Integrated analytical system and method

• US 9,822,410 B2
• Filed: 09/21/2016
• Issued: 11/21/2017
• 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, Sr., Ravi, Helgesen, Scott Edward
• Primary Examiner(s): NGUYEN, SANG H
• Application Number:
  US15/272,138
• Publication Number:
  US 20170137877A1
• Time in Patent Office: 426 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 method for nucleic acid sequencing comprising:

delivering sequencing reagents onto a sequencing chip having at least 10,000 analytical devices, each analytical device having a reaction cell, optical elements, one or more detection elements that detect light emitted from the reaction cell and convert the detected light into electrical data signals, and waveguides that deliver illumination light to the reaction cells, wherein the reaction cell, waveguides, optical elements, and detection elements, are pre-aligned and locked in during manufacturing of the sequencing chip and there is no substantial open or free space between the reaction cell, waveguides, optical elements, and detection elements;

delivering illumination light to the waveguides of the sequencing chip;

detecting the emitted light from the reaction cells using the detection elements while sequencing reactions are occurring within the reaction cells;

converting the detected light into electrical data signals using the detection elements; and

transferring the electrical data signals through electrical connections on the sequencing chip to a processor to process the electrical data signals.

2. The method of claim 1, wherein the reaction cell comprises a zero mode waveguide.

3. The method of claim 1, wherein the sequencing chip further comprises circuitry for refining the electrical data signals from the analytical devices into event pulses.

4. The method of claim 3, wherein the event pulses comprise information including temporal onset and offset times and signal strengths.

5. The method of claim 3, further comprising:

processing, using the processor, the electrical data signals, wherein the processing comprises data reduction, digitization, buffer storage, or bus arbitration.

6. The method of claim 1, wherein the sequencing reactions occurring in the reaction cells are asynchronous, and circuits on the sequencing chip align these random events to a system clock whereby the data that is transmitted off of the chip is read off in a synchronous manner.

7. The instrument of claim 1, wherein the sequencing chip has at least a million analytical devices.

8. The method of claim 1, wherein the electrical data signals from the sequencing chip comprise data from single molecule real time sequencing.

9. The method of claim 1, wherein the sequencing chip comprises a silicon chip.

10. The method of claim 1, wherein the sequencing chip is produced by forming stacks on top of a silicon chip that comprises the detection elements.

11. The method of claim 1, wherein each reaction cell is associated with a single detection element.

12. The method of claim 1, wherein each reaction cell is associated with two detection elements, each associated with a different color filter to allocate spectrally different signals to each element.

13. The method of claim 1, wherein each reaction cell is associated with four detection elements, each associated with a different color filter to allocate spectrally different signals to each element.

14. The method of claim 1, wherein the detection elements are CMOS sensors.