Identifying randomly distributed microparticles in images to sequence a polynucleotide

• US 9,135,497 B2
• Filed: 01/27/2012
• Issued: 09/15/2015
• Est. Priority Date: 01/27/2012
• Status: Active Grant

• Current Assignee: National Instruments Corporation (Emerson Electric Company)
• Original Assignee: National Instruments Corporation (Emerson Electric Company)
• Inventors: Cerna, Michael D., Nagle, James C., Ruan, Qing, Schmidt, Darren R., Wenzel, Lothar
• Primary Examiner(s): DeJong, Eric S
• Assistant Examiner(s): VANNI, GEORGE STEVEN
• Application Number:
  US13/359,950
• Publication Number:
  US 20130196330A1
• Time in Patent Office: 1,327 Days
• US Class Current: 1/1
• CPC Class Codes: G06V 20/698 Matching; Classification
• CPC Class Codes: G06V 20/80 Recognising image objects characterised by unique random patterns
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Performing sequencing of a polynucleotide. A first image of microparticles that are distributed in a random fashion on a substrate may be received. Each of the microparticles may include a plurality of similar oligonucleotides of the polynucleotide. A second image of the microparticles may be received. A plurality of first subportions of the first image may be determined. Each subportion may include a respective plurality of microparticles distributed in a random fashion. The second image may be analyzed to identify a plurality of second subportions in the second image. Each of the plurality of second subportions may correspond to a respective one of the plurality of first subportions. A plurality of the microparticles may be matched from the first and second images based on said analyzing. At least a portion of the sequence of nucleotides of the polynucleotide may be determined based on said matching.

Claims

1. A computer-implemented method for performing sequencing of a polynucleotide, comprising:

receiving, by the computer, a first image of microparticles, wherein the first image is stored in a memory of the computer, wherein the microparticles are distributed in a random fashion on a substrate wherein the microparticles have respective random positions on the substrate, wherein the respective random positions are not pre-determined and are not regularly spaced, and wherein each of the microparticles comprises a plurality of similar oligonucleotides of the polynucleotide;

receiving, by the computer, a second image of the microparticles, wherein the second image of the microparticles highlights at least some of the microparticles in response to fluorescent chemicals attached to the oligonucleotides based on terminal nucleotides of the oligonucleotides on the microparticles, and wherein the second image is stored in the memory of the computer;

determining, by the computer, a plurality of first subportions of the first image, wherein each subportion comprises a respective plurality of microparticles distributed in a random fashion, and wherein each first subportion'"'"'s random distribution comprises a respective unique pattern;

analyzing, by the computer, the second image to identify a plurality of second subportions in the second image that each corresponds to a respective one of the plurality of first subportions based on the respective unique patterns;

matching, by the computer, a plurality of the microparticles in the first and second images based on said analyzing using the respective unique patterns; and

determining, by the computer, the sequence of nucleotides of the polynucleotide based on said matching and the highlighted microparticles, wherein the sequence of nucleotides is stored in the memory of the computer.

2. The computer-implemented method of claim 1, wherein the first image and the second image differ in at least one of scale, rotation, or translation.

3. The computer-implemented method of claim 1, further comprising:

modifying, by the computer, the second image to correspond to the first image based on said analyzing using geometric relationships between the first image and the second image.

4. The computer-implemented method of claim 3, wherein the first image has a first orientation, wherein said modifying comprises rotating the second image to match the first orientation of the first image based on said analyzing using the geometric relationships between the first image and the second image.

5. The computer-implemented method of claim 3, wherein the first image has a first scale, wherein said modifying comprises scaling the second image to match the first scale of the first image based on said analyzing using the geometric relationships between the first image and the second image.

6. The computer-implemented method of claim 1, wherein said determining the sequence of the nucleotides of the polynucleotide comprises determining sequences of nucleotides of the oligonucleotides of each of the microparticles.

