HBV Probe Panel for Sensitive Viral Integration Detection
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Solution Overview
Problem
Current methods for detecting hepatitis B virus (HBV) integration, such as direct sequencing and sequence-capture probes, are inefficient and ineffective in capturing viral DNA and viral-host junctions, particularly from circulating tumor DNA samples.
Innovation Solution
A panel of probe combinations targeting HBV, including partial and full HBV probes, hotspot gene probes, and exogenous/endogenous gene probes, designed to align with specific reference sequences, ensuring optimal viral/host sequence coverage and genetic stability, allowing for sensitive and efficient detection of viral infection and integration.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If direct sequencing methods are used to detect HBV integration, then comprehensive genomic coverage is achieved, but detection efficiency and sensitivity are poor
Solution Approach 1:
The invention segments the detection approach by using targeted sequence capture probes to enrich HBV integration regions before sequencing. Instead of sequencing the entire genome, the method divides the detection process into enrichment and sequencing stages, significantly improving the proportion of HBV-related reads while maintaining comprehensive coverage of integration sites.
Solution Approach 2:
The invention performs preliminary enrichment of HBV integration sequences using capture probes before the actual sequencing step. This preliminary action concentrates the target sequences of interest, ensuring that when sequencing occurs, the majority of reads correspond to HBV integration regions rather than background genomic DNA.
2Productivity
If sequence-capture probes are used for HBV detection, then sequencing cost is reduced, but probe efficiency and detection effectiveness are poor
Solution Approach 1:
The invention applies local quality by designing capture probes with optimized characteristics specifically for HBV integration regions. The probes are engineered with appropriate length, GC content, and specificity to maximize hybridization efficiency to target sequences while minimizing off-target binding, thereby improving both enrichment efficiency and detection accuracy.
Solution Approach 2:
The invention optimizes probe parameters including sequence length, GC content, and melting temperature to enhance capture efficiency. By carefully adjusting these parameters, the probes achieve optimal binding affinity to HBV integration regions while maintaining specificity, resolving the contradiction between efficiency and effectiveness.
3Measurement precision
If high coverage sequencing is performed to ensure detection sensitivity, then comprehensive viral integration detection is achieved, but the amount of data and processing complexity increase significantly
Solution Approach 1:
The invention extracts only the relevant HBV integration sequences from the total genomic DNA using capture probes. By physically separating and enriching the target sequences before sequencing, the method reduces the proportion of background reads, thereby decreasing the total sequencing depth required while maintaining detection sensitivity and reducing data processing burden.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The probe combination significantly enhances the detection of HBV integration, achieving higher sensitivity and efficiency compared to existing methods, with improved capture rates of HBV DNA and viral-host junctions, particularly in tumor DNA samples.
Implementation Method 1
The probe combination includes one or more sets of partial hepatitis B virus (HBV) targeting probes... When sequences of each of the sets of partial HBV targeting probes are aligned, an overall sequence of the aligned set of partial HBV targeting probes matches a reference sequence
Data Source
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AI summary
A probe combination for detecting cancer includes one or more sets of partial hepatitis B virus (HBV) targeting probes. When sequences of each of the sets of partial HBV targeting probes are aligned, an overall sequence of the aligned set of probes matches a reference sequence of a genome of a HBV genotype or a direct repeat (DR) region on the genome. In the aligned set of probes, each of the probes overlap with one or two adjacent probes by a portion of a length of the probe. The probe combination may further includes one or more sets of hotspot gene targeting probes targeting cancer hotspot genes such as CTNNB1, TERT, and TP53 genes, one or more sets of exogenous gene targeting probes targeting portions of a lambda phage genome, and endogenous gene targeting probes targeting endogenous genes such as GAPDH and GdX genes.