Optimized Nucleotide Flow Orders for Sequencing Synchrony
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Sequencing-by-Synthesis (SBS) techniques face challenges with phasic synchrony errors, leading to incomplete extension and carry-forward issues that limit read length and degrade sequence data quality, as a significant fraction of template molecules lose synchrony during the sequencing process.
Innovation Solution
The implementation of recursive methods and systems to generate optimized flow orders that minimize phasic synchrony errors by simulating sequence data acquisition and selecting orderings based on read length and extension rate parameters, allowing for cyclic repetition to re-synchronize nucleotide incorporation across a population of template molecules.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional SBS techniques are used with standard nucleotide flow orders, then sequencing can be performed, but phasic synchrony errors accumulate leading to incomplete extension and carry-forward issues that limit read length and degrade data quality
Solution Approach 1:
The patent applies parameter changes by optimizing the flow order of nucleotide species introduction based on template sequence composition. By dynamically adjusting which nucleotide species are introduced at each cycle and in what order, the system maintains phasic synchrony across longer read lengths. The flow order is selected to match the expected nucleotide sequence, ensuring that the correct nucleotide is always available for incorporation, thereby preventing incomplete extension and carry-forward errors that would otherwise accumulate with longer reads.
2Measurement precision
If a large number of template molecules are sequenced simultaneously, then signal strength is sufficient for detection, but a significant fraction of molecules lose synchrony during the sequencing process
Solution Approach 1:
The patent applies local quality by tailoring the flow order to the specific sequence composition of each template molecule or population. Instead of using a universal flow order for all templates, the system determines the optimal flow order based on the expected nucleotide sequence at each position. This localized optimization ensures that each template molecule receives the correct nucleotide species at the right time, maintaining synchrony across the entire population while enabling accurate signal detection.
3Ease of manufacture
If nucleotide species are introduced in standard cyclic order, then the sequencing process is simple to implement, but incomplete extension and carry-forward errors accumulate over successive cycles
Solution Approach 1:
The patent applies dynamics by making the flow order adaptive rather than static. The system dynamically selects and changes the flow order based on the sequence position and expected nucleotide composition. This dynamic adjustment prevents the accumulation of incomplete extension and carry-forward errors that occur with fixed cyclic orders, while still maintaining a relatively simple implementation through automated flow order selection based on template sequence information.
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 extends the reliable read length and improves the accuracy of nucleic acid sequencing by reducing the accumulation of phasic synchrony errors, enabling longer high-quality reads and enhancing the synchronization of nucleotide incorporation across the sequencing process.
Implementation Method 1
the polymerase will extend the primer with the nucleotide species
Implementation Method 2
incorporation of the nucleotide species can be detected by a variety of methods known in the art, e.g. by detecting the release of pyrophosphate (PPi) or Hydrogen (H+)
Data Source
AI summary
An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.