7. The computer-implemented method of claim 6, wherein in the second image, a subset of the microparticles are illuminated corresponding to a chemical reaction used to identify one or more nucleotides of the oligonucleotides comprised on the microparticles, wherein the method further comprises:

identifying, by the computer, the subset of the microparticles that are illuminated in the second image;

wherein determining the sequence of nucleotides of the oligonucleotides of each of the microparticles is based on said identifying the subset of the microparticles that are illuminated in the second image.

8. The computer-implemented method of claim 1, further comprising:

receiving, by the computer, a plurality of additional images of the microparticles;

performing, by the computer, said analyzing and said matching for each of the plurality of additional images;

wherein said determining the sequence of nucleotides is based on said performing.

9. The computer-implemented method of claim 1, further comprising:

receiving, by the computer, a third image of the microparticles;

receiving, by the computer, a fourth image of the microparticles;

receiving, by the computer, a fifth image of the microparticles;

performing, by the computer, said analyzing and said matching for each of the third, fourth, and fifth images of the microparticles;

wherein the first image is an initial image of the microparticles, wherein the second image corresponds to a chemical reaction for identifying a first type of nucleotide, wherein the third image corresponds to a chemical reaction for identifying a second type of nucleotide, wherein the fourth image corresponds to a chemical reaction for identifying a third type of nucleotide, wherein the fifth image corresponds to a chemical reaction for identifying a fourth type of nucleotide;

wherein said determining the sequence of nucleotides of the polynucleotide comprises performing said receiving, said analyzing, and said matching for the second, third, fourth, and fifth images a plurality of times for a plurality of nucleotides of the oligonucleotides comprised on each of the microparticles.

10. The computer-implemented method of claim 9, wherein the chemical reactions for the different types of nucleotide cause illumination of the microparticles at respective, different wavelengths.

11. A non-transitory, computer accessible memory medium storing program instructions for performing sequencing of a polynucleotide, wherein the program instructions are executable to:

receive a first image of microparticles, wherein the microparticles are distributed in a random fashion on a substrate wherein the microparticles have respective random positions on the substrate, wherein the respective random positions are not pre-determined and are not regularly spaced, and wherein each of the microparticles comprise a plurality of similar oligonucleotides of the polynucleotide;

receive a second image of the microparticles, wherein the second image of the microparticles highlights at least some of the microparticles in response to fluorescent chemicals attached to the oligonucleotides based on terminal nucleotides of the oligonucleotides on the microparticles;

determine a plurality of first subportions of the first image, wherein each subportion comprises a respective plurality of microparticles distributed in a random fashion, and wherein each first subportion'"'"'s random distribution comprises a respective unique pattern;

analyze the second image to identify a plurality of second subportions in the second image that each corresponds to a respective one of the plurality of first subportions based on the respective unique patterns;

match a plurality of the microparticles in the first and second images based on said analyzing using the respective unique patterns; and

determine the sequence of nucleotides of the polynucleotide based on said matching and the highlighted microparticles.

12. The non-transitory, computer accessible memory medium of claim 11, wherein the first image and the second image differ in at least one of scale, rotation, or translation.

13. The non-transitory, computer accessible memory medium of claim 11, wherein the program instructions are further executable to:

modify the second image to correspond to the first image based on said analyzing using geometric relationships between the first image and the second image.

14. The non-transitory, computer accessible memory medium of claim 13, wherein the first image has a first orientation, wherein said modifying comprises rotating the second image to match the first orientation of the first image based on said analyzing using the geometric relationships between the first image and the second image.

15. The non-transitory, computer accessible memory medium of claim 13, wherein the first image has a first scale, wherein said modifying comprises scaling the second image to match the first scale of the first image based on said analyzing using the geometric relationships between the first image and the second image.

16. The non-transitory, computer accessible memory medium of claim 11, wherein said determining the sequence of the nucleotides of the polynucleotide comprises determining sequences of nucleotides of the oligonucleotides of each of the microparticles.

