Allele-Specific Copy Number Measurement via SNP Microarray Hybridization
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Solution Overview
Problem
Current methods for detecting single nucleotide polymorphisms (SNPs) and allele-specific copy number measurements are not high throughput and often require amplification processes like PCR, limiting their efficiency and scalability.
Innovation Solution
The use of microarray platforms that involve digesting DNA samples with restriction enzymes and hybridizing them to probes complementary to SNP sites, allowing for the detection of alleles by comparing signal intensity between digested and undigested samples, enabling the determination of allele presence and copy number.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If PCR amplification is used for SNP detection, then detection sensitivity is improved, but throughput is limited and process complexity increases
Solution Approach 1:
The invention extracts and eliminates the PCR amplification step from the SNP detection workflow. By using direct hybridization of genomic DNA to microarray probes without prior amplification, the method removes the time-consuming and low-throughput PCR process while maintaining detection capability through direct binding of target DNA to complementary probes on the array surface.
Solution Approach 2:
The invention replaces the mechanical/chemical amplification process (PCR) with a direct binding/hybridization process. Instead of using polymerase enzymes and thermal cycling to amplify DNA, the method uses complementary base pairing between genomic DNA and microarray probes to achieve detection, fundamentally changing the detection mechanism from amplification-based to hybridization-based.
2Reliability
If PCR amplification is used for SNP detection, then allele detection capability is improved, but process time and operational complexity increase
Solution Approach 1:
The invention performs preliminary preparation of the microarray probe set to cover multiple SNP loci simultaneously. By designing and synthesizing a comprehensive panel of probes before the actual detection experiment, the system enables parallel analysis of many SNPs in a single hybridization reaction, eliminating the need for sequential PCR amplifications for each SNP or small group of SNPs.
Solution Approach 2:
The invention merges multiple individual SNP detection assays into a single integrated microarray platform. Instead of performing separate PCR reactions for each SNP, the method combines hundreds or thousands of probe-based detection reactions on one array, allowing simultaneous analysis of multiple SNPs from a single genomic DNA sample preparation.
3Measurement precision
If traditional SNP detection methods are used, then accuracy is maintained, but scalability and high-throughput capability are limited
Solution Approach 1:
The invention creates a universal microarray platform that can detect multiple SNP variants across different genomic loci using a single assay system. The standardized probe design and hybridization protocol allow the same platform to be applied to diverse SNP panels, making the system scalable to different applications and gene sets without requiring method revalidation or protocol changes.
Solution Approach 2:
The invention changes the fundamental detection parameter from amplification efficiency to hybridization specificity. By shifting the basis of detection from measuring PCR product quantity to measuring probe-target binding affinity and specificity, the system achieves both high accuracy through stringent wash conditions and high scalability through parallel processing of multiple probes simultaneously.
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 rapid and high-throughput detection of SNPs and allele-specific copy number measurements, improving the efficiency and accuracy of genetic analysis, particularly in diagnosing diseases and cancer research.
Implementation Method 1
DNA samples are digested with at least one restriction enzyme, wherein the SNP site comprises a sequence that is cleaved by the restriction enzyme
Implementation Method 2
a digested and an undigested and/or reference sample are hybridized to a microarray comprising a probe complementary to a sequence comprising the SNP site
Data Source
AI summary
Methods and systems for allelic detection and allele-specific copy number are provided herein. The described methods use identification of single nucleotide polymorphism using restriction enzymes and CGH analysis. Microarrays comprising probes designed by the described methods are provided. Also included are methods for identifying SNP sites and copy number in samples obtained from patient populations.