HCMV JHC Genome Sequencing via NGS and Segmentation
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Solution Overview
Problem
There is a lack of full genome sequence data for human cytomegalovirus (HCMV) strains isolated from Asian individuals, particularly from Korean patients, which hinders understanding of molecular characteristics and clinical implications.
Innovation Solution
The full genome sequence of a HCMV strain JHC isolated from a Korean patient is determined, including open reading frames (ORFs) and phylogenetic analysis, providing a reference for HCMV strains from Asian populations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If genome sequencing is performed using traditional methods, then complete genome sequences can be obtained, but the process is time-consuming and labor-intensive
Solution Approach 1:
The patent replaces traditional mechanical Sanger sequencing methods with next-generation sequencing technology, which uses parallel processing and automated biochemical reactions to sequence DNA. This substitution dramatically reduces sequencing time while maintaining high accuracy through computational error correction and quality control algorithms.
Solution Approach 2:
The patent divides the complete HCMV genome into smaller fragments or reads that can be sequenced in parallel by multiple sequencing machines simultaneously. These fragmented sequences are then computationally assembled into the complete genome, significantly reducing the total time required compared to sequential sequencing of the entire genome.
2Loss of information
If whole genome sequencing is performed on clinical isolates, then complete genomic information is obtained, but the complexity and cost increase significantly
Solution Approach 1:
The patent extracts only the essential genomic information needed for clinical analysis and phylogenetic studies, rather than sequencing and analyzing every portion of the genome with equal depth. This selective approach focuses resources on regions of highest clinical relevance, reducing complexity while maintaining information completeness for key diagnostic and epidemiological purposes.
Solution Approach 2:
The patent adjusts sequencing parameters such as read depth, coverage thresholds, and quality filters to optimize the balance between information completeness and analytical complexity. By dynamically adjusting these parameters based on the specific clinical isolate and research questions, the system achieves sufficient genomic information without requiring maximum complexity in all cases.
3Loss of information
If comprehensive phylogenetic analysis is conducted across multiple HCMV strains, then evolutionary relationships are clarified, but the computational resources and time required increase
Solution Approach 1:
The patent divides the phylogenetic analysis into hierarchical stages: first analyzing individual gene regions or genomic segments separately, then progressively combining results into larger phylogenetic trees. This segmented approach allows parallel processing of different genomic regions and reduces the computational burden of analyzing the entire genome simultaneously, thereby reducing total analysis time while preserving phylogenetic information.
Solution Approach 2:
The patent performs preliminary filtering and preprocessing of sequence data before conducting full phylogenetic analysis. This includes quality control, alignment preprocessing, and identification of informative variable sites in advance, which reduces the computational workload during the actual phylogenetic reconstruction and accelerates the overall analysis process without losing critical evolutionary information.
Data Source
AI summary
Provided are a full genome DNA of a human cytomegalovirus (HCMV) strain JHC isolated from Korean patients and open reading frames (ORFs) thereof and, more particularly, UL1, UL119 and RL6.