Nanopore Sequencing AC Signal Differencing for Voltage Variability
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Solution Overview
Problem
Nanopore-based DNA sequencing technologies face challenges in accurately determining nucleotides due to manufacturing variability in nanopore chips, leading to inconsistent voltage measurements across cells, which complicates the identification of correct molecules.
Innovation Solution
Implementing a differencing technique using AC waveforms applied to nanopore sequencing systems to analyze voltage differences and identify threading events, allowing for the determination of nucleotides without requiring extensive filtering or external parameters, thus enhancing accuracy and robustness.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If voltage measurements are taken across nanopore cells, then nucleotide detection can be performed, but manufacturing variability causes inconsistent measurements that reduce accuracy
Solution Approach 1:
The patent creates a reference voltage trace from a first AC cycle and compares it against voltage traces from subsequent AC cycles. This copying approach allows the system to account for manufacturing variability by using the actual measured reference trace from the same chip and conditions, rather than relying on theoretical or average values. The reference trace captures the specific characteristics of that nanopore chip instance, enabling accurate comparison and nucleotide identification despite chip-to-chip variations.
2Reliability
If AC waveforms are applied to detect threading events, then nucleotide identification can be achieved, but noise and systematic variations complicate the detection process
Solution Approach 1:
The patent extracts and removes the reference trace component from the subsequent voltage traces through subtraction. By taking out the systematic variations and noise patterns that are present in the reference cycle, the system isolates the actual nucleotide-specific signals. This extraction process eliminates common-mode noise and systematic variations, leaving only the differential signals that contain the nucleotide identification information.
Solution Approach 2:
Instead of trying to detect threading events directly from the raw voltage traces, the patent inverts the approach by first establishing what the trace should look like without threading events (the reference trace), then subtracting this from the actual traces. This inversion strategy transforms the problem from direct detection to differential analysis, making the nucleotide-specific signals more prominent and easier to identify against the background noise.
3Productivity
If period-to-period differencing is performed, then the detection process is simplified and accelerated, but multiple AC cycles are required
Solution Approach 1:
The patent performs preliminary action by acquiring and storing the reference voltage trace from the first AC cycle before processing subsequent cycles. This reference trace is prepared in advance and can be reused for comparing multiple subsequent cycles, eliminating the need to re-establish baseline characteristics for each comparison. The preliminary acquisition of the reference data enables rapid differential analysis of multiple nucleotide incorporation events without repeated setup overhead.
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 simplifies and speeds up the nucleotide detection process by eliminating noise and adapting to local systematic variations, improving the accuracy and reliability of nanopore sequencing.
Implementation Method 1
When a voltage signal is applied across a nanopore immersed in a conducting fluid, the electric field can move ions in the conducting fluid through the nanopore.
Implementation Method 2
The movement of ions in the conducting fluid through the nanopore can cause a small ion current.
Implementation Method 3
The level of the ion current (or a corresponding voltage) depends on the sizes and chemical structures of the nanopore and the particular molecule that has been moved into the nanopore.
Data Source
AI summary
An alternating signal is applied across a nanopore of a sequencing cell, the nanopore being configured to receive a tag that is connected to a nucleotide, thereby creating a threading event. A first set of voltage data is acquired during a first portion of a plurality of cycles of the alternating signal. Each data point of the first set of voltage data corresponds to a value of a resistance of the nanopore at a different time, where the resistance of the nanopore changes when the tag is received within the nanopore. A shifted set of voltage data is determined from the first set of voltage data and difference data is computed by computing differences between data points of the first set of voltage data and corresponding data points of the shifted set of voltage data. Threading events may be identified based on the difference data.