Probe Set for Targeted SNP Detection and Sequencing
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current high-throughput sequencing methods for SNP detection are inefficient and costly due to the need for extensive library construction, amplification, and the requirement for large amounts of nucleic acid, especially when targeting specific genes or regions, leading to waste of sequencing space and increased complexity in data analysis.
Innovation Solution
A probe set comprising specific hybridization sequences and primers that target genetic loci, allowing for the efficient detection of SNPs or mutations by forming a sequence comprising the genetic locus, reducing the need for extensive library construction and amplification, and enabling cost-effective, high-throughput sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional library construction and amplification methods are used for SNP detection, then comprehensive genome coverage is achieved, but the process becomes time-consuming, costly, and requires large amounts of nucleic acid
Solution Approach 1:
The patent extracts and focuses only on the specific genetic loci of interest using targeted probes, eliminating the need for comprehensive library construction and whole-genome amplification. This extraction approach reduces time, cost, and material requirements while maintaining detection sensitivity for the targeted SNPs.
Solution Approach 2:
The patent segments the genome into specific target loci using probe-based enrichment, separating the detection process from whole-genome sequencing. This segmentation allows focused analysis of only the relevant genetic regions, reducing the complexity and resource requirements of the detection process.
2Productivity
If whole-genome sequencing library construction is performed, then all genome fragments are sequenced, but sequencing space is wasted on non-target regions and data analysis complexity increases
Solution Approach 1:
The patent extracts only the relevant genetic loci using specific probes, eliminating waste of sequencing space on non-target regions. This extraction ensures that all sequencing capacity is utilized efficiently for detecting SNPs in the genes of interest, improving productivity while simplifying data analysis.
3Measurement precision
If commercial custom sequence capture kits are used, then target sequence enrichment is achieved, but the kits are expensive and the target sequences are fixed and cannot be changed
Solution Approach 1:
The patent creates a universal probe system that can detect multiple different target sequences and genetic loci. The probes are designed to be adaptable and can be customized for different genes and SNP locations, providing both enrichment efficiency and flexibility. This universal approach eliminates the need for expensive custom kits while maintaining the ability to detect various target sequences.
4Quantity of substance
If PCR-based non-hybrid sequence capture is used, then amplification is achieved, but some areas are not effectively amplified and polymerase errors are introduced
Solution Approach 1:
The patent introduces hybridization probes as an intermediary step between the target DNA and PCR amplification. The probes specifically bind to the target sequences through hybridization, ensuring that only the intended regions are enriched before amplification. This intermediary step improves both the accuracy of target selection and the reliability of subsequent amplification by preventing non-specific amplification and reducing polymerase errors.
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 simplifies SNP detection, reduces sequencing costs, and enhances sensitivity, allowing for the analysis of multiple loci simultaneously with improved accuracy and reduced sample requirements, making it suitable for large-scale population screening.
Implementation Method 1
one or more first probes comprising: (1) a first hybridization sequence that specifically binds to the target polynucleotide sequence upstream of the genetic locus
Data Source
AI summary
Provided herein is a multi-sample and multi-locus method for analyzing a genetic locus. In particular, provided herein is a method for SNP detection and analysis based on high-throughput sequencing, comprising designing a probe, pre-amplification and biotin labeling, hybridization, ligation, barcode specific primer extension, sequencing and analyzing the SNP locus. A probe set is for the analysis is also provided.