Integrated analytical system and method

• US 10,640,825 B2
• Filed: 10/17/2017
• Issued: 05/05/2020
• Est. Priority Date: 02/19/2010
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: McCaffrey, Nathaniel Joseph, Turner, Stephen, Saxena, Ravi, Helgesen, Scott Edward
• Primary Examiner(s): Nguyen, Sang H
• Application Number:
  US15/786,215
• Publication Number:
  US 20180155781A1
• Time in Patent Office: 931 Days
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0663 Whole sensors
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/168 Specific optical properties, e.g. reflective coatings
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B82Y 20/00 Nanooptics, e.g. quantum optics or photonic crystals
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• 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 2021/0346 Capillary cells; Microcells
• CPC Class Codes: G01N 2021/6434 Optrodes
• 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 2021/757 using immobilised reagents
• CPC Class Codes: G01N 2021/7786 Fluorescence
• CPC Class Codes: G01N 21/03 Cuvette constructions
• CPC Class Codes: G01N 21/0303 Optical path conditioning in cuvettes, e.g. windows; adapted optical elements or systems; path modifying or adjustment G01N21/031 - G01N21/15 take precedence
• CPC Class Codes: G01N 21/05 Flow-through cuvettes G01N21/09 takes precedence; handling fluid samples G01N1/10
• CPC Class Codes: G01N 21/253 : for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• CPC Class Codes: G01N 21/64 : Fluorescence; Phosphorescence
• 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 21/645 : Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6454 : using an integrated detector array
• CPC Class Codes: G01N 21/6456 : Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 21/648 : using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• CPC Class Codes: G01N 21/75 : Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated systems in which material is burnt in a flame or plasma G01N21/72, G01N21/73
• CPC Class Codes: G01N 21/77 : by observing the effect on a chemical indicator
• CPC Class Codes: G01N 2201/067 : Electro-optic, magneto-optic, acousto-optic elements
• CPC Class Codes: G01N 2201/068 : Optics, miscellaneous
• CPC Class Codes: G01N 2201/08 : Optical fibres; light guides
• CPC Class Codes: G01N 33/54373 : involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G02B 6/1226 : involving surface plasmon interaction
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed.

Claims

1. A sequencing chip comprising:

a plurality of analytical devices, each analytical device having a reaction cell, an optical element and a detection element;

one or more integrated waveguides in optical communication with the reaction cells to deliver a pulsed illumination light to the reaction cells, wherein for each respective analytical device in the plurality of analytical devices;

a sample is disposed in the reaction cell and emits photons in response to the pulsed illumination light;

the optical element is in optical communication with the reaction cell and the detection element to deliver the photons emitted from the sample in the reaction cell to the detection element; and

the detection element comprises a plurality of storage elements, and is configured to;

convert the photons into charges;

relegate each respective charge into a storage element in the plurality of storage elements; and

integrate the charges over time in each storage element in the plurality of storage elements to generate a plurality of electrical data signals;

and

one or more electrical contacts electrically connected with the detection elements for transmitting the electrical data signals.

2. The sequencing chip of claim 1, wherein relegation of each respective charge into a storage element in the plurality of storage elements is based on at least one event associated with the photon that is converted into the respective charge.

3. The sequencing chip of claim 1, wherein:

the sample comprises a plurality of labeled species at different excitation spectra;

the pulsed illumination light comprises a plurality of excitation sources at different wavelengths; and

relegation of each respective charge into a storage element is based on the timing of a corresponding excitation source of the pulsed illumination light, a delay between the corresponding excitation and subsequent emission, an arrival time of the photon at the detection element relative to the corresponding excitation source of the pulsed illumination light, or any combination thereof.

4. The sequencing chip of claim 3, wherein the plurality of storage elements is synchronized with the plurality of excitation sources of the pulsed illumination light such that charges converted from photons emitted in response to different excitation sources are regulated into different storage elements.

5. The sequencing chip of claim 4, wherein each respective storage element in the plurality of storage elements is electrically gated by activation of a corresponding excitation source in the plurality of excitation sources of the pulsed illumination light to correlate each respective storage element with the corresponding excitation source.

6. The sequencing chip of claim 4, wherein a delay between the corresponding excitation source of the pulsed illumination light and its subsequent emission event is pre-programed in each analytical device in synchronization of the storage elements with the excitation sources.

7. The sequencing chip of claim 4, wherein each respective storage element in the plurality of storage elements is turned off during intermediate stages of the illumination process to reduce noise contribution.

