Integrated device with external light source for probing detecting and analyzing molecules

• US 9,678,012 B2
• Filed: 09/02/2016
• Issued: 06/13/2017
• Est. Priority Date: 08/08/2014
• Status: Active Grant

• Current Assignee: Quantum-Si Incorporated
• Original Assignee: Quantum-Si Incorporated
• Inventors: Rothberg, Jonathan M., Kabiri, Ali, Gyarfas, Brett J., Lackey, Jeremy, Schmid, Gerard, West, Lawrence C., Cipriany, Benjamin, Sickler, Jason W., Fife, Keith G., Ghasemi, Farshid
• Primary Examiner(s): Nur, Abdullahi
• Application Number:
  US15/255,303
• Publication Number:
  US 20160370292A1
• Time in Patent Office: 284 Days
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6463 Optics
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 21/6408 with measurement of decay time, time resolved fluorescence
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6454 using an integrated detector array
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• CPC Class Codes: G01N 2201/064 Stray light conditioning
• CPC Class Codes: G01N 2201/0696 Pulsed
• CPC Class Codes: G01N 2201/08 Optical fibres; light guides
• CPC Class Codes: G01N 2201/12 Circuits of general importance; Signal processing

Abstract

System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample.

Claims

1. An integrated device comprising:

a plurality of sample wells on a surface of the integrated device, wherein a sample well of the plurality of sample wells is configured to receive a sample;

a first grating coupler configured to receive excitation energy from an external optical source;

a reflective layer positioned to reflect light towards the first grating coupler, wherein the reflective layer includes four openings;

four sensors, each of the four sensors positioned to receive light through one of the four openings of the reflective layer, wherein signals from the four sensors provide an indication of alignment of the external optical source to the first grating coupler; and

a plurality of waveguides, wherein a first waveguide of the plurality of waveguides and a second waveguide of the plurality of waveguides are optically coupled to the first grating coupler, wherein the first waveguide and the second waveguide are configured to receive excitation energy from the first grating coupler and deliver the excitation energy to at least a portion of the plurality of sample wells.

2. The integrated device of claim 1, wherein the sample is a biological sample, the sample well is configured to retain the biological sample, and the excitation energy excites at least a portion of the biological sample.

3. The integrated device of claim 1, wherein the integrated device further comprises a second grating coupler optically coupled to an end of the first waveguide distal from the first grating coupler.

4. The integrated device of claim 3, wherein the second grating coupler is configured to direct light to a fifth sensor of the integrated device, and wherein the fifth sensor is configured to generate a signal indicative of a power of excitation energy coupled out of the first waveguide.

5. The integrated device of claim 1, wherein the integrated device further comprises a splitter optically coupled to the first grating coupler, the first waveguide, and the second waveguide, wherein the splitter is configured to receive excitation energy from the first grating coupler and direct excitation energy to the first waveguide and the second waveguide.

6. The integrated device of claim 5, wherein the splitter is selected from the group consisting of a multi-mode interference splitter, a star splitter, and a Y splitter.

7. The integrated device of claim 1, wherein the first grating coupler is positioned in the same plane of the integrated device as the first waveguide and is formed of the same layer of the integrated device as a core material of the first waveguide.

8. The integrated device of claim 1, wherein the first waveguide is tapered in a dimension perpendicular to a direction of light propagation of the first waveguide.

9. The integrated device of claim 1, wherein the first waveguide has a ridge that overlaps with at least one sample well of the plurality of sample wells.

10. The integrated device of claim 1, wherein the first waveguide is positioned to evanescently couple excitation energy to a first portion of the plurality of sample wells, and the second waveguide is positioned to evanescently couple excitation energy to a second portion of the plurality of sample wells.

11. The integrated device of claim 1, wherein the integrated device further comprises a sensor positioned to receive luminescence emitted by a sample positioned in a sample well of the plurality of sample wells.

12. The integrated device of claim 11, wherein the sensor positioned to receive luminescence emitted by a sample positioned in a sample well is configured to generate a signal indicative of lifetime of luminescence emitted by the sample in response to the excitation energy.

13. The integrated device of claim 11, wherein the sensor positioned to receive luminescence emitted by a sample positioned in a sample well is configured to aggregate charge carriers produced by received photons of the luminescence into at least two time bins over different time intervals with respect to a reference time.

14. The integrated device of claim 13, wherein the sensor positioned to receive luminescence emitted by a sample positioned in a sample well is configured to generate a signal indicative of the relative number of photons arrived within each of the different time intervals.

