Chromosomal Ploidy Detection Using Phased Allele Frequency Models
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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, and selecting a best fit model based on joint probabilities to correct for errors and detect chromosomal aneuploidy, using high-throughput nucleic acid sequence data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current methods are used to detect chromosomal deletions and duplications, then the detection process is simple, but the detection accuracy is insufficient
Solution Approach 1:
The patent segments the chromosomal analysis process into multiple independent steps: receiving allele frequency data, generating phased allelic information, calculating joint probabilities, and selecting best-fit models. Each step processes specific data aspects separately, improving overall detection accuracy while maintaining manageable complexity through modularization.
Solution Approach 2:
The patent performs preliminary phasing of allelic information before final detection analysis. By pre-processing the allele frequency data to establish phased relationships and generating expected genotype patterns in advance, the system prepares refined input data that significantly improves subsequent detection accuracy without adding excessive complexity to the core detection algorithm.
2Loss of information
If high-throughput nucleic acid sequence data is used, then more comprehensive chromosomal information is obtained, but error rates increase requiring correction
Solution Approach 1:
The patent implements feedback mechanisms by calculating joint probabilities that incorporate phased allelic information and comparing observed allele frequencies against expected patterns. This feedback loop identifies deviations caused by errors and enables correction through statistical modeling, allowing the system to maintain high information completeness while correcting reliability issues.
Solution Approach 2:
The patent changes key parameters including allele frequency thresholds, probability cutoffs for model selection, and phased allelic information criteria. By adjusting these parameters based on data quality assessment, the system optimizes the balance between retaining comprehensive chromosomal information and filtering out erroneous data points.
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.