Multi-Template Synchronous Sequencing for Paired-End Throughput
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Solution Overview
Problem
Current paired-end sequencing methods require sequential sequencing of both DNA strands, limiting throughput and increasing costs.
Innovation Solution
A method involving amplification techniques to generate sequencing chips with multiple nucleic acid templates, adjusting copy numbers or primer concentrations to achieve signal variations, and applying crosstalk and phasing correction parameters for simultaneous sequencing of multiple templates.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequential paired-end sequencing is performed on both DNA strands, then sequencing accuracy is improved, but sequencing throughput decreases and costs increase
Solution Approach 1:
The patent merges the sequencing of first strand and second strand into a single synchronous sequencing reaction. Multiple nucleic acid templates (both first strand and second strand) are loaded onto the same sequencing chip and sequenced simultaneously in one reaction cycle, eliminating the need for sequential processing while maintaining accuracy through signal differentiation techniques.
Solution Approach 2:
The patent changes the parameter of template concentration by adjusting the relative copy numbers of different nucleic acid templates within a cluster. By controlling the concentration ratios of first strand and second strand templates, the system enables signal intensity variations that allow differentiation and accurate base-calling for both strands simultaneously.
2Measurement precision
If sequential paired-end sequencing is performed on both DNA strands, then sequencing accuracy is improved, but sequencing time increases
Solution Approach 1:
The patent combines two separate sequencing reactions (first strand and second strand) into a single synchronous reaction. Both strands are sequenced in parallel on the same chip during one sequencing run, reducing the total sequencing time while maintaining accuracy through computational signal separation and crosstalk correction.
Solution Approach 2:
The patent enables continuous sequencing action by performing both first strand and second strand sequencing without interruption or intermediate steps. The synchronous sequencing approach eliminates the sequential workflow where one strand must complete before the other begins, achieving uninterrupted parallel processing.
3Measurement precision
If sequential paired-end sequencing is performed on both DNA strands, then base-calling accuracy is improved, but sequencing costs increase
Solution Approach 1:
The patent merges multiple sequencing reactions into a single synchronous reaction on one chip. By sequencing both first strand and second strand simultaneously in one run rather than requiring two separate runs, the system reduces reagent consumption, instrument time, and operational costs while maintaining base-calling accuracy through signal differentiation.
4Productivity
If multiple nucleic acid templates are sequenced simultaneously, then sequencing throughput is improved, but signal differentiation becomes more difficult
Solution Approach 1:
The patent applies local quality by creating spatial differentiation within the cluster. Different nucleic acid templates (first strand and second strand) are positioned at different locations within the same cluster, and their signal intensities are differentiated based on their specific spatial positions and concentration ratios, enabling accurate signal separation despite simultaneous sequencing.
Solution Approach 2:
The patent uses parameter changes in template concentration to enable signal differentiation. By adjusting the relative copy numbers of different nucleic acid templates, the system creates distinct signal intensity patterns that allow computational algorithms to differentiate and accurately call bases for each template type during synchronous sequencing.
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
Significantly reduces sequencing time and costs while improving throughput, making it suitable for widespread application.
Implementation Method 1
hybridizing the plurality of nucleic acid templates with corresponding sequencing primers
Implementation Method 2
performing, by use of the sequencing primers, a plurality of sequencing reaction cycles
Data Source
AI summary
Provided are a multi-template nucleic acid synchronous sequencing method and use thereof. The method includes: providing a plurality of composite nucleic acid template spots, with a plurality of nucleic acid templates being arranged in the plurality of composite nucleic acid template spots; hybridizing the plurality of nucleic acid templates with corresponding sequencing primers thereof; performing, by use of the sequencing primers, a plurality of sequencing reaction cycles on each of the plurality of nucleic acid templates hybridized with the sequencing primers, wherein in each of the plurality of sequencing reaction cycles, signal intensities generated by the plurality of nucleic acid templates exhibit variations from one another; and classifying sequencing channel signals into the plurality of nucleic acid templates based on the variations in the signal intensities for each of the plurality of sequencing reaction cycles.