Granted Patent B2

US 12,540,948 · App. 19/063,118 · Granted Feb 3, 2026

Inventors: Hei Mun Christina Fan (Palo Alto, CA); Janice Hoiyi Lai (Mountain View, CA); Sixing Li (Mountain View, CA); Stephen P.A. Fodor (Palo Alto, CA); Eleen Yee Lam Shum (San Carlos, CA)

Assignee: COUNTABLE LABS, INC.

G01N33/689C12Q1/6844G01N21/645G01N21/6486G01N2021/6482

Abstract

Claims (24)

1 . A method, comprising:

(a) distributing a sample comprising a set of targets across a set of partitions comprising at least 10 million partitions stabilized within a container, wherein a given partition of the set of partitions is surrounded by an immiscible film, and wherein the set of partitions is in a continuous phase immiscible with the immiscible film;

(b) amplifying nucleic acids associated with the set of targets within the set of partitions;

(c) in a container, detecting signals corresponding to the set of targets from multiple partitions of the set of partitions upon scanning a cross-section of the container; and

(d) using the signals detected in (c) to generate a count of the multiple partitions of the set of partitions.

2 . The method of claim 1 , wherein the set of targets comprises protein targets.

3 . The method of claim 2 , wherein (b) is performed according to a proximity ligation assay.

4 . The method of claim 1 , wherein (a) is performed using a non-microfluidic device.

5 . The method of claim 1 , wherein the set of partitions are provided as a gel-like emulsion.

6 . The method of claim 5 , wherein the gel-like emulsion has a level of clarity greater than a threshold level of clarity without refractive index matching between components of the gel-like emulsion, and wherein the threshold level of clarity comprises greater than 80% transmissivity of light.

7 . The method of claim 1 , wherein the sample is from a human subject.

8 . The method of claim 7 , further comprising detecting minimal residual disease in the human subject based on the count in (d).

9 . The method of claim 1 , wherein (b) comprises performing an isothermal amplification process.

10 . The method of claim 1 , wherein the set of targets comprises viral particles.

11 . The method of claim 1 , wherein the set of partitions comprises a set of droplets.

12 . The method of claim 1 , wherein the set of partitions are generated using a set of channels.

13 . The method of claim 1 , wherein (d) does not comprise use of Poisson statistics associated correction factors.

14 . The method of claim 1 , wherein (a) comprises driving the sample through a membrane aligned with an opening of the container.

15 . The method of claim 1 , wherein the sample comprises target nucleic acids from single cells.

16 . The method of claim 1 , wherein the container comprises wells.

17 . The method of claim 1 , wherein less than 10% of partitions of the set of partitions are occupied by a target of the set of targets.

18 . The method of claim 1 , wherein (c) comprises optically interrogating contents of the container using a 3D imaging technique.

19 . The method of claim 1 , wherein (c) comprises using a detection system for said detecting, wherein said detecting comprises optically interrogating the set of partitions using four color channels of the detection system.

20 . The method of claim 19 , wherein optically interrogating the set of the set of partitions is performed within 10 minutes.

Assignments (2)

Continuity (6)

References Cited (312)