Resolving spatial arrays using deconvolution
Inventors
Bent, Zachary • Ramachandran Iyer, Eswar Prasad • Mikkelsen, Tarjei Sigurd
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-12545949-B2
Publication Date
2026-02-10
Expiration Date
Abstract
Methods for determining a location of a feature on a spatial array include (a) providing an array of features on a substrate, where a feature of the array includes a barcoded oligonucleotide having, in a 5′ to 3′ direction, a spatial barcode, a cleavage domain, and a constant sequence; (b) hybridizing a priming oligonucleotide to the constant sequence; (c) extending the priming oligonucleotide using the barcoded oligonucleotide as a template; and (d) determining all or a portion of a sequence of the extended priming oligonucleotide corresponding to the spatial barcode, or a complement thereof, and a location of the extended priming oligonucleotide, and using the location of the extended priming oligonucleotide to determine the location of the feature on the spatial array.
Core Innovation
The invention provides a method for identifying a location of an analyte in a biological sample by using an array comprising a plurality of features on a substrate. Each feature includes an oligonucleotide comprising a first spatial barcode and a capture probe comprising a second spatial barcode and a capture domain. The first and second spatial barcodes are linked to locations on the substrate through sequence-based mapping.
A priming oligonucleotide hybridizes to the oligonucleotide by including a sequence that is substantially complementary to a portion of the oligonucleotide, and is extended using the oligonucleotide as a template to generate an extended priming oligonucleotide. The method determines all or a portion of the sequence of the extended priming oligonucleotide and determines a location of the extended priming oligonucleotide, then determines a sequence and a location of the first spatial barcode and a location of the second spatial barcode based on the location of the first spatial barcode.
The location of the extended priming oligonucleotide is associated with the location of the first spatial barcode. After the mapping, the capture domain captures the analyte from the biological sample, and the location of the analyte is identified based on the location of the second spatial barcode. The disclosure further provides embodiments in which the barcoded oligonucleotide includes a cleavage domain and constant sequence, and the cleavage domain enables release of the extended priming oligonucleotide for sequencing or partial sequencing associated with spatial barcode deconvolution.
Claims Coverage
The document includes one independent claim directed to identifying a location of an analyte in a biological sample using array features that carry two spatial barcodes and a capture domain, with barcode locations established by priming and extension and sequence and location determination of an extended priming oligonucleotide. The independent claim includes three main inventive features, with dependent refinements referenced for barcode relationships, capture-domain criteria, cleavage-domain options, and sequencing modality.
Array feature with first and second spatial barcodes
Providing an array comprising a plurality of features on a substrate, where a feature comprises an oligonucleotide comprising a first spatial barcode and a capture probe comprising a second spatial barcode and a capture domain.
Priming and extension generating an extended priming oligonucleotide
Hybridizing a priming oligonucleotide to the oligonucleotide, and extending the priming oligonucleotide using the oligonucleotide as a template to generate an extended priming oligonucleotide.
Sequence-based location mapping and analyte identification
Determining all or a portion of the sequence of the extended priming oligonucleotide and a location of the extended priming oligonucleotide; determining a sequence and a location of the first spatial barcode and a location of the second spatial barcode based on the location of the first spatial barcode; associating the location of the extended priming oligonucleotide with the location of the first spatial barcode; capturing the analyte from the biological sample with the capture domain; and identifying the location of the analyte in the biological sample based on the location of the second spatial barcode.
The claims coverage centers on mapping a spatial sequence determination from an extended priming oligonucleotide to the first spatial barcode and then using the capture domain and the second spatial barcode location to identify analyte location in a biological sample.
Stated Advantages
Improves library complexity (substrate-based isothermal nucleic acid amplification).
Provides correlative gene-expression matching across capture areas (reported correlations).
Documented Applications
Spatially barcoded analyte profiling, emphasizing RNA spatial transcriptomics.
Use with tissue workflows involving immunofluorescence/immunohistochemistry and correlation of gene-expression matching across captured regions.
Interested in licensing this patent?