invention extracts the alignment function from the fluorescence signal of probe DNAs and implements it through a separate autofocus image acquisition system. This separates the alignment function from the probe arrangement, allowing all probe positions to be used for actual analysis without reserving positions for positive control
Solution Approach 2:
The invention makes the substrate surface itself serve dual purposes: it provides the irregular shape that generates detectable autofocus signals for alignment, while simultaneously serving as the base for arranging probe DNAs. The substrate's physical characteristics are utilized for both structural support and alignment reference
2Measurement precision
If fluorescent substance is used as positive control to enable alignment, then alignment can be performed with small DNA amounts, but the fluorescent substance liberates during hybridization and contaminates the periphery
Solution Approach 1:
The invention extracts the alignment function from fluorescent substances and implements it through optical detection of the substrate's physical shape. This removes the source of contamination while preserving the alignment capability through a different mechanism
Solution Approach 2:
The invention introduces an intermediary mechanism (autofocus image acquisition based on substrate shape) that mediates between the need for alignment and the prohibition against using fluorescent substances. The substrate surface acts as the intermediary carrier that provides alignment information without contamination
3Measurement precision
If DNA sample amount is increased to ensure sufficient fluorescence for alignment, then alignment accuracy is improved, but the requirement for small sample analysis is not met
Solution Approach 1:
The invention replaces the biological/chemical mechanism (fluorescence intensity from DNA samples) with an optical/physical mechanism (autofocus detection of substrate shape). This substitution allows alignment to be performed independently of the quantity or fluorescence properties of the DNA sample
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 alignment processing even on DNA chips without positive control or with small DNA samples, improving analysis precision and reducing contamination risks while maintaining cost-effectiveness.
Implementation Method 1
a microarray obtained by arranging probes on a substrate surface having an irregular shape with a height profile is irradiated with excitation light and fluorescence amounts of the probes excited by the excitation light are obtained as numerical data
Implementation Method 2
a step (b) of receiving reflected light and/or scattered light from the substrate surface to acquire alignment image data expressing the irregular shape of the substrate surface of the microarray based on light receiving intensities of the light
Implementation Method 3
a step (b) of receiving reflected light and/or scattered light from the substrate surface to acquire alignment image data expressing the irregular shape of the substrate surface of the microarray based on light receiving intensities of the light
Data Source
Figure 1~2
Figure 3~4
Figure 5~6(c)
AI summary
In order to provide a microarray analysis method that can perform alignment processing appropriately in an analysis of a DNA chip on which no positive control is arranged or an analysis of a chip on which a sample contains a small amount of DNAs, the microarray analysis method in which a microarray obtained by arranging probes on a substrate surface having an irregular shape is irradiated with excitation light and fluorescence amounts of the probes excited by the excitation light are obtained as numerical data includes a step (a) of measuring the fluorescence amounts of the probes to acquire fluorescence image data, a step (b) of receiving reflected light and/or scattered light from the substrate surface to acquire the irregular shape of the substrate surface of the microarray as alignment image data based on the light receiving intensities of the light, and a step (c) of determining positions of the probes on the fluorescence image data based on the alignment image data.