Reflective Fiducials for Nucleic Acid Array Alignment
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Solution Overview
Problem
As the density and size of features on nucleic acid arrays increase, accurate detection and alignment become challenging, leading to issues in comparing successive images and determining molecular sequences, which complicates genetic sequencing and increases economic and time costs.
Innovation Solution
Incorporating an optically reflective fiducial feature on the array support that returns incident radiation, allowing for precise location and registration during fluorescent imaging, regardless of the biological samples' visibility, using fiducial features such as Bragg gratings or metallic materials, and encoding information in their layout and structure.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the density of features on the array increases and feature size decreases, then the array capacity and information content improve, but the accuracy of detection and alignment deteriorates
Solution Approach 1:
The patent introduces fiducial features as intermediary reference elements that are distinct from the biological samples. These fiducial features serve as mediators for alignment and registration, providing stable reference points that do not interfere with the biological samples while enabling accurate positioning even as sample density increases
Solution Approach 2:
The fiducial features utilize optical reflectivity differences to create distinguishable signals. By making fiducial features optically reflective while biological samples are fluorescent, the system creates contrasting signal types that can be easily differentiated during imaging, maintaining detection accuracy despite increased feature density
2Area of stationary object
If the overall size of the array expands, then the array capacity increases, but the difficulty of accurate detection and alignment increases
Solution Approach 1:
The patent divides the large array into multiple smaller fields of view by placing multiple fiducial features throughout the array area. Each fiducial feature serves as a local reference point for its surrounding region, allowing the imaging system to accurately locate and align each field of view independently, thereby managing the alignment complexity of large arrays
3Quantity of substance
If the number and density of sites on the array increase, then the array capacity improves, but the ability to accurately locate and align sites in successive cycles deteriorates
Solution Approach 1:
The fiducial features are permanently formed in or on the support structure, creating stable reference copies that remain unchanged across successive imaging cycles. These reference copies provide consistent alignment markers that enable accurate registration of multiple images taken at different times, maintaining alignment stability despite increased site density
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 solution enables robust and accurate registration of images across successive cycles, improving the accuracy of sequence analysis and reducing errors, thereby enhancing the efficiency and cost-effectiveness of nucleic acid sequencing processes.
Implementation Method 1
a fiducial feature that is formed in or on the support and that is optically reflective to, during imaging, return at least a portion of incident radiation
Implementation Method 2
the fiducial feature comprises a Bragg grating
Data Source
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AI summary
Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include features and materials that are provided on or in the support of the array and that return at least a portion of incident light by reflection. The fiducials may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the array.