Methods, devices, and systems for analyte detection and analysis

Patent metadata

Field	Value
Publication number	US-11268143-B2
Application number	US-202117308241-A
Country	US
Kind code	B2
Filing date	May 5, 2021
Priority date	Mar 14, 2019
Publication date	Mar 8, 2022
Grant date	Mar 8, 2022

Abstract

Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

First claim

What is claimed is:

1. A method for dispensing a sample to a substrate surface, comprising: dispensing, via a sample dispenser, a sample solution comprising a plurality of beads onto said substrate surface along a path while said substrate surface and said sample dispenser are in relative motion, wherein said substrate surface comprises a plurality of individually addressable locations that receives and immobilizes said plurality of beads, wherein said substrate surface comprises a first location and a second location, wherein said first location has a higher affinity for a bead of said plurality of beads than said second location, wherein said first location comprises an individually addressable location of said plurality of individually addressable locations, and wherein subsequent to said dispensing, said bead is immobilized at said first location.

2. The method of claim 1 , wherein said substrate surface is substantially planar.

3. The method of claim 1 , wherein said substrate surface is patterned.

4. The method of claim 3 , wherein said substrate surface is patterned using surface chemistry.

5. The method of claim 1 , wherein said path is in a substantially spiral pattern.

6. The method of claim 5 , wherein said sample solution is dispensed onto said substrate surface in said substantially spiral pattern in a radially outward direction with respect to a central axis of said substrate surface.

7. The method of claim 5 , wherein said sample solution is dispensed onto said substrate surface in said substantially spiral pattern in a radially inward direction with respect to a central axis of said substrate surface.

8. The method of claim 5 , wherein a path width of said path is greater than a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

9. The method of claim 5 , wherein a path width of said path is less than a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

10. The method of claim 5 , wherein a path width of said path is substantially the same as a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

11. The method of claim 1 , wherein during said dispensing said sample dispenser is moving.

12. The method of claim 1 , wherein during said dispensing said substrate surface is moving.

13. The method of claim 12 , wherein during said dispensing (i) said substrate surface is rotating with respect to a rotational axis and (ii) said sample dispenser is moving with respect to said rotational axis of said substrate surface or said substrate surface is moving such that said rotational axis is moving with respect to said sample dispenser.

14. The method of claim 13 , wherein said substrate surface is rotating at a rotational frequency of no more than 5 revolutions per minute (rpm).

15. The method of claim 1 , wherein said plurality of beads comprises a first subset of beads and a second subset of beads, wherein said first subset of beads each comprises a respective template nucleic acid sequence coupled thereto and said second subset of beads does not comprise a template nucleic acid sequence coupled thereto.

16. The method of claim 15 , wherein subsequent to said dispensing said first subset of beads is immobilized to individually addressable locations of said plurality of individually addressable locations and said second subset of beads is not immobilized to said plurality of individually addressable locations.

17. The method of claim 1 , wherein said bead comprises a plurality of nucleic acid molecules having sequence identity.

18. The method of claim 1 , wherein said plurality of individually addressable locations comprise at least 50,000,000,000 individually addressable locations.

19. The method of claim 1 , wherein said substrate surface comprises a set of first locations and a set of second locations different from said set of first locations, wherein said set of first locations comprises said first location, and wherein said set of second locations comprises said second location.

20. The method of claim 19 , wherein said first location is not in contact with another first location of said set of first locations.

21. The method of claim 20 , wherein said set of first locations and said set of second locations are alternating locations on said substrate surface.

22. The method of claim 19 , wherein said set of first locations carries a positive electrostatic charge with affinity towards a negative electrostatic charge, wherein said bead comprises a nucleic acid molecule coupled thereto, which nucleic acid molecule carries said negative electrostatic charge.

23. The method of claim 22 , wherein said set of first locations comprises (3-aminopropyl)triethoxysilane (APTMS), and wherein said second set of locations comprises hexamethyldisilazane (HMDS).

Assignees

• Ultima Genomics Inc

Inventors

• Beckett Nathan
• Almogy Gilad
• Caswell Nathan
• Wolf Jacob A
• Barbee Kristopher
• Pristinski Denis
• Pratt Mark
• Polovy Gene
• Schwartz Osip
• Kubecka Stephanie
• Menchen Steven
• Anthony Joseph
• Sosa Jose Martin
• Lee Phillip You Fai

Classifications

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q1/6816

  characterised by the detection means (C12Q1/6804 takes precedence) · CPC title

• G01N1/312 Primary

  for samples mounted on planar substrates · CPC title

• G01N35/1002

  Reagent dispensers · CPC title