Integrated sequencing apparatuses and methods of use

• US 8,637,242 B2
• Filed: 11/06/2012
• Issued: 01/28/2014
• Est. Priority Date: 11/07/2011
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Shen, Min-Jui Richard, Kain, Robert C., Kuhn, Kenneth M., Talasaz, AmirAli Hajhossein, Jamshidi, Arash
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): Zhang, Kaijiang
• Application Number:
  US13/670,318
• Publication Number:
  US 20130116128A1
• Time in Patent Office: 448 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: B01L 2200/0673 Handling of plugs of fluid surrounded by immiscible fluid
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/069 Absorbents; Gels to retain a fluid
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0851 Bottom walls
• CPC Class Codes: B01L 2300/165 Specific details about hydrophobic, oleophobic surfaces
• CPC Class Codes: B01L 2400/0427 Electrowetting
• CPC Class Codes: B01L 3/502792 for moving individual droplets on a plate, e.g. by locally altering surface tension
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation

Abstract

Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.

Claims

1. An apparatus for manipulating droplets comprising a substrate comprising an array of dynamic pads for performing droplet operations, wherein for at least a subset of the array of dynamic pads, each pad comprises a hydrophilic patch,

wherein the ratio of the area of the hydrophilic patch to the dynamic pad allows the droplet to move from a first dynamic pad comprising the patch to a second dynamic pad, and

wherein the dynamic pad is an electrowetting control pad comprising an electrode covered by a hydrophobic layer.

2. The apparatus of claim 1, wherein the size of the patch is smaller than the first dynamic pad.

3. The apparatus of claim 1, wherein the hydrophilic patch remains hydrophilic regardless of whether the first dynamic pad is in a hydrophilic or hydrophobic state.

4. The apparatus of claim 1, wherein the electrowetting control pad is the same size as the electrode.

5. The apparatus of claim 1, wherein the hydrophilic patch is on the same plane as the hydrophobic layer.

6. The apparatus of claim 1, wherein the first dynamic pad comprises a well comprising the hydrophilic patch.

7. The apparatus of claim 1, wherein the hydrophilic patch is comprised of one or more hydrophilic areas being separated from one another on the first dynamic pad.

8. The apparatus of claim 1, wherein the hydrophilic patch comprises a gel capable of indirect or direct nucleic acid molecule attachment.

9. The apparatus of claim 1, wherein the hydrophilic patch comprises one or more nucleic acids.

10. A method of moving a droplet, comprising the steps of:

(a) providing the apparatus of claim 1;

(b) moving a droplet on the substrate surface onto a first dynamic pad comprising a hydrophilic patch; and

(c) moving the droplet from the first dynamic pad to a second dynamic pad.

11. The method of claim 10, wherein the hydrophilic patch of step (b) comprises one or more primers.

12. The method of claim 11, wherein the droplet of step (b) comprises a plurality of nucleic acid molecules capable of hybridizing to the primers.

13. The method of claim 10, wherein the droplet of step (b) comprises one or more nucleic acid sequencing reagents.

14. The method of claim 10, wherein the droplet manipulation apparatus comprises a fill liquid that is immiscible to the droplet, and wherein the fill liquid flows past the droplet under a force that is independent of forces placed on the fluid by the droplet.

15. The method of claim 10, wherein the size of the hydrophilic patch is smaller than the first dynamic pad.

16. The method of claim 10, wherein the hydrophilic patch remains hydrophilic regardless of whether the electrowetting control pad is active.

17. The method of claim 10, wherein the electrowetting control pad is the same size as the electrode.

18. The method of claim 10, wherein the hydrophilic patch is on the same plane as the hydrophobic layer.

19. The method of claim 10, wherein the hydrophilic patch is comprised of one or more hydrophilic areas being separated from one another.

20. The method of claim 10, wherein the hydrophilic patch of step (b) comprises one or more nucleic acid molecules to be sequenced.

21. A method of sequencing a nucleic acid molecule, the method comprising the steps of:

(a) providing the apparatus of claim 1;

(b) transporting a droplet comprising one or more nucleic acid molecules to be sequenced to the hydrophilic patch;

(c) immobilizing the one or more nucleic acid molecules;

(d) sequencing the one or more nucleic acid molecules.

22. The method of claim 21, wherein the hydrophilic patch comprises one or more primers.

23. The method of claim 22, wherein step (c) includes hybridizing the nucleic acid molecules to the primers.

24. The method of claim 21, wherein prior to step (d) the nucleic acid molecules are amplified.

25. The method of claim 21, wherein the size of the patch is smaller than the first dynamic pad.

26. The method of claim 21, wherein the hydrophilic patch remains hydrophilic regardless of whether the electrowetting control pad is active.

27. The method of claim 21, wherein the electrowetting control pad is the same size as the electrode.

28. The method of claim 21, wherein the hydrophilic patch is on the same plane as the hydrophobic layer.

29. The method of claim 21, wherein the hydrophilic patch is comprised of one or more hydrophilic areas being separated from one another.