# US 2021/0172007 A1 · Methods and systems for determining spatial patterns of biological targets in a sample

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- Number: US 2021/0172007 A1
- Document ID: US20210172007A1
- Status: Published application
- Kind: A1
- Application number: 17/180,356
- Filed: 2021-02-19
- Published: 2021-06-10
- Earliest claimed: 2013-06-25
- Assignees: Prognosys Biosciences, Inc.
- Applicants: Prognosys Biosciences, Inc.
- Inventors: Mark S. CHEE; David A. ROUTENBERG
- Web page: https://patentgrep.com/patent/US20210172007A1

## CPC

- C12Q 1/6809: Methods for determination or identification of nucleic acids involving differential detection
- C12Q 1/6853: using modified primers or templates
- B01L 3/502761: {specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads or physically stretching molecules}
- C12Q 1/6841: In situ hybridisation
- B01L 3/5027: {by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip}
- B01L 2300/0636: Integrated biosensor, microarrays
- B01L 2300/0816: Cards, e.g. flat sample carriers usually with flow in two horizontal directions
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE

## Abstract

The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.

## Claims

### Claim 1

A method of determining a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample, comprising:
delivering a probe for each of one or more biological targets to multiple sites in a sample, wherein each probe comprises: (1) a target-binding moiety capable of binding to the probe's corresponding biological target; (2) an address tag that identifies each of the multiple sites to which the probe is delivered; and (3) an identity tag that identifies the probe's corresponding biological target or target-binding moiety;
allowing each probe to bind to its corresponding biological target in the sample;
analyzing the probe bound to the one or more biological targets, the analysis comprising: (1) determining abundance, expression, and/or activity of each of the one or more biological targets by assessing the amount of the probe bound to the biological target; and (2) determining the identities of the identity tag and the address tag of the probe; and
determining a spatial pattern of abundance and/or activity of the one or more biological targets across the multiple sites in the sample based on the analysis,
wherein the method does not depend on an imaging technique for determining spatial information of the one or more biological targets in the sample.