Chromosomal Ploidy Detection Using Phased Allele Frequency Data
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Solution Overview
Problem
Current methods are inadequate for accurately detecting deletions and duplications of chromosome segments or entire chromosomes, which are associated with various diseases and conditions, including cancer, mental and physical handicaps, and autoimmune disorders, necessitating improved diagnostic techniques for early detection and treatment.
Innovation Solution
A method and system for determining chromosomal ploidy by receiving allele frequency data, generating phased allelic information, correcting for errors, and selecting a best fit model to determine chromosomal ploidy, utilizing nucleic acid sequence data and considering linkage between polymorphic loci.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current methods are used to detect chromosomal abnormalities, then the diagnostic process is simpler, but the accuracy of detecting deletions and duplications is insufficient
Solution Approach 1:
The patent segments the chromosome into multiple genomic bins and analyzes copy number variations in each bin independently. This segmentation allows for more precise detection of chromosomal abnormalities by examining specific regions rather than treating the entire chromosome as a single unit, thereby improving measurement precision while managing complexity through systematic division.
Solution Approach 2:
The patent introduces a new dimension of analysis by examining allele frequency distributions and phased allelic information across multiple loci simultaneously. This multi-dimensional approach enables more accurate detection of chromosomal abnormalities by considering not just copy number but also allelic composition and phase relationships, resolving the contradiction between accuracy and complexity.
2Measurement precision
If phased allelic information is generated and error correction is applied, then the precision of ploidy determination is improved, but the computational complexity increases
Solution Approach 1:
The patent performs error correction and phase estimation as preliminary steps before final ploidy determination. By correcting errors in allele frequency data and establishing phase relationships in advance, the method improves precision of subsequent ploidy calls while organizing the computational complexity into manageable sequential stages rather than a single complex operation.
Solution Approach 2:
The patent employs iterative refinement where initial ploidy estimates are used to inform subsequent error correction and phase estimation steps. This feedback loop allows the system to progressively improve precision by using intermediate results to guide further analysis, managing computational complexity through iterative rather than exhaustive processing.
Data Source
AI summary
The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.