Polymorphism Detection via Consensus Flanking Regions
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Solution Overview
Problem
Existing methods for identifying polymorphisms in nucleic acid sequences are hindered by secondary polymorphisms near primary polymorphisms, which can inhibit probe binding and result in false negatives.
Innovation Solution
Introducing known 5' and 3' flanking regions into amplicons based on consensus sequences to create a known probe binding site, ensuring the probe is an exact match and enhancing binding efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If probe binding is used to identify polymorphisms, then polymorphism detection is achieved, but secondary polymorphisms inhibit probe binding causing false negatives
Solution Approach 1:
The method segments the target nucleic acid sequence into a known flanking region and a variable region containing the polymorphism. By designing probes to bind only to the known flanking region (which is identical across all variants), the method isolates the polymorphism detection from the interfering secondary polymorphisms in the variable region, thereby eliminating false negatives while maintaining detection accuracy
Solution Approach 2:
The method extracts and removes the known flanking region from the target nucleic acid sequence to create a separate probe binding site. This extracted flanking region is used to design probes that are complementary only to this conserved sequence, effectively taking out the polymorphism-containing regions that cause inhibition and using only the clean, known sequence for probe binding, thus resolving the contradiction between detection accuracy and false negative rate
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 reduces false negatives and improves the detection of primary polymorphisms by eliminating the inhibitory effect of secondary polymorphisms, allowing for more accurate identification of target nucleic acids.
Implementation Method 1
A probe may be designed having a probe sequence which is complementary to the exact sequence of a known probe binding site
Data Source
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AI summary
Methods and compositions for determining the presence of a polymorphism at a target nucleotide position in a plurality of target nucleic acid sequences is provided.