Analyte Mislocalization Measurement Using Capture Probe Arrays
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Solution Overview
Problem
Existing spatial analysis techniques fail to provide information on the position of single cells within a biological sample, requiring time and resource-intensive sequencing to determine analyte sequence and spatial location, and there is a need to assess spatial preservation and presence of analytes prior to traditional analysis.
Innovation Solution
A method involving hybridization of analytes to capture probes on an array, extending and circularizing padlock or snail probes, amplifying, and detecting signals to determine mislocalization by comparing images, using techniques such as rolling circle amplification and enzymatic ligation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional spatial analysis techniques are used to determine analyte sequence and spatial location, then complete spatial information is obtained, but the process becomes time and resource intensive
Solution Approach 1:
The patent extracts only the essential spatial information needed for analysis by using capture probes that bind to analytes at their original locations, followed by amplification and detection that retrieves spatial coordinates without requiring complete sequencing of all analyte molecules. This extraction approach obtains sufficient spatial data while avoiding the time-consuming nature of traditional comprehensive sequencing methods.
2Loss of information
If sequencing is performed to determine analyte sequence and spatial barcode, then complete spatial analysis is achieved, but resources are consumed excessively
Solution Approach 1:
The patent employs universal capture probes that can bind to multiple different analyte types through common structural features, allowing a single set of probes to retrieve spatial information for various analytes simultaneously. The amplification and detection system also serves multiple functions by amplifying captured analytes and generating detectable signals, thereby reducing resource consumption while maintaining complete spatial information acquisition.
3Productivity
If permeabilization is increased to improve analyte accessibility, then more analytes are captured, but mislocalization increases
Solution Approach 1:
The patent optimizes permeabilization parameters (such as enzyme concentration, treatment time, and temperature) to achieve the minimum effective level needed for analyte accessibility. This parameter optimization ensures sufficient analyte capture efficiency while minimizing excessive permeabilization that would cause analyte displacement and mislocalization, thereby balancing productivity and 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
Provides high-resolution analyte data while retaining native spatial context, minimizing mislocalization, and optimizing permeabilization conditions for accurate analyte localization.
Implementation Method 1
hybridizing the analyte to a capture probe on an array
Implementation Method 2
extending the capture probe using the analyte as a template
Implementation Method 3
circularizing the padlock probe or the snail probe
Implementation Method 4
amplifying the padlock probe or the snail probe
Implementation Method 5
hybridizing a plurality of detection probes to the amplified circularized padlock probe or the amplified circularized snail probe
Data Source
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AI summary
Provided herein are methods for determining the mislocalization of an analyte by capturing the analyte on an array and measuring the mislocalization distance.