17. The non-transitory, computer accessible memory medium of claim 16, wherein in the second image, a subset of the microparticles are illuminated corresponding to a chemical reaction used to identify one or more nucleotides of the oligonucleotides comprised on the microparticles, wherein the program instructions are further executable to:

identify the subset of the microparticles that are illuminated in the second image;

wherein determining the sequence of nucleotides of the oligonucleotides of each of the microparticles is based on said identifying the subset of the microparticles that are illuminated in the second image.

18. The non-transitory, computer accessible memory medium of claim 11, wherein the program instructions are further executable to:

receive a plurality of additional images of the microparticles;

perform said analyzing and said matching for each of the plurality of additional images;

wherein said determining the sequence of nucleotides is based on said performing.

19. The non-transitory, computer accessible memory medium of claim 11, wherein the program instructions are further executable to:

receive a third image of the microparticles;

receive a fourth image of the microparticles;

receive a fifth image of the microparticles;

perform said analyzing and said matching for each of the third, fourth, and fifth images of the microparticles;

wherein the first image is an initial image of the microparticles, wherein the second image corresponds to a reaction for identifying a first type of nucleotide, wherein the third image corresponds to a reaction for identifying a second type of nucleotide, wherein the fourth image corresponds to a reaction for identifying a third type of nucleotide, wherein the fifth image corresponds to a reaction for identifying a fourth type of nucleotide;

wherein said determining the sequence of nucleotides of the polynucleotide comprises performing said receiving, said analyzing, and said matching for the second, third, fourth, and fifth images a plurality of times for a plurality of nucleotides of the oligonucleotides comprised on each of the microparticles.

20. The non-transitory, computer accessible memory medium of claim 19, wherein the chemical reactions for the different types of nucleotide cause illumination of the microparticles at respective, different wavelengths.

21. A system for performing sequencing of a polynucleotide, comprising:

an image acquisition apparatus, wherein the image acquisition apparatus is configured to acquire images of microparticles, wherein the microparticles are distributed in a random fashion on a substrate wherein the microparticles have respective random positions on the substrate, wherein the respective random positions are not pre-determined and are not regularly spaced, and wherein each of the microparticles comprise a plurality of similar oligonucleotides of the polynucleotide;

a processor coupled to the image acquisition device;

a memory medium coupled to the processor, wherein the memory medium stores program instructions that are executable by the processor to;

receive a first image of microparticles via the image acquisition apparatus at a first time;

receive a second image of the microparticles via the image acquisition apparatus at a second time wherein the second image of the microparticles highlights at least some of the microparticles in response to fluorescent chemicals attached to the oligonucleotides based on terminal nucleotides of the oligonucleotides on the microparticles;

determine a plurality of first subportions of the first image, wherein each subportion comprises a respective plurality of microparticles distributed in a random fashion, and wherein each first subportion'"'"'s random distribution comprises a respective unique pattern;

analyze the second image to identify a plurality of second subportions in the second image that each corresponds to a respective one of the plurality of first subportions based on the respective unique patterns;

match a plurality of the microparticles in the first and second images based on said analyzing using the respective unique patterns; and

determine the sequence of nucleotides of the polynucleotide based on said matching and the highlighted microparticles.

22. The system of claim 21, further comprising:

a chemical reaction apparatus coupled to the image acquisition device, wherein the chemical reaction apparatus comprises the substrate comprising the microparticles, wherein the chemical reaction apparatus is configured to expose the microparticles to a plurality of chemical reactions to determine the sequence of nucleotides of the polynucleotide.

23. The system of claim 22, wherein the first image is of the microparticles prior to a first chemical reaction, wherein the second image is of the microparticles after the first chemical reaction, wherein the chemical reaction apparatus is configured to perform the first chemical reaction to identify at least a first type of nucleotide.

24. The system of claim 21, wherein the program instructions are executable by the processor to cause the chemical reaction apparatus to perform the plurality of chemical reactions.

25. The system of claim 21, wherein the first image and the second image differ in at least one of scale, rotation, or translation.