Cell-free nucleic acid analysis for non-invasive pathogen integration detection
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Solution Overview
Problem
Current methods for detecting chromosomal rearrangements and pathogen integration in humans, such as those associated with cancer, are invasive, costly, and painful, relying on tissue biopsies which are not always effective or efficient.
Innovation Solution
A method involving the analysis of cell-free nucleic acid molecules from biological samples to identify organism-pathogen chimeric nucleic acid fragments through paired-end sequencing, aligning sequence reads to reference genomes, and determining a pathogen integration index to classify pathology, thereby detecting chromosomal rearrangements and nucleic acid integration events non-invasively.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If tissue biopsy methods are used to detect chromosomal rearrangements and pathogen integration, then detection capability is achieved, but the procedure becomes invasive, risky, costly, and painful
Solution Approach 1:
The patent uses cell-free nucleic acid molecules as an intermediary medium to detect pathogen integration and chromosomal rearrangements. Instead of directly biopsying tissue, the method analyzes circulating cell-free DNA that contains integration junctions, serving as a non-invasive proxy for detecting the underlying pathology without requiring tissue penetration
Solution Approach 2:
The patent replaces the mechanical tissue biopsy procedure with a molecular sequencing approach. Instead of physically extracting tissue samples through needles or endoscopes, the method uses paired-end sequencing to detect chimeric reads that span pathogen-host integration junctions in cell-free nucleic acids
2Loss of information
If tissue biopsy is performed to analyze chromosomal rearrangements, then diagnostic information is obtained, but the procedure is costly and time-consuming
Solution Approach 1:
The patent performs preliminary enrichment and selection of cell-free nucleic acid molecules containing pathogen integration signals before full sequencing analysis. By pre-filtering for chimeric reads that span integration junctions, the method reduces the computational and temporal resources needed for complete genomic sequencing while maintaining diagnostic accuracy
3Measurement precision
If paired-end sequencing is used to analyze cell-free nucleic acid molecules, then detection sensitivity is improved, but the complexity of the analysis process increases
Solution Approach 1:
The patent segments the complex paired-end sequencing analysis into distinct functional steps: (1) identifying chimeric reads that span pathogen-host junctions, (2) determining integration breakpoints within specific genomic regions, and (3) classifying pathology based on integration patterns. This segmentation simplifies the overall workflow while maintaining high detection sensitivity through systematic processing of sequencing data
Data Source
AI summary
Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed.