DNA sequencing system with stacked BSI global shutter image sensor

• US 10,670,526 B2
• Filed: 03/05/2018
• Issued: 06/02/2020
• Est. Priority Date: 03/05/2018
• Status: Active Grant

• Current Assignee: Smartsens Technology (Cayman) Co., Ltd.
• Original Assignee: Smartsens Technology (Cayman) Co., Ltd.
• Inventors: Xu, Chen, Mo, Yaowu, Shao, Zexu, Zhang, Zhengmin, Ma, Weijian
• Primary Examiner(s): Prieto, Violeta A
• Application Number:
  US15/911,661
• Publication Number:
  US 20190271645A1
• Time in Patent Office: 820 Days
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 2021/1765 Method using an image detector and processing of image signal
• CPC Class Codes: G01N 2021/637 Lasing effect used for analysis
• CPC Class Codes: G01N 2021/6415 with two excitations, e.g. strong pump/probe flash
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 2021/6493 by alternating fluorescence/transmission or fluorescence/reflection
• CPC Class Codes: G01N 21/636 using an arrangement of pump beam and probe beam; using the measurement of optical non-linear properties; non-linear optics per se G02F1/35
• CPC Class Codes: G01N 21/6402 Atomic fluorescence; Laser induced 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 21/6456 Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 2201/0697 Pulsed lasers
• CPC Class Codes: H04N 25/42 by switching between different modes of operation using different resolutions or aspect ratios, e.g. switching between interlaced and non-interlaced mode
• CPC Class Codes: H04N 25/778 comprising amplifiers shared between a plurality of pixels, i.e. at least one part of the amplifier must be on the sensor array itself
• CPC Class Codes: H04N 25/79 Arrangements of circuitry being divided between different or multiple substrates, chips or circuit boards, e.g. stacked image sensors

Abstract

An improved DNA sequencing system comprising a DNA sample holder residing on a stacked BSI global shutter image sensor illuminated by a pulsed laser for fluorescent illumination detection. The pulsed laser has on and off periods wherein during the laser on period a Fluorophore tag attached to a DNA sample is excited to produce fluorescence emission while the imaging system captures no illumination and during the off period the global shutter imaging system captures persistent fluorescent emission from the DNA sample and reads out an imaging signal.

Claims

1. An apparatus for identifying the presence of fluorophore tagged nucleotide bases in a sample, the apparatus comprising:

a laser illumination source configured to emit pulses of radiation;

an optically transparent sample holding chamber adapted to receive the sample, the sample holding chamber having a transparent top side to receive the pulses of radiation from the laser illumination source into the sample holding chamber, in order to identify the presence of the fluorophore tagged nucleotide bases by imaging the fluorescent emissions which may persist after the laser illumination ceases;

an image sensor chip including an array of image sensing pixels with its image sensing surface stacked immediately adjacent and under the sample holding chamber and configured with in-pixel global shutter for accumulating and transferring an image signal in response to persistent fluorescent emission light incident upon the image sensor;

a circuit chip with circuit blocks disposed within a second substrate stacked immediately adjacent and upon the other surface of the image sensor chip for coupling out the image signal through the second substrate to information processing and analysis component circuit blocks;

wherein the image sensor global shutter pixels are open to accumulate persistent fluorescent emission and transfer out a related image signal when no laser radiation is directed into the sample holding chamber; and

wherein the image sensor global shutter pixels are closed or in reset mode when the laser radiation pulse is directed into the sample holding chamber.

2. The apparatus of claim 1, wherein the image sensor chip comprises a backside illuminated image sensor.

3. The apparatus of claim 1, wherein the image sensor chip comprises a frontside illuminated image sensor.

4. The apparatus of claim 1, wherein on the imaging side of the image sensor is disposed an antireflective layer.

5. The apparatus of claim 4, wherein on the antireflective layer are disposed on optical filers comprising a color filter pattern.

6. The apparatus of claim 4, wherein on the antireflective layer are disposed microlenses positioned above each sensor element.

7. The apparatus of claim 5, wherein the microlenses are covered with a planarizing layer stacked immediately adjacent and under the base sample holding chamber.

8. The apparatus of claim 1, wherein the circuit blocks disposed on the second substrate comprise one of an ARM core, a GPU core and a FPGA core.

9. The apparatus of claim 1, wherein the in-pixel global shutter employs an in-pixel capacitor as the global shutter storage element.

10. The apparatus of claim 1, wherein the in-pixel global shutter employs an in-pixel anti-blooming gate for reset operation.

11. A method for identifying the presence of fluorophore tagged nucleotide bases, the method comprising the steps of:

providing a laser illumination source configured to emit pulsed laser radiation;

providing a sample of fluorophore tagged nucleotide bases;

providing an optically transparent sample holding chamber that has an upper side, the sample holding chamber being adapted for receiving the sample of fluorophore tagged nucleotide bases;

providing an image sensor chip including an array of image sensing pixels with its image sensing surface stacked immediately adjacent and under the base sample holding chamber;

providing a circuit chip with circuit blocks disposed within a second substrate stacked immediately adjacent and upon the other surface of the image sensor chip;

placing the sample of fluorophore tagged nucleotide bases into the sample holding chamber;

exposing the sample in the sample holding chamber to the pulsed laser radiation such that the pulsed laser radiation passes through the sample and into the upper side of the sample holding chamber, thereby identifying the presence of fluorophore tagged nucleotide bases by imaging the release of fluorescent emissions which may persist after the pulsed laser radiation ceases;

accumulating and transferring, via the image sensor chip configured with in-pixel global shutter, an image signal in response to fluorescent emissions emitted from the sample and incident upon the image sensor;

coupling out the image signal through the second substrate to the circuit blocks of the circuit chip;

closing the image sensor global shutter when the laser radiation pulse is incident on the sample;

opening the image sensor global shutter to accumulate persistent fluorescent emission and transfer out a related image signal during the subsequent period between laser radiation pulses when no laser radiation is incident on the sample; and

executing signal processing on the image signal within the circuit blocks to identify the presence of fluorophore tagged bases within the sample.

12. The method of claim 11, wherein the image sensing chip further comprises a backside illuminated image sensor including an array of image sensing pixels with its image sensing surface stacked immediately adjacent and under the base sample holding chamber.

13. The method of claim 11, wherein the image sensing chip further comprises a frontside illuminated image sensor including an array of image sensing pixels with its image sensing surface stacked immediately adjacent and under the base sample holding chamber.