Spatially Encoded Biological Assays
Patent No. US11008607 (titled "Spatially Encoded Biological Assays") was filed by Prognosys Biosciences Inc on Nov 13, 2020.
What is this patent about?
’607 is related to the field of biological assays, specifically those designed to determine the spatial distribution of biological molecules within a sample. Traditional methods like in situ hybridization and microarrays lack the ability to simultaneously measure many genes or proteins across numerous spatial locations with high resolution. This patent addresses the need for a reproducible, high-resolution method to map biological molecules in tissues.
The underlying idea behind ’607 is to create a spatially encoded assay system that combines high-throughput multiplexing with spatial information. This is achieved by delivering encoded probes to a biological sample in defined spatial patterns. Each probe interacts with a specific biological target (e.g., mRNA), and its associated coding tag identifies the location within the sample where the interaction occurred. By decoding these tags, the abundance and location of multiple targets can be simultaneously determined.
The claims of ’607 focus on a method for detecting a target mRNA in a tissue sample. This involves contacting the tissue with probes that have a capture agent (binding to the target mRNA) and an oligonucleotide sequence. The method then generates a nucleic acid molecule that includes the oligonucleotide sequence and one or more nucleic acid tags that indicate the location of the target mRNA. Finally, the sequence of this nucleic acid molecule is determined to both detect the target mRNA and pinpoint its location within the tissue sample.
In practice, the method involves several key steps. First, a tissue sample is treated with a set of probes, each designed to bind to a specific mRNA target. These probes are linked to oligonucleotides. Next, a nucleic acid molecule is created that incorporates the probe's oligonucleotide sequence along with spatial location tags. This molecule is then sequenced using high-throughput methods, allowing for the simultaneous identification of the target mRNA and its location within the tissue.
This approach differs significantly from prior methods by enabling highly multiplexed spatial analysis. Unlike traditional in situ hybridization, which is limited in the number of targets that can be simultaneously analyzed, ’607 allows for the detection of many targets at once. Furthermore, the use of high-throughput sequencing for decoding provides a digital readout, enabling quantitative analysis of target abundance at each spatial location. The spatial encoding scheme allows for the creation of detailed spatial maps of biological activity within tissues, opening new avenues for research and diagnostics.
How does this patent fit in bigger picture?
Technical landscape at the time
In the early 2010s when ’607 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 a time when technologies such as microarrays, SAGE, high-throughput implementations of qPCR and in situ PCR were available, no practical method existed to analyze at high resolution the spatial expression patterns of large numbers of genes, proteins, or other biologically active molecules simultaneously.
Novelty and Inventive Step
Claims were rejected during prosecution. Specifically, claims 2-10 and 13-33 were rejected under pre-AIA 35 U.S.C. § 102(b) as being anticipated by prior art. The prosecution record does NOT describe the technical reasoning or specific claim changes that led to allowance.
Claims
This patent contains 29 claims, with claim 1 being the only independent claim. Independent claim 1 focuses on a method for detecting a target mRNA in a tissue sample using probes with capture agents and oligonucleotide sequences, generating tagged nucleic acid molecules, and determining the sequence to detect the mRNA and its location. The dependent claims generally elaborate on and refine the method described in the independent claim, adding details such as separation steps, imaging, multiple probes, sequencing adapters, analysis of multiple regions, and tissue sample types.
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Date
Description
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US11008607
- Application Number
- US17097824
- Filing Date
- Nov 13, 2020
- Status
- Granted
- Expiry Date
- Apr 5, 2031
- External Links
- Slate, USPTO, Google Patents