Chromosomal Ploidy Analysis with Phased Allelic Error Correction
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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 high-throughput nucleic acid sequence data to detect allele frequencies and allelic imbalance.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current methods are used for detecting 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 chromosomal analysis into multiple independent steps: receiving allele frequency data, generating phased allelic information, correcting for errors, and selecting a best fit model. This segmentation allows each step to be optimized independently while maintaining overall accuracy in detecting chromosomal abnormalities.
Solution Approach 2:
The patent performs preliminary actions by generating phased allelic information and correcting for errors before final analysis. These preparatory steps ensure that the data is properly conditioned and corrected for known biases, thereby improving the accuracy of subsequent chromosomal abnormality detection.
2Measurement precision
If high-throughput nucleic acid sequence data is used, then the detection accuracy improves, but the data processing complexity increases
Solution Approach 1:
The patent introduces intermediate processing steps including generating phased allelic information and correcting for errors as mediators between raw high-throughput sequencing data and final chromosomal analysis. These intermediaries transform complex raw data into standardized, corrected formats that are easier to analyze accurately.
Solution Approach 2:
The patent implements feedback mechanisms by selecting a best fit model that compares observed allele frequencies against expected patterns. This feedback loop allows the system to iteratively refine its analysis and correct for systematic errors, thereby improving detection accuracy despite the complexity of high-throughput data.
3Reliability
If comprehensive error correction is performed, then the diagnostic reliability improves, but the processing time increases
Solution Approach 1:
The patent performs error correction as a preliminary action before final diagnostic interpretation. By correcting for errors in advance and generating phased allelic information upfront, the system ensures reliable data without requiring time-consuming corrections during the actual diagnostic process.
Solution Approach 2:
The patent changes parameters by selecting a best fit model that optimizes the balance between correction comprehensiveness and processing efficiency. This allows the system to adjust the level of error correction applied based on the specific data characteristics, maintaining high reliability while minimizing unnecessary processing time.
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.