Cell-free Nucleic Acid Microbiome Analysis via Bioinformatics Extraction
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Solution Overview
Problem
Current methods for monitoring the microbiome and immunocompetence in organ transplant patients are invasive, costly, and lack sensitivity, particularly in diagnosing infections and predicting transplant rejection, as they rely on specific targets and invasive biopsies, and fail to account for patient-to-patient variability in immunosuppressive drug sensitivity.
Innovation Solution
High-throughput sequencing of cell-free nucleic acids from plasma, followed by bioinformatics analysis to subtract host sequences and determine microbial prevalence, allowing for unbiased analysis of the microbiome and virome, which can predict immunocompetence and transplant outcomes by measuring viral and bacterial loads.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If high-throughput sequencing of cell-free nucleic acids is performed, then sensitivity and non-invasiveness are improved, but device complexity and cost increase
Solution Approach 1:
The patent extracts only the necessary microbial sequences from the complex cell-free nucleic acid mixture through bioinformatics filtering. By separating host sequences from microbial sequences and focusing analysis only on the relevant microbial portion, the system achieves high detection sensitivity without requiring equally high sequencing depth across the entire genome, thereby reducing the effective complexity burden.
Solution Approach 2:
The patent employs universal primers that can amplify a broad range of microbial DNA sequences without requiring specific knowledge of each pathogen. This multi-functional approach allows a single sequencing system to detect diverse microorganisms (bacteria, viruses, fungi) simultaneously, improving sensitivity across multiple targets while avoiding the need for multiple specialized diagnostic systems.
2Adaptability or versatility
If unbiased amplification with universal primers is used, then all microbiome sequences are included, but bioinformatics analysis complexity increases to identify sequences of interest in a dataset predominated by host sequences
Solution Approach 1:
The patent extracts microbial sequences from the overwhelming host background through targeted bioinformatics filtering. By using reference genomes to identify and isolate sequences that match known microbial pathogens, the system recovers only the relevant diagnostic information from the unbiased amplification data, making the analysis tractable despite the initial complexity.
Solution Approach 2:
The patent performs preliminary host sequence subtraction before detailed microbial analysis. By removing all sequences that match the host genome in an initial filtering step, the system reduces the data complexity early in the analysis pipeline, making subsequent microbial sequence identification more efficient and less computationally intensive.
3Measurement precision
If specific target methods are used for monitoring infections, then diagnostic specificity is improved, but sensitivity and ability to detect unknown pathogens deteriorate
Solution Approach 1:
The patent uses universal primers that can bind to conserved regions across diverse microbial genomes, enabling a single diagnostic test to detect both known and unknown pathogens. This universal approach maintains diagnostic specificity through subsequent bioinformatics matching while dramatically expanding the detection range to include any microorganism with the targeted genetic marker.
Solution Approach 2:
The patent performs preliminary unbiased amplification of all microbial DNA before specific identification. This allows the system to capture all pathogen types in the sample first, then apply specific identification methods afterward, ensuring that neither sensitivity nor specificity is compromised by the ordering of operations.
Data Source
AI summary
Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.