Spatially encoded biological assays

Patent No. US11001879 (titled "Spatially encoded biological assays") on Jan 8, 2021. The application was issued on May 11, 2021.

’879 is related to the field of spatial genomics and high-resolution biological assays. It addresses the technical challenge of mapping the distribution and abundance of biological molecules, such as nucleic acids and proteins, within a complex tissue structure while maintaining the original spatial context of those molecules.

The underlying idea behind ’879 is the use of spatially encoded probes that link a biological target's identity to its physical coordinates in a sample. By delivering unique coding tags to specific locations in a defined pattern, the invention allows researchers to pool assay products for efficient analysis without losing the information regarding where each molecule originated.

The claims of ’879 focus on a method for determining the presence or abundance of a nucleic acid at a specific location in a tissue section using a capture agent array. This process involves contacting the tissue with an array of features, where each feature contains a capture agent comprising a target-binding sequence and a location-specific coding tag.

In practice, the invention functions by capturing target molecules directly from a tissue section onto a support. Once the targets are bound to the capture agents, the resulting constructs—containing both the target sequence and the spatial tag—are sequenced. This digital readout allows the abundance of specific transcripts or proteins to be computationally mapped back to their precise coordinates in the tissue.

This approach differs from prior methods like laser capture microdissection or standard in situ hybridization by enabling high-level multiplexing and random access to tissue samples. Unlike traditional assays that require physical separation of tissue into wells, this system uses combinatorial tagging and high-throughput sequencing to provide a scalable, high-resolution map of cellular function across a large area.

How does this patent fit in bigger picture?

Technical Landscape

In the early 2010s when ’879 was filed, the analysis of biological molecules in tissue samples was typically implemented using in situ hybridization or laser capture microdissection, which provided spatial information but suffered from limited multiplexing capabilities. At a time when systems commonly relied on the physical transference of tissue into discrete wells for quantitative analysis, achieving high spatial resolution across a large number of targets was restricted by the labor-intensive nature of sample preparation and the scaling limitations of existing hardware. Furthermore, when software and hardware constraints made the simultaneous measurement of thousands of gene expression patterns across a two-dimensional sample non-trivial, researchers were often forced to choose between high-resolution spatial mapping and the comprehensive data depth provided by bulk sequencing methods.

Prosecution Position

The disclosed invention represents a meaningful technical advancement through the integration of spatial encoding schemes with high-throughput digital sequencing to enable highly multiplexed, high-resolution mapping of biological targets. By utilizing an architectural shift where encoded probes—comprising both a target-binding region and a location-specific coding tag—are delivered to a sample in a known spatial pattern, the system overcomes the technical constraint of losing positional context during large-scale analysis. This approach enables the simultaneous detection of thousands of biological targets across multiple sites by pooling reaction products for parallel sequencing and subsequently mapping the digital readout back to the original coordinates. The resulting technical effect is the ability to generate reproducible, high-resolution spatial maps of cellular function and regulation that combine the visual resolution of histology with the massive data capacity of next-generation sequencing.

Claims

This patent contains 30 claims, with claim 1 serving as the sole independent claim. The independent claim focuses on a method for determining the presence or abundance of a nucleic acid at specific locations within a tissue section by using an array of features containing capture agents that include both a binding sequence and a location-specific coding tag. The dependent claims serve to specify various technical parameters, such as the types of nucleic acids and tissue sections used, the physical structure of the array features, the specific steps for sequencing and amplification, and methods for imaging or mapping the resulting data.

Key Claim Terms New

Definitions of key terms used in the patent claims.

Term (Source)	Support for Specification	Interpretation
Array (Claim 1)	The assay system can utilize an encoding scheme that comprises a 2-dimensional grid format based on the discrete positioning of the binding agents in the substrate surfaces. In another example, the spatial patterns may be based on more randomized cell locations, e.g., the patterns on the substrate surface follow an underlying biological structure rather than a strict, x,y grid pattern. The assay system and methods of the invention are based on relational, solid-state substrates with positions that represent specific spatial locations within a biological sample, e.g., a cell, organelle or tissue.	A substrate surface containing a plurality of discrete features or sites arranged in a known spatial pattern for localized reagent delivery or target capture.
Capture agent (Claim 1)	The assay systems utilize one or more binding agents that specifically bind to the biological molecule of interest and unique coding identifiers associated with specific binding agents. In specific aspects of the invention, the binding agents are nucleic acids immobilized directly or indirectly to the substrate surface, e.g., directly through the use of amino groups on the substrate surface or indirectly through the use of a linker. Each encoded probe comprises a probe region that may interact with the biological targets and a coding tag that identifies a location of the site to which the encoded probe was delivered.	A molecular construct, typically an oligonucleotide, designed to specifically bind a target nucleic acid and provide a spatial identifier for that interaction.
Coding tag (Claim 1)	An encoding scheme used in these assay systems allows one to determine the location of biological targets or activity (or lack thereof) in the biological samples after the products of the multiplexed assay are removed from the biological sample and pooled for analysis. The encoding scheme of the assay system comprises the use of two or more coding patterns, each comprising regions defined by spatial patterns on the substrate surface. The ability to use encoding features to represent locations allows high-throughput analysis of the presence or absence, and relative amount, of a biological molecule at more than one spatial location in a sample.	A unique nucleotide sequence identifier that corresponds to a specific spatial location on the array, allowing for the decoding of positional information.
Determining the sequence (Claim 1)	“Sequencing”, “sequence determination” and the like means determination of information relating to the nucleotide base sequence of a nucleic acid. Decoding of the encoding scheme can be performed by, e.g., next-generation sequencing, which easily provides millions to trillions of data points at low cost. “High throughput digital sequencing” or “next generation sequencing” means sequence determination using methods that determine many (typically thousands to billions) of nucleic acid sequences in an intrinsically parallel manner.	The process of identifying the nucleotide base order of the coding tag and the target nucleic acid, typically using high-throughput parallel methods.
Tissue section (Claim 1)	The assay systems of the invention detect the presence or absence and relative amount of a biological target or biological activity indicative of a biological target, as well as the location of the biological target or activity in a biological sample, e.g., a tissue section or other biological structure disposed upon a support such as a microscope slide or culture dish. For example, the assay may be designed to preserve the relative position of cells in a tissue, and the assay may interrogate the individual cells for genomic DNA variation (including epigenetic modifications), and RNA and protein expression. Furthermore, the spatial organization of mutant cells can be observed, which may be particularly important in detecting key mutations in tissue sections in cancer.	A biological sample consisting of a slice or layer of tissue that preserves the spatial organization of its constituent cells and molecules for analysis.

Litigation Cases New

US Latest litigation cases involving this patent.

Case Number	Filing Date	Title
1:23-cv-01375	Dec 1, 2023	10X Genomics, Inc. V. Curio Bioscience, Inc.

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US11001879

Application Number: US17144971A
Filing Date: Jan 8, 2021
Publication Date: May 11, 2021
External Links: Slate, USPTO , Google Patents

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