Single Cell Nucleic Acid Sequencing via Contiguity Preserving Elements
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Solution Overview
Problem
Existing nucleic acid sequencing methods struggle to efficiently analyze and distinguish nucleic acid components from a single cell, particularly in high-throughput applications, leading to errors and inefficiencies in sequence assembly and haplotype determination.
Innovation Solution
The use of contiguity preserving elements (CE) that compartmentalize and label nucleic acid components within a single cell with unique barcodes and reporter moieties, allowing for precise sequencing and analysis of multiple analytes, including nucleic acids and proteins, by maintaining physical proximity and using combinatorial indexing to assemble sequence information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional nucleic acid sequencing methods are used to analyze single cell components, then sequencing can be performed, but error rates increase and efficiency decreases due to inability to properly compartmentalize and distinguish nucleic acid components
Solution Approach 1:
The patent divides the single cell into multiple compartments using droplets or beads, where each compartment contains a subset of nucleic acid components. This segmentation allows parallel processing of multiple samples simultaneously while maintaining the ability to trace back to individual cell components, thereby improving both accuracy through reduced contamination and efficiency through multiplexing
Solution Approach 2:
The patent introduces unique barcodes and reporter moieties as intermediary elements that link nucleic acid components to their cellular origins. These intermediaries enable the sequencing system to distinguish between different cellular components without direct physical separation during sequencing, resolving the contradiction by adding informational layers that improve both accuracy and throughput
2Productivity
If high-throughput sequencing is implemented to increase productivity, then more samples can be processed, but error rates and inefficiencies in sequence assembly increase
Solution Approach 1:
By segmenting samples into droplet-based compartments, the system enables high-throughput processing while maintaining data quality. Each droplet acts as an independent unit that can be processed in parallel, and the segmented nature allows for better control over sequencing depth and quality metrics for each individual sample
Solution Approach 2:
The patent incorporates unique barcodes that provide feedback about the origin and quality of each nucleic acid component. This feedback mechanism allows for real-time quality control and error correction during assembly, enabling high throughput while maintaining reliability through continuous monitoring and verification of sequence data
3Device complexity
If single cell analysis is performed without compartmentalization, then analysis can be simplified, but the ability to distinguish and analyze multiple analytes is compromised
Solution Approach 1:
The patent creates a universal platform where the same droplet-based compartmentalization system can analyze multiple types of analytes (nucleic acids, proteins, metabolites) simultaneously. The unique barcoding system serves multiple functions: it tracks cellular origin, enables multiplexing, and provides quality control, thereby achieving multi-analyte capability without proportionally increasing complexity
Solution Approach 2:
The patent implements nested structures where multiple analysis layers are contained within the same droplet compartment. Different analytes can be processed in parallel within the same physical compartment, with each analyte receiving its own unique barcode. This nesting allows the system to maintain simplicity at the physical level while achieving versatility at the analytical level
Data Source
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AI summary
Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.