NGS Trio Analysis for Direct UPD Detection and Pathogenic Mutation Identification
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Solution Overview
Problem
Current methods for detecting uniparental disomy (UPD) are inefficient and costly, particularly for genome-wide screening, and often require multiple experiments, with existing techniques only able to indirectly deduce UPDs through loss of heterozygosity (LOH) analysis, failing to directly determine genetic origin and pathogenic mutations.
Innovation Solution
A method utilizing Next-Generation Sequencing (NGS) trio data to directly detect UPDs by classifying mutation sites, merging data from trio samples, and analyzing inheritance patterns to identify uniparental fragments, thereby determining the genetic origin of chromosomes and identifying pathogenic UPDs without additional cost or experiments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If methylation method is used to detect UPDs, then detection of small regions on chromosomes is possible, but different experiments are required for different regions resulting in low efficiency
Solution Approach 1:
The patent applies universality by using a single NGS-based inheritance pattern analysis method to detect UPDs across the entire genome, replacing the need for multiple region-specific methylation experiments. The method universally analyzes inheritance patterns at mutation sites throughout the genome, achieving both detection capability and efficiency.
Solution Approach 2:
The patent substitutes the mechanical/molecular methylation detection system with an NGS-based genetic inheritance pattern analysis system. Instead of detecting methylation levels directly, the method uses sequencing data to infer UPD status through inheritance pattern classification, achieving higher efficiency and genome-wide coverage.
2Productivity
If SNP chip-based method is used, then genome-wide screening is possible, but cost is high and pathogenic micro-mutations cannot be detected
Solution Approach 1:
The patent makes the NGS-based method universal by using it to simultaneously achieve genome-wide UPD screening and pathogenic mutation detection. The same sequencing data and inheritance pattern analysis are used for both purposes, eliminating the need for separate SNP chip assays and reducing overall cost while maintaining comprehensive detection capability.
Solution Approach 2:
The patent merges the functions of UPD detection and pathogenic mutation detection into a single NGS-based analysis pipeline. By combining inheritance pattern analysis with mutation screening, the method achieves genome-wide coverage at lower cost than separate SNP chip approaches, while also identifying pathogenic micro-mutations that SNP chips cannot detect.
3Measurement precision
If WES is used to detect gene defeat diseases, then pathogenic point mutations and copy number variations can be detected, but UPDs can only be indirectly deduced by LOH based on single sample sequencing data
Solution Approach 1:
The patent introduces parent samples as intermediaries to bridge the gap between single-sample WES data and direct UPD determination. By incorporating parental sequencing data, the method enables direct inference of chromosomal origin through inheritance pattern analysis, transforming indirect LOH deduction into direct genetic origin determination while maintaining pathogenic mutation detection capability.
Solution Approach 2:
The patent uses the parental genomes as reference copies to determine the proband's chromosomal origin. By comparing inheritance patterns against the parental copies, the method directly identifies which chromosome segments came from which parent, enabling direct UPD determination without relying on indirect LOH inference from single-sample data.
4Measurement precision
If LOH detection is used to indirectly detect UPDs, then monosomy rescue UPDs can be detected, but trisomy rescue UPDs cannot be clearly identified due to local LOH from recombination
Solution Approach 1:
The patent uses parental inheritance patterns as an intermediary reference to distinguish between different types of UPDs. By analyzing which parent transmitted which chromosome segments, the method can reliably identify trisomy rescue UPDs even when local recombination causes LOH, something indirect LOH detection cannot achieve.
Solution Approach 2:
Instead of detecting UPDs by looking for loss of heterozygosity (the conventional approach), the patent inverts the logic by directly detecting which parent transmitted each chromosome segment through inheritance pattern analysis. This inversion allows clear differentiation between monosomy and trisomy rescue mechanisms, eliminating the ambiguity caused by recombination-related LOH.
Data Source
AI summary
A method for detecting a uniparental disomy based upon NGS-trio and a use thereof, which belongs to the technical field of bioinformatics analysis is provided. The method can directly deduce the genetic origin of chromosome for proband through obtaining NGS-trio sequencing data, analyzing and judging, so as to directly judge whether UPD occurs in the sample (rather than indirectly deduce whether UPD occurs in the sample through LOH), thereby improving positive diagnosis rate without increasing any cost. Further, the method also can assist in the judgment of loss of heterozygosity of large fragments, and its resolution can reach 1 Mbp according to the density of mutation sites, showing excellent detection performance.