Single-pass primary analysis

Patent metadata

Field	Value
Publication number	US-11397870-B2
Application number	US-202117547602-A
Country	US
Kind code	B2
Filing date	Dec 10, 2021
Priority date	Aug 31, 2020
Publication date	Jul 26, 2022
Grant date	Jul 26, 2022

Abstract

Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.

First claim

What is claimed is:

1. A method for identifying a set of base-calling locations in a flow cell comprising:
capturing a first plurality of flow cell images from a single flow cycle, wherein each of the first plurality of flow cell images corresponds to a different wavelength of fluorescent elements and each different wavelength corresponds to a respective nucleotide base;
applying, to the first plurality of flow cell images, a spot-finding algorithm, wherein the spot-finding algorithm uses pixel intensity and relative color purity to identify DNA cluster centers on the flow cell;
mapping, onto a template, a plurality of base-calling locations corresponding to the DNA cluster centers identified by applying the spot-finding algorithm to the first plurality of flow cell images from the single flow cycle;
registering a second plurality of flow cell images from one or more subsequent flow cycles to the template mapped from the single flow cycle; and
identifying nucleotide bases added at each of the plurality base-calling locations in the subsequent flow cycles based on the template mapped from the single flow cycle.

2. The method of claim 1 , wherein the spot-finding algorithm detects each DNA cluster center at a sub-pixel resolution.

3. The method of claim 1 , wherein a wavelength of an optical signal detected at a particular DNA cluster center in a given flow cycle correlates to a nucleotide base added to the particular DNA cluster center in the given flow cycle.

4. The method of claim 1 , wherein registering a second plurality of flow cell images comprises aligning each flow cell image in the second plurality of flow cell images with the template mapped from the single flow cycle.

5. The method of claim 1 , wherein the pixel intensity is determined based on a comparison of a set of channel intensities at the DNA cluster centers, each channel intensity in the set of channel intensities corresponding to a respective different wavelength of fluorescent elements.

6. The method of claim 1 , wherein the plurality of images are captured according to a coordinate system.

7. The method of claim 1 , wherein the method is performed by a configurable processor.

8. A system for identifying a set of base-calling locations in a flow cell, the system comprising:
data storage; and
one or more dedicated processing units configured to:
capture a first plurality of flow cell images from a single flow cycle, wherein each of the first plurality of flow cell images corresponds to a different wavelength of fluorescent elements and each different wavelengths corresponds to a respective nucleotide base;
apply, to the first plurality of flow cell images, a spot-finding algorithm, wherein the spot-finding algorithm uses pixel intensity and relative color purity to identify DNA cluster centers of DNA clusters on the flow cell;
map, onto a template, a plurality of base-calling locations corresponding to the DNA cluster centers identified by applying the spot-finding algorithm to the first plurality of flow cell images from the single flow cycle;
register a second plurality of flow cell images from one or more subsequent flow cycles to the template mapped from the single flow cycle; and
identify nucleotide bases added at each of the plurality base-calling locations in the subsequent flow cycles based on the template mapped from the single flow cycle.

9. The system of claim 8 , wherein the spot-finding algorithm detects each DNA cluster center at a sub-pixel resolution.

10. The system of claim 8 , wherein a wavelength of an optical signal detected at a particular DNA cluster in a given flow cycle correlates to a nucleotide base added to the particular DNA cluster center in the given flow cycle.

11. The system of claim 8 , wherein registration of a second plurality of flow cell images comprises aligning each flow cell image in the second plurality of flow cell images with the template mapped from the single flow cycle.

12. The system of claim 8 , wherein the pixel intensity is determined based on a comparison of a set of channel intensities at the DNA cluster centers, each channel intensity in the set of channel intensities corresponding to a respective different wavelength of fluorescent elements.

13. The system of claim 9 , wherein the plurality of images are captured according to a coordinate system.

14. The system of claim 8 , wherein the one or more dedicated processing units comprises a configurable processor.

15. A non-transitory computer readable storage medium having computer readable code thereon, the non-transitory computer readable medium including instructions configured to cause a computer system to perform operations comprising:
capturing a first plurality of flow cell images from a single flow cycle, wherein each of the first plurality of flow cell images corresponds to a different wavelength of fluorescent elements and each different wavelength corresponds to a respective nucleotide base;
applying, to the first plurality of flow cell images, a spot-finding algorithm, wherein the spot-finding algorithm uses pixel intensity and relative color purity to identify DNA cluster centers on the flow cell;
mapping, onto a template, a plurality of base-calling locations corresponding to the DNA cluster centers identified by applying the spot-finding algorithm to the first plurality of flow cell images from the single flow cycle
registering a second plurality of flow cell images from one or more subsequent flow cycles on the template mapped from the single flow cycle; and
identifying nucleotide bases added at each of the plurality of base-calling locations in the subsequent flow cycles based on the template generated from the single flow cycle.

16. The non-transitory computer readable storage medium of claim 15 , wherein the spot-finding algorithm detects each DNA cluster center at a sub-pixel resolution.

17. The non-transitory computer readable storage medium of claim 15 , wherein a wavelength of an optical signal detected at a particular DNA cluster center in a given flow cycle correlates to a nucleotide base added to the particular DNA cluster center in the given flow cycle.

18. The non-transitory computer readable storage medium of claim 15 , wherein registering a second plurality of flow cell images comprises aligning each flow cell image in the second plurality of flow cell images with the template mapped from the single flow cycle.

19. The non-transitory computer readable storage medium of claim 15 , wherein the pixel intensity is determined based on a comparison of a set of channel intensities at the DNA cluster center, each channel intensity in the set of channel intensities corresponding to a respective different wavelength of fluorescent elements.

20. The non-transitory computer readable storage medium of claim 15 , wherein the plurality of images are captured according to a coordinate system.

21. The non-transitory computer readable storage medium of claim 15 , wherein the computer system comprises a configurable processor.

Assignees

• Element Biosciences Inc

Inventors

• Zhou Chunhong
• Kruglyak Semyon
• Garcia Francisco
• Guo Minghao
• Wang Haosen
• Kelly Ryan

Classifications

• G06V20/69

  Microscopic objects, e.g. biological cells or cellular parts · CPC title

• G06F18/23211

  with adaptive number of clusters · CPC title

• G06V10/751

  Comparing pixel values or logical combinations thereof, or feature values having positional relevance, e.g. template matching · CPC title

• G06T7/30

  Determination of transform parameters for the alignment of images, i.e. image registration · CPC title

• G06T2207/30072

  Microarray; Biochip, DNA array; Well plate · CPC title