Fixed Sequence Oligonucleotides for Copy Number Variation Detection
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Solution Overview
Problem
Current methods for detecting genetic abnormalities such as copy number variations (CNVs) are inefficient and lack reproducibility, particularly in identifying fetal aneuploidy and other genetic disorders.
Innovation Solution
The method involves interrogating loci from target genomic regions using fixed sequence oligonucleotides that hybridize and ligate, with capture regions binding to complementary probes on a solid support, allowing for the detection of copy number variations, insertions, deletions, translocations, polymorphisms, and mutations by quantifying relative frequencies of ligation products.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Difficulty of detecting and measuring
If ligation methods are used for evaluating polymorphisms and copy number variations, then detection capability is improved, but assay efficiency and reproducibility deteriorate
Solution Approach 1:
The assay is divided into distinct modular steps: hybridization of fixed sequence oligonucleotides to target loci, ligation to form concatemers, amplification, and detection. Each step can be optimized independently, improving overall efficiency while maintaining detection capability for copy number variations and polymorphisms.
Solution Approach 2:
Fixed sequence oligonucleotides are designed with predetermined sequences that hybridize to specific target loci before ligation. This preliminary hybridization step ensures specific binding and reduces non-specific ligation, improving both efficiency and reproducibility of the assay.
2Difficulty of detecting and measuring
If ligation methods are used for evaluating polymorphisms and copy number variations, then detection capability is improved, but assay reproducibility deteriorates
Solution Approach 1:
The assay separates detection into distinct steps (hybridization, ligation, amplification, detection) with defined conditions for each, reducing variability between runs and improving reproducibility while maintaining ability to detect copy number variations and polymorphisms.
Solution Approach 2:
The assay optimizes specific parameters including hybridization temperature, salt concentration, and ligation buffer conditions to ensure consistent and reproducible results across different runs while maintaining high detection capability for genetic abnormalities.
3Reliability
If fixed sequence oligonucleotides with capture regions are used, then detection reliability is improved, but assay complexity increases
Solution Approach 1:
Fixed sequence oligonucleotides are designed with multiple functional regions: a target-binding region for specific hybridization to loci and a capture region for subsequent detection. This multi-functionality improves detection reliability across different target sequences while using a standardized assay platform, reducing overall complexity.
Solution Approach 2:
The capture region on fixed sequence oligonucleotides serves as an intermediary element that bridges target binding and detection steps. This mediator improves reliability by ensuring specific target capture while allowing the use of standardized detection reagents, simplifying the overall assay design.
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 provides a reliable and efficient method for detecting genetic characteristics, including fetal aneuploidy, by quantifying relative frequencies of target genomic regions, enabling accurate diagnosis and treatment options.
Implementation Method 1
interrogating loci from target genomic regions using fixed sequence oligonucleotides that hybridize and ligate
Implementation Method 2
joining the fixed sequence oligonucleotides either directly or indirectly via ligation
Data Source
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AI summary
The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.