Split Probe DNA Fragment Joining Detection Method
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Solution Overview
Problem
Current methods for detecting DNA fragment joining events and alternative splicing are either costly, time-consuming, or require specialized expertise, limiting their clinical application in precision medicine, especially for cancer diagnosis and treatment.
Innovation Solution
A method involving the use of split probes and gene-specific primers to enrich and detect DNA fragment joining events, which includes obtaining DNA or RNA from a sample, enriching with oligonucleotides, and using split probes to bind and detect specific nucleic acid sequences, allowing for the identification of DNA fragment joining and alternative splicing events through PCR and probe hybridization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next-generation sequencing (NGS) is used to detect DNA fragment joining events, then comprehensive information with details is provided, but the method is costly and time-consuming
Solution Approach 1:
The invention divides the detection process into two stages: first using a rapid screening method with split probes to identify potential DNA fragment joining events, then applying NGS only to confirmed cases for detailed analysis. This segmentation reduces overall detection time while maintaining comprehensive information gathering where needed.
Solution Approach 2:
The split probe method applies local quality by targeting specific regions of interest with high precision probes rather than sequencing entire genomes. This allows accurate detection of DNA fragment joining events at specific loci without the time and cost burden of comprehensive NGS across the whole genome.
2Measurement precision
If next-generation sequencing (NGS) is used to detect DNA fragment joining events, then comprehensive information with details is provided, but the method is costly
Solution Approach 1:
The detection workflow is segmented into a low-cost screening phase using split probes followed by expensive NGS only when necessary. This reduces overall cost while preserving detection accuracy for confirmed cases.
Solution Approach 2:
The invention uses inexpensive split probes as disposable screening tools that can be synthesized at low cost. These probes serve as a cheap first line of detection, eliminating the need for costly NGS in routine screening while maintaining high detection accuracy through the subsequent use of NGS only for confirmed positive cases.
3Ease of operation
If immunohistochemistry (IHC) is used to detect DNA fragment joining events, then the presence of produced proteins is detected, but it is challenging to distinguish the relationship between genotype mutations and phenotype variations
Solution Approach 1:
The invention introduces split probes as an intermediary detection tool that bridges the gap between simple protein detection (IHC) and complex genomic analysis (NGS). The probes hybridize to specific DNA sequences at fragment joining sites, providing direct genotypic information while maintaining operational simplicity similar to IHC.
4Measurement precision
If fluorescent in situ hybridization (FISH) is used to detect gene fusions, then gene fusion detection is achieved, but separate reactions are required for each fusion type and highly-trained specialists are needed to analyze results
Solution Approach 1:
The split probe system is designed with universal applicability to detect multiple types of DNA fragment joining events and alternative splicing across different genes using the same basic methodology. A single probe design strategy can target various fusion types without requiring separate specialized reactions for each, reducing system complexity while maintaining detection precision.
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 method provides a more accurate, comprehensive, and efficient way to detect DNA fragment joining and alternative splicing events, enabling better diagnosis and potential targeted treatments for cancer by identifying specific genetic variations.
Implementation Method 1
probing the target nucleic acid with a split probe including: (i) a first split probe being complementary to the 3′ end of a partner DNA fragment, a second split probe being complementary to the 5′ end of a target DNA fragment
Data Source
AI summary
The present disclosure relates to the fields of a method a kit for molecular diagnostics and genomics. More particularly, this disclosure relates to a method and a kit fir detecting a DNA fragment joining event or distinguishing an alternative splicing event. The present disclosure also relates to a method for administering a subject with proper treatment by steps of determining the risk of a particular cancer type or genotype.