Methods, devices, and systems for analyte detection and analysis
Inventors
Beckett, Nathan • Almogy, Gilad • Caswell, Nathan • WOLF, Jacob A. • Barbee, Kristopher • Pristinski, Denis • Pratt, Mark • Polovy, Gene • Schwartz, Osip • KUBECKA, Stephanie • Menchen, Steven • Anthony, Joseph • SOSA, Jose Martin • Lee, Phillip You Fai
Assignees
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Publication Number
US-12031180-B2
Publication Date
2024-07-09
Expiration Date
Abstract
Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
Core Innovation
The invention relates to methods for applying sequencing reagents to an open substrate that is moving relative to multiple dispensers during or after dispensing. A first solution comprising a plurality of labeled nucleotides of a base type is dispensed from a first dispenser to the open substrate, and a second solution comprising a plurality of unlabeled nucleotides of the same base type is dispensed from a second dispenser to the open substrate.
During or subsequent to dispensing, the open substrate is moving relative to the first dispenser and the second dispenser to disperse the first solution and the second solution, respectively, across the open substrate. The disclosure includes rotating planar arrays and patterned deposition concepts, including spiral, circular, and linear, striped, cross-hatched, and diagonal patterns.
In a sequencing-by-synthesis context, the document describes directing nucleotide solutions to rotating planar arrays, optionally combining labeled and unlabeled nucleotides on the substrate, and performing washing and signal detection. It also describes optical or fluorescence imaging, label cleavage or muting signal concepts, iterative cycles, and timing or synchronization between dispensing and imaging.
The document further describes system architectures for high-throughput sequencing on an open, moving substrate using multi-fluid channels or nozzles for multiple solutions, recycling with filtering, rotating and/or translating fluidics and detector systems, environmental control or barrier systems for open substrate operation, and imaging-system concepts for continuous area scanning and mitigation of tangential velocity blur for fluorescence detection.
Claims Coverage
The independent claim covers a dispensing method using two dispensers that deliver labeled and unlabeled nucleotide solutions of the same base type to an open substrate while the substrate moves relative to the dispensers to disperse both solutions across the substrate. Dependent claims narrow the motion geometry, timing relationship of dispensing, formation of labeled and unlabeled mixtures on the substrate, additional processing using a washing solution, and optional imaging synchronization.
Dispensing labeled and unlabeled nucleotide solutions to an open moving substrate
Dispensing a first solution comprising a plurality of labeled nucleotides of a base type from a first dispenser to an open substrate, and dispensing a second solution comprising a plurality of unlabeled nucleotides of said base type from a second dispenser to said open substrate, wherein the open substrate is moving relative to said first dispenser and said second dispenser during or subsequent to each of said dispensing to disperse said first solution and said second solution, respectively, across said open substrate.
Rotating the open substrate about a perpendicular axis
Moving the open substrate by rotating it about a rotational axis perpendicular to the surface.
Simultaneous dispensing of first and second nucleotide solutions
Dispensing the first solution and the second solution at substantially the same time.
Dispensing first and second nucleotide solutions at different time points
Dispensing the first solution and the second solution at different time points.
Forming a labeled and unlabeled nucleotide mixture on the open substrate
Forming a mixture on the open substrate that includes labeled nucleotides and unlabeled nucleotides.
Synchronizing imaging with dispensing
Synchronizing imaging of the open substrate with dispensing the first solution.
Compensating for tangential velocity differences across radial positions
The apparatus compensates for differences in tangential velocity across radial positions by scan-rate changes and processing, with anamorphic magnification gradients associated with different illuminated regions and radial positions.
Across the independent and dependent claims, the core coverage is the use of two dispensers delivering labeled and unlabeled nucleotides of the same base type to an open substrate while the substrate moves to disperse both solutions across the substrate. Dependent refinements specify rotation geometry, concurrent versus different-time dispensing, forming mixtures of labeled and unlabeled nucleotides on the substrate, synchronization of imaging with dispensing, and compensation for tangential velocity differences across radial positions.
Stated Advantages
Reducing or avoiding barcoding.
Documented Applications
Nucleic-acid sequencing using nucleic acids immobilized on an uncovered/open array and detecting incorporation signals as nucleotide solutions are dispensed across the moving open substrate.
Multiplex sample processing using spatial indexing, including avoiding barcoding.
Nucleic-acid sequencing/imaging [procedural detail omitted for safety].
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