Allele-Specific Probe Array for Mixed Nucleic Acid Analysis
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Solution Overview
Problem
Current microarray technologies face challenges in accurately detecting genetic abnormalities in mixed nucleic acid populations, particularly in non-invasive samples like maternal blood for fetal aneuploidy and tumor DNA in cancer patients, due to low concentrations and high similarity between subpopulations, leading to high false-positive and false-negative rates.
Innovation Solution
A method using a probe array to measure copy numbers and genotypes in mixed nucleic acid samples by analyzing signals from polymorphic sites, allowing for the estimation of fetal fraction and detection of copy number variations, even at low levels, through oligonucleotide probes and detectors, enabling discrimination between major and minor subpopulations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional microarray technology is used to analyze mixed nucleic acid populations, then the analysis can be performed, but the sensitivity and specificity are insufficient leading to high false-positive and false-negative rates
Solution Approach 1:
The method segments the mixed nucleic acid population analysis into distinct genotyping and copy number analysis components. By using allele-specific probes that target specific polymorphic sites, the system can separately analyze maternal and fetal DNA signals, improving the ability to detect fetal aneuploidies without being confounded by the dominant maternal signal.
Solution Approach 2:
The invention applies local quality by using probes with specific affinities for different alleles at polymorphic sites. The probes are designed to selectively bind to specific nucleotide variants (e.g., A allele vs B allele), enabling differentiation between maternal and fetal DNA based on local sequence variations rather than requiring global differences.
2Ease of operation
If non-invasive sampling methods are used to obtain nucleic acid samples, then the sampling is easier and less risky, but the concentration of target DNA is very low making detection difficult
Solution Approach 1:
The method changes the detection parameters by using allele-specific probes that can detect minor variations in the nucleic acid population. Instead of requiring high concentrations of target DNA, the system uses polymorphic site analysis to identify fetal DNA sequences within the mixed population, enabling detection at low fetal DNA fractions (as low as 4-15% of total cell-free DNA).
3Device complexity
If single or low multiplex assays are used, then the assay complexity is reduced, but the ability to differentiate between aneuploid and euploid fetuses is insufficient
Solution Approach 1:
The microarray system provides multi-functionality by simultaneously performing genotyping and copy number analysis using the same allele-specific probes. The probes can identify both the presence of specific alleles and the copy number of chromosomal regions, enabling comprehensive fetal aneuploidy detection without requiring separate assays for each function.
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 enhances the sensitivity and specificity of genetic abnormality detection in non-invasive samples, reducing false-positive and false-negative rates and enabling early and accurate diagnosis of fetal aneuploidies and cancer, while minimizing the need for invasive procedures.
Implementation Method 1
conducting a first assay comprising (a) contacting the population of nucleic acid fragments with an oligonucleotide array containing a first oligonucleotide probe configured to hybridize to the target nucleic acid sequence containing the polymorphic site of the SNP
Data Source
AI summary
Provided includes methods and systems useful in array-based analysis of mixed nucleic acid populations, including for genotyping and copy number analysis of the various subpopulations of the mixed nucleic acid population. Also provided includes methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken from an organism.