8. The sequencing chip of claim 4, wherein the electrical data signals are used to classify the plurality of labeled species in the sample.

9. The sequencing chip of claim 1, wherein:

the sample comprises a plurality of labeled species at different excitation spectra;

the pulsed illumination light comprises a plurality of excitation sources at different wavelengths; and

the detection element is configured as a vertical detector, and relegation of each respective charge into a storage element is based on a depth of absorption of the photon that relates to an energy level of the photon.

10. The sequencing chip of claim 1, wherein relegation of each respective charge into a storage element is based on an arrival time of the photon at the detection element relative to a corresponding pulse of the pulsed illumination light.

11. The sequencing chip of claim 10, wherein the electrical data signals are representative of a decay of a labeled species in the sample.

12. The sequencing chip of claim 1, wherein the sequencing chip comprises at least 1000 analytical devices, at least 10,000 analytical devices, at least 100,000analytical devices, or at least 1,000,000 analytical devices.

13. A nucleic acid sequencing instrument, comprising:

the sequencing chip of claim 1,

a fluidic sample delivery device in fluidic communication with the sequencing chip to deliver the sample to the sequencing chip;

an illumination source in optical communication with the integrated waveguides of the sequencing chip to provide the pulsed illumination light for sequencing the sample on the sequencing chip; and

a processing system in electrical communication with the one or more electrical contacts of the sequencing chip to retrieve the electrical data signals from the sequencing chip, and classify species in accord with the retrieved electrical data signals.

16. The nucleic acid sequencing instrument of claim 13, wherein relegation of each respective charge into a storage element in the plurality of storage elements is based on at least one event associated with the photon that is converted into the respective charge.

17. The nucleic acid sequencing instrument of claim 13, wherein:

the sample comprises a plurality of labeled species at different excitation spectra;

the pulsed illumination light comprises a plurality of excitation sources at different wavelengths; and

relegation of each respective charge into a storage element is based on the timing of a corresponding excitation source of the pulsed illumination light, a delay between the corresponding excitation and subsequent emission, an arrival time of the photon at the detection element relative to the corresponding excitation source of the pulsed illumination light, or any combination thereof.

18. The nucleic acid sequencing instrument of claim 17, wherein the plurality of storage elements is synchronized with the plurality of excitation sources of the pulsed illumination light such that charges converted from photons emitted in response to different excitation sources are regulated into different storage elements.

19. The nucleic acid sequencing instrument of claim 18, wherein each respective storage element in the plurality of storage elements is electrically gated by activation of a corresponding excitation source in the plurality of excitation sources of the pulsed illumination light to correlate each respective storage element with the corresponding excitation source.

20. The nucleic acid sequencing instrument of claim 18, wherein a delay between the corresponding excitation source of the pulsed illumination light and its subsequent emission event is pre-programed in each analytical device in synchronization of the storage elements with the excitation sources.

21. The nucleic acid sequencing instrument of claim 18, wherein each respective storage element in the plurality of storage elements is turned off during intermediate stages of the illumination process to reduce noise contribution.

22. The nucleic acid sequencing instrument of claim 18, wherein the electrical data signals are used to classify the plurality of labeled species in the sample.

23. The nucleic acid sequencing instrument of claim 13, wherein:

the sample comprises a plurality of labeled species at different excitation spectra;

the pulsed illumination light comprises a plurality of excitation sources at different wavelengths; and

the detection element is configured as a vertical detector, and relegation of each respective charge into a storage element is based on a depth of absorption of the photon that relates to an energy level of the photon.

24. The nucleic acid sequencing instrument of claim 13, wherein relegation of each respective charge into a storage element is based on an arrival time of the photon at the detection element relative to a corresponding pulse of the pulsed illumination light.

25. The nucleic acid sequencing instrument of claim 13, wherein the electrical data signals are representative of a decay of a labeled species in the sample.

26. The nucleic acid sequencing instrument of claim 13, wherein the sequencing chip comprises at least 1000 analytical devices, at least 10,000 analytical devices, at least 100,000 analytical devices, or at least 1,000,000 analytical devices.

14. The nucleic acid sequencing instrument of 13, wherein the processing system comprises:

a camera board in contact with the one or more electrical contacts of the sequencing chip, the camera board comprising a circuitry for processing the electrical data signals from the sequencing chip.

15. The nucleic acid sequencing instrument of 13, wherein the processing system further comprises:

a downstream processing system in electrical communication with the camera board to receive data from the camera board and to perform further analysis.