Spatially encoded biological assays

What is this patent about?

’030 is related to the field of spatially encoded biological assays and high-resolution mapping of biological molecules within a sample. Traditional methods like laser capture microdissection or standard in situ hybridization often struggle to balance high levels of multiplexing with the preservation of precise spatial context. The invention addresses the need for a scalable system that can simultaneously measure the abundance and location of thousands of different nucleic acids or proteins across a tissue section, effectively merging the visual resolution of histology with the data density of modern sequencing.

The underlying idea behind ’030 is the use of a substrate-bound array of capture probes that act as localized anchors for biological targets, where each anchor is pre-encoded with a unique digital address. By utilizing a surface populated with beads that carry these specific capture sequences, the system can trap target molecules from an overlying tissue section while simultaneously tagging them with a location-specific barcode. This allows the spatial organization of the sample to be preserved in a digital format, enabling the researcher to pool all reacted probes for efficient analysis without losing the information regarding where each molecule originated in the original tissue structure.

The claims of ’030 focus on a composition featuring an array where a plurality of beads is attached to a substrate in a random pattern, each carrying specialized capture probes. These probes are structured linearly from the bead surface to include a primer binding site, a spatial nucleic acid sequence that identifies the bead's unique location, and a target-binding domain designed to hybridize with specific nucleic acids. Crucially, the independent claims specify that the location-identifying sequence is distinct and not intended to hybridize with the target itself, and they further cover the integration of this bead-based array with a tissue section disposed directly onto the surface.

In practice, the invention functions by placing a biological sample, such as a thin tissue slice, in direct contact with the bead array. The biological targets—typically RNA or DNA—are released from the tissue and hybridize to the target nucleic acid-binding domain of the adjacent capture probes. Once the targets are captured, the spatial information is locked to the biological data through enzymatic extension or ligation. The resulting chimeric molecules, containing both the target sequence and the unique location identifier, are then collected and analyzed using high-throughput sequencing to reconstruct a high-definition map of the sample’s molecular landscape.

This approach differentiates itself from prior art by moving away from rigid, pre-defined grids or labor-intensive physical microdissection. By employing a random pattern of beads that are subsequently decoded, the system achieves a high density of sampling points that can resolve features at or near the single-cell level. Unlike conventional microarrays that require specific targets to be directed to specific spots, this architecture allows for a universal capture surface where the spatial barcode is the primary mechanism for reassembling the tissue image, providing a digital readout that is both highly multiplexed and spatially precise.