Image Sensor Nanowell Layout for Simultaneous Paired-End Sequencing
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Solution Overview
Problem
Current image sensor structures for sequencing polynucleotide strands are time-consuming due to serial synthesis of forward and reverse strands, and suffer from increased probability of polyclonality and crosstalk with larger nanowells and closely spaced clusters.
Innovation Solution
The image sensor structure enables simultaneous paired-end sequencing by incorporating an array of light detectors, light guides, and nanowells with distinct primer sets in adjacent well regions, allowing for simultaneous attachment and sequencing of forward and reverse strand clusters.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If serial synthesis of forward and reverse strands is used, then sequencing can be performed, but the process is very time consuming
Solution Approach 1:
The patent divides a single nanowell into two distinct well regions (first well region and second well region), with each region containing different primer sets. This segmentation allows forward strands and reverse strands to be synthesized and sequenced simultaneously in separate regions, eliminating the time-consuming serial process while maintaining controlled reaction conditions in each region.
2Quantity of substance
If larger nanowells are used to accommodate larger clusters, then more polynucleotide strands can be sequenced, but the probability of polyclonality increases
Solution Approach 1:
By dividing the nanowell into two separate well regions with distinct primer sets, the patent effectively creates two independent reaction zones. This segmentation allows each region to maintain lower effective concentrations of polynucleotide strands, reducing the probability of multiple different strands being amplified simultaneously (polyclonality), while the overall nanowell size can still be large enough to accommodate sufficient clusters for high throughput sequencing.
3Productivity
If clusters are placed closer to each other to increase density, then throughput increases, but the probability of crosstalk increases
Solution Approach 1:
The division of the nanowell into two well regions with different primer sets creates distinct spatial zones for forward and reverse strand synthesis. This segmentation reduces light emission crosstalk between adjacent clusters by nearly half, as each cluster's signal is more localized to its specific region, allowing higher cluster density and improved throughput without sacrificing signal accuracy.
4Loss of time
If distinct primer sets are used in adjacent well regions for simultaneous sequencing, then sequencing time is reduced, but device complexity increases
Solution Approach 1:
The patent merges multiple functions into a single nanowell structure: both forward and reverse strand synthesis and sequencing occur within the same physical nanowell, but in separate well regions. This merging approach achieves simultaneous paired-end sequencing (reducing time) while avoiding the need for completely separate physical wells or complex additional components, thus limiting the increase in device complexity.
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 significantly reduces the time required for sequencing, minimizes the probability of polyclonality, and decreases crosstalk between adjacent clusters, thereby enhancing the throughput and accuracy of the sequencing process.
Implementation Method 1
The labeled strands may then emit photons of an emissive light, indicative of the order of nucleotide bases in the strand, which may be transmitted through the passivation stack and into light guides of the image sensor structure that are associated (e.g., located directly below) with each nanowell.
Implementation Method 2
The light guides direct the emissive light photons to light detectors disposed within the image sensor structure and associated with the light guides. The light detectors detect the emissive light photons.
Implementation Method 3
One or more excitation lights may then be directed onto the labeled strands within the nanowells. The labeled strands may then emit photons of an emissive light, indicative of the order of nucleotide bases in the strand
Data Source
AI summary
An image sensor structure includes an image layer having an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.