NGS Genome Instability Detection via Segmented Sequencing
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Solution Overview
Problem
Current methods for detecting homologous recombination deficiency (HRD) are inadequate as they fail to consider other genes in the homologous recombination pathway, do not utilize mutational signatures, and lack calculation of biallelic pathogenic mutation load, leading to low sensitivity and specificity, and struggle with capturing genomic structural variations in telomeric regions due to low capture efficiency and probe density.
Innovation Solution
A method and kit using next-generation sequencing (NGS) that calculates pathogenic point mutations, biallelic pathogenic mutation burden, mutational signatures, copy number variations, and genomic structural variations by designing probes to optimize capture efficiency and incorporating whole-genome sequencing for comprehensive analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If targeted sequencing is used to detect homologous recombination pathway genes, then sequencing depth is high, but capture efficiency is low and probe density is insufficient due to repetitive sequences in telomeric regions
Solution Approach 1:
The patent segments the detection approach by separating targeted sequencing (for high-depth gene mutation detection) from whole-genome sequencing (for structural variation detection in telomeric regions). This allows each method to be applied where it is most effective, overcoming the limitation of targeted sequencing in capturing telomeric structural variations.
Solution Approach 2:
The patent implements a multi-functional detection system that combines targeted sequencing and whole-genome sequencing to achieve both high sequencing depth for gene mutations and comprehensive coverage for structural variations. The NGS platform is configured to perform multiple detection functions simultaneously, resolving the trade-off between precision and productivity.
2Device complexity
If only exon regions of BRCA1 and BRCA2 genes are captured, then detection is simpler, but accuracy of detecting cnv and large fragment deletion is reduced
Solution Approach 1:
The patent performs preliminary whole-genome sequencing to obtain comprehensive genomic information before focused analysis. By first capturing the entire genome including introns and telomeric regions, the system ensures that no potential structural variations are missed, then proceeds with detailed analysis of specific regions of interest.
Solution Approach 2:
The patent expands the detection dimension from only exon regions to include introns, telomeric regions, and structural variations. This dimensional expansion allows detection of a broader range of genomic abnormalities including large fragment deletions and CNVs that would be invisible in exon-only sequencing.
3Loss of time
If current detection methods are used for homologous recombination pathway, then detection is faster, but sensitivity and specificity are low due to not considering other pathway genes, mutational signatures, and biallelic pathogenic mutation load
Solution Approach 1:
The patent merges multiple detection dimensions into a unified HRD assessment: gene mutations, mutational signatures, structural variations, and biallelic pathogenic mutation load are integrated into a single comprehensive evaluation system. This combination maintains efficiency while dramatically improving sensitivity and specificity through multi-parameter analysis.
Solution Approach 2:
The patent creates a composite detection approach that combines multiple types of genomic data (sequence variations, structural variations, mutational signatures) into a unified HRD score. This composite methodology leverages the strengths of each detection type to achieve high sensitivity and specificity while maintaining practical detection speed.
Data Source
AI summary
A method and a kit for determining genome instability based on next generation sequencing (NGS) are disclosed. The new method is used to determine whether there is homologous recombination defect by calculating a comprehensive value of one or more of pathogenic germline and somatic mutations, such as SNV, indels, and CNVs, and Biallelic germline and somatic mutations, pathogenic mutational signature, copy number variation (CNV) in homologous recombination repair (HRR) gene, genomic structural variation and genome instability. The genomics DNA is interrupted and added with an A adapter; then corresponding polymerase chain reaction (PCR) is conducted, and Whole genome sequencing is performed; the hybrid capture is conducted with designed probes of HRR genes and SNPs, and a captured DNA library is subjected to amplification and library sequencing; and then professional bioinformatics software is used for evaluation to determine the homologous recombination deficiency (HRD) status.