15. The integrated device of claim 11, wherein the sensor positioned to receive luminescence emitted by a sample positioned in a sample well is configured to detect the luminescence after the excitation energy has substantially turned off at the sample well.

16. The integrated device of claim 1, wherein the integrated device further comprises a metal layer on the surface of the integrated device, wherein the plurality of sample wells extend below the metal layer.

17. The integrated device of claim 1, wherein a depth of a sample well of the plurality of sample wells is between 50 nanometers (nm) to 500 nm.

18. The integrated device of claim 1, wherein a surface of the sample well is positioned from the first waveguide by a distance between 50 nm to 250 nm.

19. The integrated device of claim 1, wherein the sidewalls of a sample well of the plurality of sample wells are tapered.

20. A method of fabricating an integrated device, the method comprising:

forming a layer having a plurality of grating couplers and a plurality of waveguides, wherein a first waveguide of the plurality of waveguides and a second waveguide of the plurality of waveguides are optically coupled to a first grating coupler of the plurality of grating couplers;

forming a reflective layer positioned to reflect light towards the first grating coupler, wherein the reflective layer includes four openings;

forming four sensors, each of the four sensors positioned to receive light through one of the four openings of the reflective layer, wherein signals from the four sensors provide an indication of alignment of excitation energy to the first grating coupler; and

forming a plurality of sample wells on a surface of the integrated device, wherein a sample well of the plurality of sample wells is configured to receive a sample, and the first waveguide and the second waveguide are configured to receive excitation energy from the first grating coupler and deliver excitation energy to at least a portion of the plurality of sample wells.

21. The method of claim 20, wherein forming the layer having the plurality of grating couplers and the plurality of waveguides further comprises forming a second grating coupler of the plurality of grating couplers optically coupled to an end of the first waveguide distal from the first grating coupler.

22. A system comprising:

an excitation source module comprising;

an optical source configured to generate a beam of excitation energy; and

an alignment mechanism configured to position the beam of excitation energy relative to the integrated device; and

an integrated device comprising;

a plurality of sample wells on a surface of the integrated device, wherein a sample well of the plurality of sample wells is configured to receive a sample;

a first grating coupler configured to receive the excitation energy;

at least one sensor positioned to receive light that passes through the first grating coupler, wherein the at least one sensor is configured to generate a signal indicative of alignment of the beam of excitation energy to the first grating coupler; and

a plurality of waveguides, wherein a first waveguide of the plurality of waveguides and a second waveguide of the plurality of waveguides are optically coupled to the first grating coupler, wherein the first waveguide and the second waveguide are configured to receive excitation energy from the first grating coupler and deliver excitation energy to at least a portion of the plurality of sample wells.

23. The system of claim 22, wherein the integrated device further comprises:

a second grating coupler optically coupled to an end of the first waveguide distal from the first grating coupler; and

a second sensor configured to detect light directed from the second grating coupler and generate a signal indicative of the power of the excitation energy coupled out of the first waveguide.

24. A method for exciting a sample, the method comprising:

providing a sample in a sample well of a plurality of sample wells on a surface of an integrated device, wherein the integrated device further comprises;

a first grating coupler configured to receive excitation energy from an external optical source;

at least one sensor configured to receive light that passes through the first grating coupler and generate a signal indicative of alignment of a beam of excitation energy to the first grating coupler; and

a plurality of waveguides, wherein a first waveguide of the plurality of waveguides and a second waveguide of the plurality of waveguides are optically coupled to the first grating coupler, wherein the first waveguide and the second waveguide are configured to receive excitation energy from the first grating coupler and deliver the excitation energy to at least a portion of the plurality of sample wells including the sample well; and

coupling excitation energy from the external optical source to the first grating coupler to deliver excitation energy to the at least a portion of the plurality of sample wells by using an alignment mechanism configured to position a beam of excitation energy relative to the integrated device, wherein the first sample well is positioned to receive excitation energy from the first waveguide and the excitation energy is configured to optically excite the sample.

25. The method of claim 24, wherein the integrated device further comprises a second grating coupler optically coupled to an end of the first waveguide distal from the first grating coupler.

26. The method of claim 25, wherein the second grating coupler is configured to direct light to a second sensor of the integrated device, and wherein a signal from the second sensor is indicative of a power of the excitation energy coupled out of the first waveguide.