Spatially Encoded Biological Assays
Patent No. US11549138 (titled "Spatially Encoded Biological Assays") was filed by Prognosys Biosciences Inc on May 26, 2022.
What is this patent about?
’138 is related to the field of biological assays, specifically those used to determine the spatial distribution of biological molecules within a sample. Traditional methods like in situ hybridization and microarrays have limitations in simultaneously measuring multiple targets at numerous spatial locations. There is a need for high-resolution spatial maps of biological molecules in tissues.
The underlying idea behind ’138 is to create a system that combines high-throughput multiplexing with spatial encoding to map biological activity in tissues. This is achieved by delivering encoded probes to a biological sample in defined spatial patterns. Each probe has a region that interacts with a biological target and a coding tag that identifies the location where the probe was delivered. By sequencing these tags, the abundance or activity of the targets can be mapped back to their original locations in the sample.
The claims of ’138 focus on an array comprising a substrate and a plurality of capture probes. Each capture probe has a target-binding domain, a nucleic acid sequence that identifies a unique location on the substrate, and a primer binding site. The target-binding domain includes a nucleic acid sequence complementary to at least a portion of the nucleic acid that binds to the target-binding domain. The capture probes are immobilized on the substrate in a random pattern. A related claim covers the same array with a tissue section disposed on it.
In practice, the system works by affixing a biological sample, such as a tissue section, to the array. The encoded probes are then delivered to the sample in a controlled manner, allowing them to interact with the biological targets of interest. After washing away unbound probes, the coding tags of the bound probes are sequenced using high-throughput sequencing. The resulting sequence data is then used to create a spatial map of the biological targets within the sample, showing their abundance or activity at different locations.
This approach differs from prior methods by enabling simultaneous measurement of many biological targets at many spatial locations with high resolution. Unlike laser capture microdissection, it is scalable and less laborious. The use of high-throughput sequencing for decoding the spatial information allows for a digital readout with millions or even billions of data points. The combinatorial encoding scheme , using pairs of coding tags, maximizes the efficiency of encoding and reduces the number of oligonucleotides required.
How does this patent fit in bigger picture?
Technical landscape at the time
In the early 2010s when ’138 was filed, comprehensive gene expression analysis and protein analysis were useful tools in understanding mechanisms of biology, at a time when in situ hybridization and multiplexed detection of different transcripts revealed spatial patterns of gene expression. At that time, technologies that enabled the quantitative analysis of many RNA sequences per sample included microarrays, serial analysis of gene expression (SAGE), high-throughput implementations of qPCR and in situ PCR.
Novelty and Inventive Step
The examiner allowed the claims because the prior art, taken alone or in combination, including the art cited in the Information Disclosure Statement, does not teach a composition comprising an array with a substrate and capture probes. Each capture probe has: (i) a target-binding domain, (ii) a unique nucleic acid sequence that identifies a location on the substrate and does not hybridize to a nucleic acid that binds to the target-binding domain, and (iii) a primer binding site. The target-binding domain has a nucleic acid sequence complementary to at least part of the nucleic acid that binds to the target-binding domain. The capture probes are immobilized on the substrate in a random pattern.
Claims
This patent contains 30 claims, with claims 1 and 17 being independent. The independent claims are directed to compositions comprising arrays with capture probes immobilized on a substrate in a random pattern, with claim 17 further including a tissue section disposed on the array. The dependent claims generally specify details and variations of the composition, such as the pattern of immobilization, attachment methods, array components, and the nature of the biological sample or nucleic acids.
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Date
Description
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US11549138
- Application Number
- US17825719
- Filing Date
- May 26, 2022
- Status
- Granted
- Expiry Date
- Apr 5, 2031
- External Links
- Slate, USPTO, Google Patents