HaploDissection Method for High-Throughput Haplotype Determination
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Solution Overview
Problem
Current methods for haplotyping are limited by chromosome breakdown, are time-consuming and labor-intensive, and not suitable for high-throughput analysis, making them impractical for molecular diagnosis in personalized medicine and genetic studies.
Innovation Solution
The HaploDissection method introduces an imbalance in the chromosome ratio by randomly selecting and collecting chromosomes from diploid cells into sample tubes, allowing for genotyping and determining haplotypes based on allele nucleotide sequence information and signal intensities, which maintains phase information and enables long-range haplotype determination without physical separation of chromosomes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If physical separation of chromosomes is used to determine haplotype, then phase information can be obtained, but the method is time-consuming and labor-intensive
Solution Approach 1:
The patent replaces mechanical chromosome separation with molecular-level SNP genotyping. By using genotyping assays to detect SNP alleles and their signal intensities, the method obtains phase information without physical chromosome manipulation, significantly reducing time and labor requirements while maintaining accuracy.
Solution Approach 2:
The patent uses signal intensity data as a proxy or copy of chromosome presence information. Instead of physically tracking chromosomes, the method measures allele signal intensities that represent the presence of maternal or paternal chromosomes at heterozygous SNP loci, enabling indirect but accurate phase determination.
2Measurement precision
If physical separation of chromosomes is used to determine haplotype, then phase information can be obtained, but the method is not suitable for high-throughput analysis
Solution Approach 1:
The patent replaces manual chromosome separation with automated genotyping assays that can process numerous samples simultaneously. The use of SNP genotyping platforms enables high-throughput analysis by measuring multiple SNP loci across many samples in parallel, maintaining phase information accuracy while dramatically increasing productivity.
Solution Approach 2:
The patent employs a universal genotyping approach that can analyze multiple SNP loci across the entire chromosome range using the same assay platform. This multi-functional method handles diverse samples and genomic regions without requiring separate procedures, enabling scalable high-throughput haplotype determination.
3Measurement precision
If physical separation of chromosomes is used to determine haplotype, then phase information can be obtained, but costs are increased
Solution Approach 1:
The patent replaces expensive and labor-intensive chromosome separation procedures with cost-effective genotyping assays. By using molecular biology techniques to detect SNP alleles directly from DNA extracts, the method achieves the same phase information goal at significantly lower material and operational costs.
Solution Approach 2:
The patent uses disposable DNA extracts and standard genotyping reagents instead of requiring complex, expensive chromosome separation equipment and materials. The approach relies on readily available, low-cost molecular biology tools that can be discarded after use, reducing overall operational expenses.
4Ease of operation
If conventional genotyping assays are used, then analysis is simplified, but phase information is lost
Solution Approach 1:
The patent uses signal intensity measurements as feedback to determine chromosome origin. By analyzing the relative intensities of allele signals at heterozygous SNP loci, the method infers whether alleles come from maternal or paternal chromosomes, thereby recovering phase information that would otherwise be lost in conventional genotyping.
Solution Approach 2:
The patent extends conventional genotyping by utilizing signal intensity parameters in addition to simple allele presence/absence detection. This additional parameter measurement enables the distinction between maternal and paternal chromosome contributions while maintaining the simplicity of the genotyping assay framework.
Data Source
AI summary
A method for molecular haplotyping of a subject is disclosed. The method comprises: randomly selecting a set of chromosomes in each of a plurality of lyzed diploid cells of the subject, collecting the selected chromosomes from said plurality of cells into a plurality of sample tubes, wherein each sample tube contains chromosomes selected from one or more cells, genotyping genomic DNA in each sample tube, and determining haplotype of the alleles based on allele nucleotide sequence information and corresponding nucleotide signal intensities from genotyping data. Other methods for molecular haplotyping using single cell lysate or single cell microdissection are also disclosed.