Barcoded Probe Hybridization for Single-Cell Transcriptomics
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Solution Overview
Problem
Current methods for single-cell omics analysis, such as transcriptome sequencing, are inefficient, costly, and prone to information loss and systematic bias due to the need for reverse transcription, limiting high-throughput analysis capabilities.
Innovation Solution
A method involving hybridization of probes with target molecules in a sample without reverse transcription, using barcoded probes to detect and sequence target molecules, allowing for efficient and accurate analysis of transcriptomics information from single cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If reverse transcription is performed to amplify target nucleic acid before sequencing, then single-cell omics analysis can be conducted, but the process becomes slow, inefficient, and costly
Solution Approach 1:
The patent extracts and sequences only the probe molecules themselves rather than the entire cDNA transcriptome. By taking out only the necessary probe sequences that contain target molecule information, the method eliminates the need for time-consuming reverse transcription and full-length cDNA sequencing, achieving high-throughput analysis of single-cell omics data
Solution Approach 2:
The patent performs preliminary hybridization of probes with target molecules before sequencing. By pre-forming the probe-target complex and attaching probes to barcodes, the method prepares the sample in advance so that sequencing only needs to read the probe sequences, skipping the reverse transcription step and significantly reducing analysis time
2Measurement precision
If reverse transcription is performed to amplify target nucleic acid, then sequencing can be conducted, but information loss and systematic bias occur
Solution Approach 1:
The patent uses probes as intermediary molecules that specifically bind to target molecules through hybridization. These probes serve as mediators that transfer target molecule information to barcodes without requiring reverse transcription. The probes act as faithful intermediaries that preserve original target sequence information while enabling efficient sequencing, eliminating the information loss and bias associated with reverse transcription
Solution Approach 2:
Instead of copying the entire cDNA transcriptome through reverse transcription, the patent creates targeted copies by sequencing only the probe sequences that contain encoded target molecule information. This selective copying approach maintains measurement precision by sequencing only the necessary information carriers (probes) rather than attempting to replicate the entire original transcriptome
3Productivity
If full-length cDNA sequencing is performed, then gene expression products can be determined, but the process becomes inefficient and costly
Solution Approach 1:
The patent applies partial action by sequencing only the probe sequences rather than full-length cDNA. Instead of sequencing the entire transcriptome (excessive action), the method sequences only the necessary probe portions that contain target molecule identification information, significantly reducing sequencing costs and increasing throughput while maintaining analytical accuracy
4Adaptability or versatility
If traditional reverse transcription method is used, then single-cell analysis can be performed, but simultaneous high-throughput analysis of multiple omics is not possible
Solution Approach 1:
The patent creates a universal platform where the same probe-based approach can simultaneously analyze multiple types of omics (transcriptome, proteome, metabolome, lipidome) by designing probes that target different molecular types. This multi-functional system enables simultaneous high-throughput analysis of multiple omics from single cells, as the probe hybridization and barcode attachment processes work universally across different molecule types
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 high-throughput, efficient, and cost-effective analysis of single-cell transcriptomics information, eliminating the need for reverse transcription and reducing systematic biases, thereby improving detection accuracy and scalability.
Implementation Method 1
contacting at least one target molecule in the sample with at least one probe, which contains a target molecule binding domain
Data Source
AI summary
A method for analyzing a target molecule from a sample, including contacting at least one target molecule in the sample with at least one probe, where the at least one probe contains a target molecule binding domain, and the target molecule binding domain is capable of specifically recognizing the at least one target molecule in the sample, attaching the at least one probe to a sample-specific barcode to obtain a barcoded probe, determining a composition of the barcoded probe, and determining a presence and/or content of the at least one target molecule in the sample from the composition of the barcoded probe.