Adaptive Sequencing by Synthesis Feedback Control
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Solution Overview
Problem
Current sequencing by synthesis methods are inefficient due to the repetitive cycling through all four nucleotides, which can result in low nucleotide incorporation rates and increased time requirements, especially when the sequence to be detected is partially or fully known.
Innovation Solution
The method optimizes nucleotide flow by selecting a predetermined order based on predicted sequences, using feedback from the reaction to revise the sequence and adapt the nucleotide order, allowing for higher incorporation rates and reduced reagent use.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If nucleotides are added in a continuous repeat of all four nucleotides (A, C, G, T), then the sequencing reaction can proceed through the template strand, but the nucleotide incorporation efficiency is low (1 in 4) and the sequencing time is increased
Solution Approach 1:
The patent applies preliminary action by predicting the sequence of the polynucleotide strand before sequencing begins. Based on this predicted sequence, the nucleotide dispensation order is pre-optimized to match the expected sequence pattern. This allows the sequencing reaction to proceed with much higher efficiency (potentially 1 in 1 incorporation) rather than the conventional 1 in 4 efficiency, significantly reducing sequencing time while maintaining accuracy through feedback mechanisms.
2Measurement precision
If a single type of nucleotide is added at a time to the polymerase reaction, then the specific nucleotide incorporated can be detected, but multiple nucleotide flows are necessary to obtain information on a single base
Solution Approach 1:
The patent applies dynamics by making the nucleotide dispensation order adaptive rather than static. The system continuously monitors the sequencing reaction and uses feedback to revise the predicted sequence and adjust the nucleotide dispensation order in real-time. This dynamic approach maintains measurement precision by accurately detecting which nucleotide is incorporated while simultaneously improving productivity by optimizing the dispensation order based on actual sequence information gained during the reaction.
3Productivity
If the nucleotide flow order is optimized based on predicted sequence, then the sequencing efficiency increases, but the system complexity increases due to feedback mechanisms and sequence revision
Solution Approach 1:
The patent applies feedback by continuously monitoring the sequencing reaction to detect which nucleotide is incorporated at each position. This experimental sequence information is used to revise the predicted sequence and adjust the nucleotide dispensation order for subsequent cycles. The feedback mechanism resolves the contradiction by enabling high sequencing efficiency through optimized nucleotide flow while maintaining system manageability through iterative refinement rather than requiring complete prior knowledge of the sequence.
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 increases the efficiency of nucleotide incorporation from 1 in 4 to potentially 1 in 1, reducing sequencing time and reagent consumption, while enabling more accurate and efficient sequencing of targeted sequences.
Implementation Method 1
Nucleotide strands complementary to a target polynucleotide fragment are extended by incorporation of nucleotides (eg, dNTPs) by a polymerase enzyme
Implementation Method 2
the incorporation is detected; for example, by fluorescence or by detection of hydrogen ions released during polymerisation
Data Source
AI summary
Described is a method for sequencing a polynucleotide strand by sequencing by synthesis, the method including selecting a predetermined order of nucleotides to provide to a sequencing reaction, the order being selected to correlate with a predicted sequence for the polynucleotide strand;monitoring the reaction to detect incorporation of a nucleotide into a synthesised polynucleotide strand;wherein, in the event that nucleotide incorporation is detected, proceeding to provide the next nucleotide in the predetermined order.In the event that nucleotide incorporation is not detected, the predicted sequence for the polynucleotide strand may be revised and a new predetermined order of nucleotides selected, wherein the new predetermined order is selected to correlate with the revised predicted sequence.In this way, the sequencing reaction provides feedback to modify the order of nucleotides provided, thereby improving the efficiency of the sequencing reaction.