cfDNA Cell Origin Mapping with Molecular Counting and TF Footprints
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Solution Overview
Problem
Existing methods for determining the cellular origin of circulating cell-free DNA (cfDNA) in bodily fluids face limitations due to the reliance on genotypic differences, which are ineffective in distinguishing cell populations with identical or nearly identical genomes, particularly in conditions where tissue damage or inflammation alters the tissue-of-origin composition.
Innovation Solution
The method involves extracting and purifying cfDNA, tagging it with unique molecular identifiers (UMIs), sequencing, and analyzing transcription factor (TF) footprints in short cfDNA fragments to determine the cellular origin by comparing these footprints to existing compendia, allowing for the differentiation of cell types based on TF occupancy patterns.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If genotypic differences are used to distinguish cell populations in cfDNA, then cell type origin can be determined in cases with genomic variations, but the method becomes ineffective when cell populations have identical or nearly identical genomes
Solution Approach 1:
The patent shifts from analyzing genotypic parameters (DNA sequence variations) to epigenetic parameters (nucleosome positioning patterns). By changing the measurement parameter from genetic sequence to chromatin structure, the method can distinguish cell types even when their genomes are identical, as epigenetic marks differ between cell types.
Solution Approach 2:
The patent introduces nucleosome positioning patterns as an intermediary marker to indirectly indicate cell type origin. Instead of directly detecting cell type-specific genetic markers, the method uses nucleosome occupancy patterns at specific genomic loci as a mediator that reflects the epigenetic state of the parent cell type.
2Measurement precision
If deep sequencing is performed to detect rare mutations and determine cell origin, then detection sensitivity is improved, but the cost and complexity of the procedure increases
Solution Approach 1:
The patent extracts and focuses on specific informative loci in the genome where nucleosome positioning patterns are highly cell type-specific. By selecting only these key loci for analysis rather than performing whole-genome deep sequencing, the method achieves high detection sensitivity while reducing sequencing depth requirements and overall complexity.
Solution Approach 2:
The patent develops a universal approach using nucleosome positioning patterns that can be applied across multiple clinical scenarios (cancer detection, fetal aneuploidy screening, transplant monitoring) without requiring scenario-specific genomic markers. This universal epigenetic marker system simplifies the overall diagnostic workflow compared to multiple specialized genetic testing protocols.
3Ease of operation
If cfDNA concentration is low in circulating plasma, then non-invasive diagnostics is advantageous, but the low concentration makes detection and analysis more challenging
Solution Approach 1:
The patent applies local quality enrichment by focusing sequencing efforts on specific genomic loci where cell type-specific nucleosome patterns are most pronounced. Rather than attempting to analyze the entire cfDNA population uniformly, the method concentrates analytical resources on informative regions, improving detection accuracy from low-concentration samples.
Solution Approach 2:
The patent performs preliminary computational analysis to identify cell type-specific nucleosome positioning patterns at key loci before full sequencing. This preliminary step allows for targeted enrichment and focused sequencing of informative regions, maximizing the information extracted from low-concentration cfDNA samples while minimizing sequencing requirements.
Data Source
AI summary
Provided herein are compounds, methods, and compositions for use in determining the cellular origin of circulating cell-free DNA.