Single-Cell Polynucleotide Processing for Extracellular Nucleic Acid Screening
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Solution Overview
Problem
Existing systems for large-scale, automated processing of single cells in genomic and transcriptomic analyses are hindered by the presence of extracellular analytes, such as DNA or RNA, which can contaminate data and obscure the distinction between cellular and extracellular nucleotide sequences, leading to poor data quality.
Innovation Solution
Methods and kits are developed to rapidly detect and quantify extracellular nucleic acids in cell samples using binding agents, such as oligonucleotides, attached to supports like beads, and detect bound analytes using analytical flow cytometry, allowing for the partitioning of cells with low extracellular nucleic acid levels into discrete droplets for library creation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If cell samples are processed in large-scale automated single cell systems, then throughput and productivity are improved, but data quality deteriorates due to extracellular nucleic acid contamination
Solution Approach 1:
The patent applies preliminary action by performing quality assessment of cell samples before they are processed in the single cell system. The method detects extracellular nucleic acid contamination levels in advance, allowing researchers to identify and exclude poor-quality samples before they enter the main processing workflow, thereby preventing data quality deterioration while maintaining high throughput
2Productivity
If extracellular nucleic acid contamination is present in cell samples, then productivity is maintained, but measurement precision deteriorates due to inability to distinguish cellular from extracellular sequences
Solution Approach 1:
The patent implements feedback by using the detected extracellular nucleic acid contamination levels to inform subsequent processing decisions. The quality assessment provides feedback about sample suitability, allowing the system to adjust processing parameters or exclude samples, thereby maintaining measurement precision while preserving overall productivity
3Manufacturing precision
If rapid quality testing is implemented before library generation, then manufacturing precision is improved, but device complexity increases due to additional testing equipment and protocols
Solution Approach 1:
The patent uses an intermediary approach by introducing a separate quality assessment step that mediates between sample preparation and library generation. This intermediary testing step provides a simple, rapid assessment of extracellular nucleic acid contamination that informs whether samples should proceed to library generation, improving manufacturing precision without requiring complex integration into the main processing system
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 approach ensures high-quality cell samples by reducing extracellular nucleic acid contamination, enabling accurate gene expression library generation and improving data precision in single cell-based analyses.
Implementation Method 1
An oligonucleotide binding agent may encode a first nucleotide sequence complementary to a second nucleotide sequence in an analyte. The first nucleotide sequence may hybridize to the second nucleotide sequence.
Data Source
AI summary
The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.