RHD/RHCE Gene Conversion Detection with Differentiating Sites
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Solution Overview
Problem
Existing methods struggle to accurately detect RHCE*CE-D(2)-CE gene conversion events in nucleic acid samples due to high sequence similarity between RHD and RHCE genes, leading to misalignment and false negatives in variant calling.
Innovation Solution
A method involving receiving sequence reads that align to RHD or RHCE genes, estimating combined copy numbers, identifying pre-determined differentiating sites, and calculating the probability of gene conversion based on RHD-specific and RHCE-specific base counts, while constructing candidate haplotypes to confirm breakpoints.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequence reads are aligned to RHD or RHCE genes using conventional methods, then alignment is performed, but misalignment occurs due to high sequence similarity between the genes
Solution Approach 1:
The patent segments the alignment process by first aligning sequence reads to a combined reference sequence containing both RHD and RHCE genes, then uses differentiating sites to assign reads to specific genes. This segmentation approach resolves the misalignment problem caused by high sequence similarity by systematically dividing the reference space and using distinctive markers (differentiating sites) to correctly attribute reads to their source gene.
Solution Approach 2:
The patent introduces differentiating sites as an intermediary element to mediate between the sequence reads and the RHD/RHCE genes. These differentiating sites serve as unique identifiers that facilitate accurate assignment of aligned reads to the correct gene, acting as a bridge that overcomes the high sequence similarity barrier and enables precise variant calling.
2Device complexity
If conventional variant calling methods are used, then processing is simpler, but false negatives increase due to inability to distinguish gene conversion events
Solution Approach 1:
The patent performs preliminary actions by first estimating combined copy numbers of RHD and RHCE genes, then identifying differentiating sites and estimating their copy numbers before calculating gene conversion probabilities. This preliminary estimation and identification of key parameters enables accurate detection of gene conversion events while maintaining a systematic and manageable workflow that balances complexity with detection accuracy.
Solution Approach 2:
The patent changes the analytical parameters from simple variant presence/absence to probabilistic gene conversion assessment based on multiple parameters including copy number estimates at differentiating sites. This parameter transformation enables the detection of subtle gene conversion events that would be indistinguishable using conventional binary variant calling, thereby reducing false negatives while maintaining computational feasibility.
3Measurement precision
If copy number estimation is performed at multiple differentiating sites, then detection sensitivity improves, but computational load increases
Solution Approach 1:
The patent extracts and focuses analysis on specific differentiating sites that are most informative for detecting gene conversion events, rather than analyzing all possible positions. By selecting and extracting key differentiating sites where RHD and RHCE genes have distinct copy number patterns, the method achieves high detection sensitivity while reducing computational burden by eliminating redundant analysis of non-informative regions.
Data Source
AI summary
Disclosed herein are systems, devices, and methods for identifying recombinant variants (such as gene conversion variants) of genes such as RHD gene and RHCE gene, the copy numbers of recombinant variants, and gene variant status (for example, heterozygous or homozygous). In some embodiments, the disclosed systems, devices, and methods include steps of receiving sequence reads which align to a RHD gene or a RHCE gene, estimating a combined copy number of a RHD gene and a RHCE gene, estimating copy numbers of a RHD-specific base and a RHCE-specific base at each of a plurality of pre-determined differentiating sites of the RHD gene and the RHCE gene, and calculating a probability of a RHCE*CE-D(2)-CE gene conversion in the nucleic acid sample.