Nucleic Acid Microarray Verification Signal Normalization
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Solution Overview
Problem
Current nucleic acid microarray methods face challenges in accurately detecting genomic DNA aberrancies due to differences in labeling efficiency and hybridization between arrays, leading to data fluctuations and the need for complex correction methods.
Innovation Solution
Incorporating a verification nucleic acid with a sequence capable of hybridizing across all spots on the array, allowing it to coexist with the sample and standard, and using its binding amount to correct differences between spots, thereby stabilizing data by calculating fluorescence ratios.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If different labeling compounds are used for sample and standard, then hybridization can be carried out simultaneously, but difference in labeling efficiency and detection system exerts influence on data
Solution Approach 1:
A verification nucleic acid is introduced as an intermediary element that hybridizes to all spots on the array. This verification nucleic acid serves as a mediator to detect and correct spot-to-spot variations, allowing the system to maintain the benefits of simultaneous hybridization while compensating for its drawbacks through normalization using the verification signal.
2Measurement precision
If same labeling compound is used for sample and standard, then difference in labeling is eliminated, but difference in spot exerts influence on data when carrying out separate hybridization
Solution Approach 1:
The verification nucleic acid acts as a mediator that is present in both separate hybridization experiments. By comparing the verification nucleic acid signals between the two arrays, the system can normalize for spot-to-spot variations and enable accurate comparison between sample and standard even when hybridized separately.
3Measurement precision
If correction spot is mounted on microarray, then difference between arrays can be corrected, but difference between separate spots cannot be corrected
Solution Approach 1:
The verification nucleic acid sequence is designed to be universal, hybridizing to all spots on the array rather than being restricted to a single correction spot. This multi-functional verification approach enables simultaneous correction of both array-to-array and spot-to-spot variations, making the normalization process more comprehensive and reliable.
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 effectively reduces data fluctuations and simplifies the correction process by using a verification nucleic acid to normalize fluorescence values across the array, enhancing the accuracy of nucleic acid microarray measurements.
Implementation Method 1
allowing a labeled sample nucleic acid (A1) of a sample to be tested to hybridize with at least a first probe nucleic acid immobilized onto a spot (X1); providing the spot (X1) with a labeled verification nucleic acid (B)... and allowing the labeled verification nucleic acid (B) to hybridize with at least the first probe nucleic acid at all spots
Data Source
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AI summary
An analytical method aided with a nucleic acid microarray, the nucleic acid microarray having a spot (X 1) onto which a first probe nucleic acid is immobilized, the method includes: allowing a labeled sample nucleic acid (A 1) of a sample to be tested to hybridize with the first probe nucleic acid; providing the spot (X 1) with a labeled verification nucleic acid (B) that has a sequence capable of hybridizing with at least a part of the first probe nucleic acid and is labeled with a label different from the labeled sample nucleic acid (A 1), and allowing the labeled verification nucleic acid (B) to hybridize with at least the first probe nucleic acid at all spots; measuring a labeled quantity value (F 1) of the labeled sample nucleic acid (A 1); and measuring a labeled quantity value (Fc 1) of the labeled verification nucleic acid (B).