Spatially encoded biological assays

What is this patent about?

’022 is related to the field of spatially encoded biological assays and high-throughput molecular analysis. 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. Traditional methods like in situ hybridization provide spatial context but lack the ability to analyze thousands of targets simultaneously, while sequencing methods offer high multiplexing but typically lose the original spatial orientation of the molecules during sample processing.

The underlying idea behind ’022 is the decoupling of target detection from spatial localization through a programmable encoding scheme. Instead of relying on physical isolation of tissue segments, the invention uses probes that capture biological information and are subsequently tagged with location-specific nucleic acid sequences. This allows the spatial context of a molecule to be converted into a digital barcode that can be read by standard high-throughput sequencing instruments, effectively turning a 2D tissue map into a pool of searchable, sequenceable data.

The claims of ’022 focus on a method for determining the spatial location of a biological molecule using a plurality of beads. These beads serve as the physical carriers for binding agents, where each agent includes a coding identifier—a specific nucleic acid sequence—that corresponds to a known location. By contacting these beads with a tissue sample, the binding agents interact with their respective biological targets. The spatial origin of each target is then reconstructed by identifying the associated coding identifier during the analysis phase.

In practice, the system utilizes instrumentation to deliver reagents or beads in defined spatial patterns, such as an x,y grid, onto a tissue section affixed to a support. When the probes interact with the targets, they are either pre-coupled to their coding identifiers or tagged in situ. Once the interaction is complete, the tagged probes are collected, pooled, and analyzed via next-generation sequencing. The resulting data set contains both the identity of the biological molecule and the coordinate-specific barcode, allowing software to map the quantitative expression levels back onto the original tissue architecture.

This approach differs from prior art by enabling massive multiplexing without the labor-intensive requirements of laser capture microdissection or the resolution limits of physical tissue transfer. By using digital nucleic acid sequencing as the readout, the invention provides a high dynamic range and the sensitivity to detect rare mutations or low-abundance transcripts. The use of combinatorial tagging—where different sets of tags define rows and columns—further optimizes the process, allowing a small number of unique sequences to define a vast number of discrete spatial locations across the sample.