Biosensors for biological or chemical analysis and systems and methods for same

Patent metadata

Field	Value
Publication number	US-11604775-B2
Application number	US-202117304758-A
Country	US
Kind code	B2
Filing date	Jun 25, 2021
Priority date	Apr 16, 2012
Publication date	Mar 14, 2023
Grant date	Mar 14, 2023

Abstract

A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer that is configured to at least one of (a) filter unwanted excitation light signals; (b) direct emission signals from a designated reaction site toward one or more associated light detectors that are configured to detect the emission signals from the designated reaction site; or (c) block or prevent detection of crosstalk emission signals from adjacent reaction sites.

First claim

What is claimed is:

1. A method comprising:
illuminating a plurality of reaction sites of a detection device with excitation light, where the detection device comprises a plurality of stacked layers under the plurality of reaction sites, where at least some of the reaction sites have one or more analytes-of-interest, the stacked layers including a filter layer and a solid-state imager coupled to the filter layer, where the solid state imager comprises light detectors, the filter layer comprising filter walls and a light-absorbing material that is deposited between adjacent filter walls, the light-absorbing material configured to prevent transmission of excitation light and permit transmission of light emissions, wherein the adjacent filter walls define a detection path therebetween through the corresponding light-absorbing material toward the solid-state imager, the filter walls configured to reflect the light emissions toward the light detectors, and the filter walls include first and second interior portions, the first interior portion extending in a direction from the reaction sites toward the light detectors, the second interior portion extending in a direction from the first interior portion toward the light detectors; and
detecting the light emissions by the light detectors.

2. The method of claim 1 , wherein at least a portion of the light emissions detected by the light detectors include crosstalk light emissions from a non-associated reaction site.

3. The method of claim 2 , further comprising:
obtaining the signal data from the light detectors, the signal data including light scores that are based on an amount of the light emissions detected by the light detectors during a plurality of imaging events;
analyzing the light scores from a group of light detectors for each of the plurality of the imaging events;
determining respective crosstalk functions of the light detectors in the group from the analyzing the light scores from the group of light detectors for each of the plurality of the imaging events, wherein each of the crosstalk functions for a corresponding light detector in the group is based on the amount of the light emissions detected by other light detectors in the group; and
analyzing the signal data for each of the imaging events using the crosstalk functions to determine characteristics of the analytes-of-interest.

4. The method of claim 3 , wherein the determining respective crosstalk functions of the light detectors in the group includes:
for each imaging event in the plurality of imaging events:
determining a light score for each of the light detectors in the group from the imaging event;
identifying, as emitting, the at least one reaction site associated with the respective light detectors in the group having the light score for the respective imaging event greater than or equal to a predetermined score value;
identifying, as non-emitting, the reaction sites associated with the respective light detectors in the group having the light score for the respective imaging event less than the predetermined score value;
determining that the light score of the light detectors associated with non-emitting reaction sites is entirely from crosstalk emissions; and
determining, for each of the non-emitting reaction sites, the number of adjacent reaction sites identified as emitting and the position of each adjacent reaction site relative to each non-emitting reaction site; and
comparing the light scores of non-emitting reaction sites from the plurality of imaging events to determine crosstalk portions of the light scores provided by the adjacent reaction sites.

5. The method of claim 3 , wherein each of the crosstalk functions of the light detectors in the group is based on a number of adjacent reaction sites that provided the light emissions and locations of the adjacent reaction sites that provided the light emissions.

6. The method of claim 1 , wherein the analytes-of-interest are nucleic acids.

7. The method of claim 3 , wherein the light scores correspond to voltage signals.

8. The method of claim 1 , wherein the light emissions detected by the light detectors includes fluorescence emission signals.

9. The method of claim 1 , wherein the reaction sites include discrete metal regions on the detector surface having discrete clusters of nucleic acids.

10. The method of claim 1 , wherein the reaction sites include discrete metal regions on the detector surface.

11. The method of claim 1 , wherein the reaction sites include discrete clusters of nucleic acids.

12. The method of claim 1 , wherein a density of the reaction sites is at least one million reaction sites per square millimeter.

13. The method of claim 1 , wherein the light detectors have detection areas that are less than about 50 μm 2 .

14. The method of claim 3 , wherein the analytes-of-interest are nucleic acids that form clusters at the reaction sites and the plurality of imaging events occur in accordance with a sequencing-by-synthesis protocol in which fluorescently-labeled nucleotides are incorporated into the nucleic acids prior to each imaging event.

15. The method of claim 1 , wherein the detection device includes a passivation layer that defines the detector surface, the analytes-of-interest being immobilized to the detector surface and exposed to a flow channel above the detector surface, the light emissions propagating through the passivation layer toward the light detectors.

16. The method of claim 15 , wherein the passivation layer extends between the filter layer and the flow channel, and at least some of the crosstalk light emissions propagate through the flow channel and the passivation layer and over one or more of the filter walls.

17. The method of claim 15 , wherein the passivation layer extends between the filter layer and the flow channel; the light-absorbing material filters the excitation light; and the crosstalk light emissions propagate through the flow channel, the passivation layer, and the light-absorbing material to the light detectors.

18. The method of claim 1 , wherein the second interior portion is to attenuate the light emissions from the reaction sites more than the first interior portion.

19. The method of claim 1 , wherein the first interior portion is coated with a reflective coating material and the second interior portion is not coated or is coated with a different material; and the light emissions from the reaction sites that are reflected by the coating are less attenuated than the light emissions that are reflected by the second interior portion of the filter walls.

20. The method of claim 1 , wherein a width for each of the detection paths decreases as the detection path extends toward the light detector; a thickness of the filter wall begins to increase as the filter wall transitions from the first interior portion to the second interior portion; and as the thickness of the filter wall increases, the width for the respective detection path decreases.

Assignees

• Illumina Inc

Inventors

• Eltoukhy Helmy A
• Kain Robert C
• Feng Wenyi
• Pratt Mark
• Hirschbein Bernard
• Sabounchi Poorya
• Khurana Tarun

Classifications

• G01N21/6486

  Measuring fluorescence of biological material, e.g. DNA, RNA, cells (G01N21/6428 takes precedence) · CPC title

• G06F16/214 Primary

  Database migration support · CPC title

• G01N33/6875

  Nucleoproteins · CPC title

• B01L3/502715

  characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces · CPC title

• B01L2300/0654

  Lenses; Optical fibres · CPC title