Granted Patent B2

US 12,319,964 · App. 18/745,574 · Granted Jun 3, 2025

Inventors: Eleen Yee Lam Shum (San Carlos, CA); Hei Mun Christina Fan (Palo Alto, CA); Stephen P.A. Fodor (Palo Alto, CA); Janice Hoiyi Lai (Mountain View, CA); Jung Won Keum (Palo Alto, CA); Haeun Grace Lee (Palo Alto, CA)

Assignee: Countable Labs, Inc.

C12Q1/6876G01N21/6428G01N33/542C12Q2600/156C12Q2600/16G01N2021/6439

Abstract

Claims (27)

1. A method comprising:

(a) providing a plurality of partitions comprising at least 500,000 partitions, wherein the plurality of partitions comprises:

(i) a plurality of target nucleic acid molecules; and

(ii) processing materials,

wherein a partition of the plurality of partitions comprises two or fewer target nucleic acid molecules of the plurality of target nucleic acid molecules;

(b) in the plurality of partitions, reacting the processing materials with the nucleic acid molecules;

(c) using an imaging system to scan the plurality of partitions across a set of channels to detect signals from at least a subset of the plurality of partitions, wherein each channel of the set of channels comprises a different filter configuration, wherein the number of targets of the set of targets is greater than the number of channels of the set of channels; and

(d) using the signals detected in (c) to identify at least a subset of the plurality of target nucleic acid molecules.

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

3. The method of claim 2 , wherein the droplets are in an emulsion.

4. The method of claim 1 , wherein (b) comprises binding the nucleic acid molecules with probes.

5. The method of claim 4 , wherein the probes comprise hydrolysis probes.

6. The method of claim 4 , wherein the probes comprise TaqMan™ probes.

7. The method of claim 1 , wherein (d) comprises processing the signals detected in (c) against a set of pre-determined signal combinations to identify the at least the subset of the plurality of target nucleic acid molecules.

8. The method of claim 7 , wherein a first signal combination of the set of signal combinations comprises a first color and first signal amplitude and a second signal combination of the set of signal combinations comprises the first color and second signal amplitude, wherein the first signal amplitude and second signal amplitude are different.

9. The method of claim 1 , wherein the set of partitions comprises a set of wells.

10. The method of claim 1 , wherein the plurality of target nucleic acid molecules comprise cell-free nucleic acid molecules.

11. The method of claim 10 , wherein the cell-free nucleic acid molecules are human cell-free nucleic acid molecules.

12. The method of claim 11 , wherein the human cell-free nucleic acid molecules are derived from a cancer.

13. The method of claim 1 , wherein the processing materials comprise a dye.

14. The method of claim 13 , wherein the dye comprises an EvaGreen® dye.

15. The method of claim 1 , wherein the set of channels comprise at least four channels.

16. The method of claim 1 , wherein the set of channels comprise at least six channels.

17. The method of claim 1 , wherein the target nucleic acid molecules are viral nucleic acid molecules.

18. The method of claim 1 , further comprising determining a copy number variation (CNV) of a target nucleic acid molecule of the plurality of target nucleic acid milecules based at least on part on (c).

19. The method of claim 1 , wherein (a) comprises generating the set of partitions, wherein at least 20,000 partitions of the at least 500,000 partitions are generated from a sample volume of less than 50 microliters.

20. The method of claim 1 , wherein the set of partitions comprises at least 1 million partitions.

Assignments (2)

Continuity (5)

References Cited (248)