Partitioned Probe Barcoding for Sensitive Multiplex Biomolecule Analysis
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Solution Overview
Problem
Existing methods for processing biological samples, such as nucleic acids and proteins, face challenges in achieving high sensitivity and multiplexed analysis while minimizing reagent usage and optimizing partition utilization.
Innovation Solution
A method involving hybridization of probes to target regions of nucleic acid molecules, followed by barcoding and extension processes, is performed within partitions like droplets or wells, allowing for the generation of barcoded nucleic acid molecules that can be further processed and analyzed.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional methods are used for processing biological samples, then basic detection can be achieved, but sensitivity and multiplexed analysis capability are limited
Solution Approach 1:
The patent divides the biological sample into multiple discrete partitions (droplets or wells), with each partition capable of independent processing. This segmentation enables parallel multiplexed analysis of multiple targets simultaneously, improving detection sensitivity through pooled signal accumulation while maintaining manageable complexity through standardized partition protocols
Solution Approach 2:
The patent implements nested barcoding where multiple levels of barcodes are combined - partition-level barcodes identify the specific partition, while sample-level barcodes identify individual samples within partitions. This nested structure enables high-dimensional multiplexed analysis without proportionally increasing operational complexity, as the hierarchical organization allows systematic data deconvolution
2Adaptability or versatility
If more partitions are used for multiplexed analysis, then analysis capability increases, but reagent usage increases
Solution Approach 1:
The patent merges multiple samples and multiple targets into shared partitions through pooled processing. Multiple barcoded samples can be combined in the same partition for simultaneous analysis of multiple nucleic acid targets, reducing total reagent consumption while maintaining multiplexed analysis capability through computational deconvolution of barcode signals
Solution Approach 2:
The patent employs universal reagents and protocols that function across all partitions and all sample types. The same barcoding chemistry, hybridization conditions, and detection methods are applied universally regardless of partition number or sample identity, enabling scalable multiplexed analysis without proportional increases in reagent complexity or usage
3Productivity
If partitions are optimized for high-throughput analysis, then productivity increases, but partition utilization efficiency decreases
Solution Approach 1:
The patent implements dynamic partition allocation where the number of samples per partition is not fixed but adapts based on sample availability and analysis requirements. Partitions can be dynamically filled to optimal capacity levels, and unused partition capacity can be utilized through pooled processing of additional samples, maintaining high throughput while maximizing utilization efficiency
Solution Approach 2:
The patent varies key parameters such as partition size, sample concentration, and barcode combination strategies to optimize the balance between throughput and utilization. By adjusting these parameters based on specific experimental needs, the system can maximize partition occupancy without compromising analysis quality or increasing reagent consumption
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 enhances sensitivity in genomic, transcriptomic, and exomic profiling, enabling efficient detection of variants and minimizing reagent usage by optimizing partition utilization.
Implementation Method 1
hybridizing a probe to a molecule of interest
Data Source
AI summary
Provided herein are systems and methods for processing biomolecules (e.g., nucleic acid molecules, proteins) from a sample. A method for processing biomolecules may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule) and barcoding the probe-nucleic acid molecule complex or derivatives thereof. Such a method can comprise performing a nucleic acid reaction, e.g., extension, denaturation, and amplification. A method for processing a sample may comprise hybridizing probes to (i) target regions of a nucleic acid molecule (e.g., RNA molecule) and (ii) a reporter oligonucleotide of a feature binding group, and barcoding the probe-associated molecules. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well.