Scanning system and method for imaging and sequencing

• US 10,107,758 B2
• Filed: 07/03/2014
• Issued: 10/23/2018
• Est. Priority Date: 04/04/2008
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Oldham, Mark F., Nordman, Eric S., Sun, Hongye, Boege, Steven J.
• Primary Examiner(s): Hixson, Christopher Adam
• Application Number:
  US14/323,203
• Publication Number:
  US 20140315206A1
• Time in Patent Office: 1,573 Days
• 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 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6456 Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 21/6486 Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence

Abstract

A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.

Claims

1. A system for detecting emissions from a plurality of fixed locations on a substrate, the system comprising:

a first irradiation source configured to irradiate the substrate and disposed for irradiating a first group of fixed locations of the plurality of fixed locations, wherein the first irradiation source comprises at least one laser source and a holographic beam shaper;

a second irradiation source configured to irradiate a second group of fixed locations of the plurality of fixed locations, the second irradiation source being fixed with respect to the first irradiation source such that the second group of fixed locations is spaced from and excludes the first group of fixed locations on the substrate;

a scanning detector array positioned with respect to the first irradiation source and the second irradiation source so as to collect emission from the first group of fixed locations without collecting emission from the second group of fixed locations;

modulating optics disposed between the first irradiation source and the scanning detector array, wherein the modulating optics comprise a set of prisms including a first prism, a second prism, and a trombone prism configured to operate in conjunction to render intensity consistent across the fixed locations irradiated by the first irradiation source; and

a translation stage configured to move the first irradiation source, the second irradiation source, and the scanning detector array, together.

2. The system of claim 1, wherein at each location a polynucleotide is disposed and at least some of the polynucleotides are labeled with respective markers that fluoresce when exposed to excitation light.

3. The system of claim 1, further comprising a substrate, wherein the substrate is positioned with respect to the first irradiation source so as to be irradiated by the first irradiation source.

4. The system of claim 3, wherein the substrate comprises a flow cell and a plurality of labeled polynucleotides disposed in the flow cell, wherein the flow cell comprises a plurality of channels or grooves.

5. The system of claim 1, wherein the scanning detector array comprises a two dimensional charge-coupled device.

6. The system of claim 1, wherein the scanning detector array comprises a point detector.

7. The system of claim 1, wherein the scanning detector array comprises a time-delay integration image detector.

17. The system of claim 4, wherein the flow cell comprises from 10,000 to 1,000,000,000 grooves for containing individual strands of DNA.

8. A system for detecting emissions from a plurality of fixed locations on a substrate, the system comprising:

a first irradiation source configured to irradiate the substrate and disposed for irradiating a first group of fixed locations of the plurality of fixed locations, wherein the first irradiation source comprises at least one laser source;

a second irradiation source configured to irradiate a second group of fixed locations of the plurality of fixed locations, the second irradiation source being fixed with respect to the first irradiation source;

a scanning detector array positioned with respect to the first irradiation source and the second irradiation source so as to collect emission from the first group of fixed locations without collecting emission from the second group of fixed locations;

modulating optics disposed between the first irradiation source and the scanning detector array, wherein the modulating optics comprise a set of prisms comprising at least one trombone prism, the set of prisms configured to operate such that a distance traveled by an irradiating beam from the first irradiation source to any one of the fixed locations irradiated by the first irradiation source can be the same; and

a translation stage configured to move the first irradiation source, the second irradiation source, and the scanning detector array, together.

9. The system of claim 8, wherein the first irradiation source further comprises a holographic beam shaper.

10. The system of claim 8, wherein the second group of fixed locations is spaced from and excludes the first group of fixed locations on the substrate.

11. The system of claim 8, wherein at each location a polynucleotide is disposed and at least some of the polynucleotides are labeled with respective markers that fluoresce when exposed to excitation light.

12. The system of claim 8, wherein the substrate is positioned with respect to the first irradiation source so as to be irradiated by the first irradiation source.

13. The system of claim 8, wherein the substrate comprises a flow cell and a plurality of labeled polynucleotides disposed in the flow cell, wherein the flow cell comprises a plurality of channels or grooves.

14. The system of claim 8, wherein the scanning detector array comprises a two dimensional charge-coupled device.

15. The system of claim 8, wherein the scanning detector array comprises a point detector.

16. The system of claim 8, wherein the scanning detector array comprises a time-delay integration image detector.

18. The system of claim 13, wherein the flow cell comprises from 10,000 to 1,000,000,000 grooves for containing individual strands of DNA.