Integrated Flow Cell Photonics for Fluorescence Lifetime Sequencing
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Solution Overview
Problem
Current sequencing methods and systems face challenges in real-time single molecule sequencing due to complex chemistry and system implementations, which can be sub-optimal and inefficient.
Innovation Solution
An integrated detection, flow cell, and photonics (DFP) device is developed, comprising a substrate with photon-sensing pixel elements, waveguides for optical isolation, and a functionalization layer for sample binding, enabling efficient detection and analysis of fluorescence signals.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If real-time single molecule sequencing is implemented, then sequencing speed and real-time detection capability are improved, but system complexity and chemical process complexity increase
Solution Approach 1:
The system divides the sequencing process into discrete cycles, each handling a single nucleotide type (A, T, G, or C). Each cycle is self-contained with specific reagents and detection parameters, allowing modular implementation and reducing overall system complexity while maintaining high throughput sequencing capability
Solution Approach 2:
The system performs preliminary preparation of nucleotides with reversible terminators and fluorescent labels before the sequencing reaction. This pre-preparation allows the actual sequencing to proceed in a streamlined fashion, reducing real-time complexity while maintaining speed
2Measurement precision
If reversible terminator chemistry is used for single-base incorporation, then sequencing accuracy is improved, but chemical complexity and reaction time increase
Solution Approach 1:
The system modifies nucleotide parameters by incorporating reversible terminators that control the reactivity of the 3'-OH group. This parameter change ensures that only one nucleotide can be incorporated per cycle, improving accuracy while the terminator can be easily removed in the next cycle, reducing chemical complexity
Solution Approach 2:
The reversible terminator acts as an intermediary that temporarily blocks further nucleotide incorporation after a single base is added. This intermediary structure ensures precise single-base incorporation accuracy while being designed for easy removal, balancing accuracy requirements with chemical simplicity
3Measurement precision
If fluorescent labels are used for nucleotide identification, then detection capability is improved, but background noise and signal interference increase
Solution Approach 1:
The system uses periodic excitation of fluorescent labels with synchronized detection windows. By exciting fluorophores at specific times and detecting signals during defined periods, the system maximizes signal capture while minimizing background noise from continuous illumination
Solution Approach 2:
The system replaces continuous illumination with pulsed optical excitation. This substitution reduces background noise by eliminating continuous light exposure while maintaining detection capability through timed fluorescence excitation and detection cycles
4Loss of information
If multiple sequencing cycles are performed, then complete sequence information is obtained, but total time and resource consumption increase
Solution Approach 1:
The system maintains continuous sequencing action by immediately transitioning from one nucleotide incorporation cycle to the next after terminator removal. Reagents are continuously flowed through the system, and detection parameters are continuously adjusted, eliminating idle time between cycles and reducing total sequencing time while obtaining complete 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
The DFP device enhances the efficiency and accuracy of sequencing by enabling real-time detection of single molecules, improving system complexity and optimizing set-up for more effective sequencing processes.
Implementation Method 1
a photonics layer for conveying excitation light to sample sites
Implementation Method 2
a substrate having an array of pixel elements that sense photons during active periods
Implementation Method 3
fluorescence chemistry and fluorescence lifetime decay information
Data Source
AI summary
An integrated detection, flow cell and photonics (DFP) device is provided that comprises a substrate having an array of pixel elements that sense photons during active periods. The substrate and pixel elements form an IC photon detection layer. At least one wave guide is formed on the IC photo detection layer as a photonics layer. An optical isolation layer is formed over at least a portion of the wave guide. A collection of photo resist (PR) walls patterned to define at least one flow cell channel that is configured to direct fluid along a fluid flow path. The wave guides align to extend along the fluid flow path. The flow cell channel is configured to receive samples at sample sites that align with the array of pixel elements.