Barcoded Oligonucleotide Labelling for Single-Cell Analyte Sequencing
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Solution Overview
Problem
Existing technologies face challenges in efficiently analyzing genomic and proteomic information from individual cells or small populations of cells, particularly in contexts such as cancer cells, fetal cells, and immune cells, due to limitations in nucleic acid sequencing and characterization methods.
Innovation Solution
A method involving the use of labelling agents that bind to cell surface features and are coupled to reporter oligonucleotides with barcode sequences, allowing for the synthesis and sequencing of nucleic acid molecules to identify these cells, along with systems and compositions that facilitate this process, including the use of anchor oligonucleotides and beads for primer extension reactions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If nucleic acid sequencing is performed on individual cells or small populations of cells, then detailed genomic and proteomic information can be obtained, but the complexity of the analysis and characterization process increases significantly
Solution Approach 1:
The patent segments the complex analysis process into distinct modular steps: cell partitioning into droplets, individual cell lysis, nucleic acid extraction, barcode sequencing, and data analysis. Each module handles a specific aspect of the workflow, making the overall complex process more manageable and automatable while maintaining high measurement precision for genomic and proteomic information
Solution Approach 2:
The patent introduces barcode sequences as intermediary elements that facilitate the connection between individual cells and their genomic/proteomic characteristics. These barcodes serve as mediators that enable tracking and identification of nucleic acids from specific cells throughout the complex sequencing and analysis process, simplifying the overall workflow while maintaining precision
2Measurement precision
If labelling agents with barcode sequences are used to identify cell surface features, then cell characterization accuracy is improved, but the device and reagent complexity increases
Solution Approach 1:
The patent employs universal barcode sequences that can be applied across different cell types and surface features. The same basic barcode structure and sequencing approach works for identifying various cell surface features, reducing the need for cell-type-specific complex reagents and simplifying the overall system while maintaining high identification accuracy
Solution Approach 2:
The patent uses barcode sequences as information copies that represent cell surface features without requiring direct physical manipulation of the cells themselves. The barcodes are synthesized copies of cellular information that can be sequenced and analyzed using standard nucleic acid sequencing technologies, reducing device complexity while improving measurement precision
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
Enables detailed characterization of individual cells by identifying cell surface features and determining the abundance of specific markers, facilitating accurate sequencing and analysis of nucleic acids and proteins from these cells.
Implementation Method 1
labelling agents that bind to cell surface features
Implementation Method 2
synthesizing a nucleic acid molecule comprising at least a portion of the nucleic acid barcode sequence
Implementation Method 3
subjecting the nucleic acid molecule to sequencing to identify the labelling agent or the cell
Data Source
AI summary
The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.