Nanoball Combinatorial Identifiers for Spatial Single-Cell Sequencing
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Solution Overview
Problem
Current single-cell sequencing technologies lack the ability to provide spatial context, failing to map cellular states within tissues effectively, and existing imaging-based methods struggle with comprehensive genome-wide coverage and multi-modal capabilities.
Innovation Solution
A method using nanoball combinatorial identifiers to correlate microscopy images with genomics, epigenomics, or proteomics information by generating unique nanoballs within cells or nuclei, allowing for spatial indexing and sequencing to integrate spatial coordinates with single-cell sequencing data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If NGS-based single-cell sequencing is used, then comprehensive genome-wide coverage and multi-modal capabilities are achieved, but spatial context information is lost
Solution Approach 1:
The patent introduces nanoballs as intermediary objects that carry spatial information. Each nanoball is positioned at a known location within a cell and contains a unique identifier sequence. This intermediary carrier allows the coupling of spatial coordinates with genomic data without requiring complex microstructures, resolving the contradiction between comprehensive sequencing and spatial context preservation.
Solution Approach 2:
The patent segments the spatial indexing function into discrete nanoballs distributed throughout the cell. Each nanoball independently carries spatial and identification information, allowing the system to maintain spatial context while enabling comprehensive genome-wide sequencing through multiple sequencing libraries that can be correlated via these segmented identifiers.
2Loss of information
If imaging-based spatial biology platforms are used, then spatial context is provided, but comprehensive genome-wide coverage is restricted
Solution Approach 1:
The nanoballs serve multiple functions simultaneously: they act as spatial markers for imaging, carry unique identification sequences for sequencing, and enable both optical microscopy and NGS-based analysis. This multi-functionality allows the system to achieve both spatial context and comprehensive genome-wide coverage in a single integrated platform.
3Loss of information
If fabricated microstructures are used to capture or label nucleotides, then spatial information is preserved, but manufacturing cost becomes prohibitively high
Solution Approach 1:
The patent replaces expensive, complex fabricated microstructures with simple, inexpensive nanoballs that can be easily synthesized. These nanoballs serve as disposable spatial markers that are much cheaper to produce while achieving the same spatial information preservation function, dramatically reducing manufacturing costs.
Solution Approach 2:
The patent changes the physical and chemical parameters of the spatial markers from complex microstructures to simple nanoscale objects. By altering the size, composition, and synthesis method of the markers, the system achieves spatial information preservation at a fraction of the manufacturing cost, making the technology more accessible.
Data Source
AI summary
The present disclosure relates to a method for spatial single-cell sequencing. The method includes collecting a sample comprising a plurality of cells or nuclei. The method also includes amplifying oligos and generating a plurality of nanoballs within each of the cell or nucleus. The method also includes creating a nanoball combinatorial identifier (NCI) or a unique nanoball combinatorial identifier (UNCI) for each of the cell or nucleus based on the combination of the nanoballs. The method also includes identifying the nanoballs using both optical microscopy and next-generation sequencing (NGS)-based single-cell or single-nucleus sequencing assays. The method also includes dissociating the cells or nuclei from tissues, and the dissociated cells or nuclei are subjected to the single-cell or single-nucleus sequencing. The method also includes subsequently sequencing the nanoballs to correlate the spatial location/coordinates of each cell or nuclei with the single-cell or single-nucleus sequencing data.