Genomic Copy Number Detection via Target-Control Amplicon Sequencing
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Solution Overview
Problem
Current methods for detecting genomic copy number changes, such as CGH and FISH, face limitations including false positives due to GC-waves and lack of fine resolution, while next-generation sequencing offers higher multiplexing capabilities but is time-consuming and expensive.
Innovation Solution
A method involving amplification of nucleic acid regions of interest and control regions, followed by next-generation sequencing to compare target and control amplicon ratios, allowing for precise detection of chromosomal or gene expression changes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If comparative genomic hybridization (CGH) is used to detect copy number changes, then the method can identify genomic aberrations, but GC-wave artifacts cause false positives and reduce measurement precision
Solution Approach 1:
The patent extracts and removes the problematic GC-wave artifact from the analysis by using control regions that are specifically chosen to be free from such artifacts. By comparing target regions against these purified control regions, the harmful GC-wave effects are excluded from the ratio calculation, thereby improving measurement precision while maintaining detection accuracy.
Solution Approach 2:
The patent introduces control regions as intermediary elements that mediate the comparison between different target regions. These control regions serve as a reference baseline that is deliberately selected to be free from GC-wave artifacts and other variations, allowing accurate normalization and elimination of systematic errors in the copy number detection process.
2Measurement precision
If whole genome sequencing is used to detect copy number variations, then comprehensive coverage is achieved, but the process becomes time-consuming and expensive
Solution Approach 1:
The patent segments the genome into specific regions of interest and control regions, rather than sequencing the entire genome. This segmentation allows focused sequencing efforts on only the necessary portions, significantly reducing the time and computational resources required while maintaining high measurement precision for the targeted copy number variations.
Solution Approach 2:
The patent applies partial action by sequencing only the essential target and control regions rather than performing complete whole-genome sequencing. This partial approach provides sufficient data for accurate copy number detection in the regions of interest while avoiding the excessive time and cost burden of comprehensive genomic analysis.
3Productivity
If FISH is used to detect gene copy number changes, then the method is relatively quick, but it lacks fine resolution to distinguish closely residing local variations
Solution Approach 1:
The patent replaces the mechanical FISH imaging system with a sequencing-based detection system. Instead of relying on fluorescent signal visualization which has inherent resolution limits, the invention uses nucleic acid sequencing and computational analysis to achieve fine spatial resolution, thereby maintaining quick detection while dramatically improving the ability to distinguish closely residing local variations.
4Adaptability or versatility
If multiplexing is increased in FISH, real time PCR, and digital PCR, then more samples and regions can be analyzed, but the degree of multiplexing remains limited
Solution Approach 1:
The patent implements a universal sequencing-based platform that can simultaneously analyze multiple samples, regions, and variant types through a single assay design. By using universal primers and control regions that work across different genomic targets, the system achieves high multiplexing capability while maintaining assay accuracy through consistent sequencing-based detection methodology.
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 enables accurate and efficient detection of copy number variations with improved resolution and multiplexing capabilities, reducing the time and cost associated with whole-genome sequencing.
Implementation Method 1
nucleic acids from both samples are typically hybridized to a microarray of probes. Signals are then detected from nucleic acids hybridized to the microarray.
Implementation Method 2
nucleic acids from the test sample are differentially labeled from nucleic acids from the reference sample
Data Source
AI summary
The present invention relates to systems and methods for detecting genomic copy number changes. In particular, the present invention relates to next generation sequencing methods for detection of copy number changes.