Barcoded Affinity Probes for Circulating Microparticle Analysis
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Solution Overview
Problem
Current methods for analyzing cell-free DNA (cfDNA) lack sensitivity and accuracy in detecting long-range genetic information and differentiating between fetal and maternal DNA, particularly in non-invasive prenatal testing (NIPT) and cancer diagnosis, due to the low fraction of cfDNA in circulation.
Innovation Solution
A multi-parametric measurement approach that links signals from genomic DNA fragments and target polypeptides within single circulating microparticles, using barcoded affinity probes and sequencing, to produce linked signals providing cellular context and enhancing diagnostic accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional cfDNA sequencing methods are used, then the analysis can be performed with existing technology, but the sensitivity and accuracy for detecting long-range genetic information is insufficient
Solution Approach 1:
The patent segments the analysis by isolating and analyzing individual microparticles separately rather than analyzing bulk cfDNA. Each microparticle is captured, barcoded, and sequenced independently, allowing detection of long-range genetic information while maintaining manageable complexity through automated processing of discrete units.
Solution Approach 2:
The patent implements a nested structure where barcoded oligonucleotides are embedded within microparticles, and multiple barcodes (first and second barcodes) are nested within each other to provide hierarchical information about microparticle origin and identity, enabling precise tracking and analysis.
2Measurement precision
If bulk cfDNA analysis is performed, then the procedure is simpler, but the ability to differentiate between fetal and maternal DNA is reduced
Solution Approach 1:
By segmenting the cfDNA into individual microparticle units and analyzing them separately with unique barcodes, the method achieves precise differentiation of fetal from maternal DNA while maintaining efficiency through high-throughput automated processing of multiple microparticles in parallel.
Solution Approach 2:
The patent introduces barcoded oligonucleotides as intermediaries that capture and tag cfDNA from specific microparticles. These barcodes serve as mediators that link the physical microparticle to its digital identifier, enabling precise tracking and differentiation without direct manual intervention.
3Loss of information
If cfDNA is analyzed without microparticle isolation, then the workflow is shorter, but the detection of long-range genetic information is limited
Solution Approach 1:
The patent segments cfDNA into microparticle-associated units, allowing preservation and analysis of long-range genetic information that would be lost in bulk analysis. The segmentation enables maintenance of spatial and contextual information while managing complexity through standardized processing protocols.
Solution Approach 2:
The patent performs preliminary actions by capturing and barcoding microparticles before sequencing. This preliminary isolation and tagging preserves long-range genetic information and contextual data, enabling more informative downstream analysis without requiring complex real-time processing during sequencing.
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
This method offers highly sensitive and precise analysis of cfDNA, enabling the detection of long-range genetic information and distinguishing between fetal and maternal DNA, improving diagnostic accuracy in NIPT and cancer monitoring.
Implementation Method 1
the affinity moiety is capable of binding to the target biomolecule
Data Source
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AI summary
Reagents and methods for the analysis of cell free biomolecules (e.g. cell free nucleic acid molecules and cell free polypeptides) of circulating microparticles (i.e. microparticles originating from blood) are provided. The methods comprise analysing a sample that comprises a circulating microparticle or a sample derived from a circulating microparticle. The methods include methods of measuring at least two linked signals, each signal corresponding to the presence, absence and/or level of a biomolecule of a circulating microparticle. The methods also include methods of determining the presence, absence and/or level of a biomolecule of a ciruclatling microparticle using a barcoded affinity probe. In certain methods both nucleic acid biomolecules and non-nucleic acid biomolecules of a circulatling microparticle are analysed together. Reagents for use in the methods are also provided.