Methods, carrier assemblies, and systems for imaging samples for biological or chemical analysis

Patent metadata

Field	Value
Publication number	US-11479808-B2
Application number	US-202016810326-A
Country	US
Kind code	B2
Filing date	Mar 5, 2020
Priority date	Mar 24, 2015
Publication date	Oct 25, 2022
Grant date	Oct 25, 2022

Abstract

Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.

First claim

What is claimed is:

1. A method of sequencing nucleic acids of a sample, comprising:
providing an assay system comprising a stage, an optical system, a detector assembly, and a controller;
positioning a substrate on the stage within an imaging zone of the optical system, the substrate comprising a microarray of reaction sites to receive at least one sample;
capturing a series of images by moving the substrate relative to the optical system, each images of the series of images comprising an overlapping portion of a microarray of reaction sites;
detecting light intensities associated with respective reaction sites in the images by the detector assembly to determine data representations of the images, each data representation corresponding to one of the images and comprising signal values based on light intensities associated with the respective reaction sites;
combining the data representations of adjacent images based on a comparison of the signal values of the data representations of the adjacent images by the controller, thereby generating a stitched data representation of the adjacent images of the microarray; and
determining properties or characteristics of the at least one sample by the controller using the stitched data representations.

2. The method of claim 1 , wherein each of the reaction sites has designated probe molecules immobilized thereto.

3. The method of claim 1 , wherein the microarray has target analytes attached thereto.

4. The method of claim 1 , wherein the data representations of the adjacent images have respective sub-arrays that are based on respective reaction sites of the microarray.

5. The method of claim 1 , wherein each of the data representations of the adjacent images further comprises a corresponding location relative to other reaction sites.

6. The method of claim 1 , wherein each of the data representations of the adjacent images includes a plurality of columns of the reaction sites.

7. The method of claim 1 , wherein the comparison of signal values includes comparing signal values of a column of one data representation of adjacent images to the signal values of a column of the adjacent data representation of the adjacent images.

8. The method of claim 7 , further including calculating a correlation value using at least the comparison of signal values by the controller.

9. The method of claim 8 , wherein the columns are designated as overlapping columns that have the same reaction sites if the correlation value satisfies a designated threshold.

10. The method of claim 1 , wherein the comparison of signal values includes comparing the signal values of a plurality of columns of one data representation of adjacent images to the signal values of a plurality of columns of the adjacent data representation of the adjacent images.

11. The method of claim 10 , further comprising calculating a correlation value using at least the comparison of signal values by the controller.

12. The method of claim 11 , wherein the columns are designated as overlapping columns that have the same reaction sites if the correlation value satisfies a designated threshold.

13. The method of claim 1 , wherein combining the data representations of adjacent images is repeated for each pair of adjacent images, thereby generating the data representation of the microarray.

14. The method of claim 1 , wherein determining properties or characteristics of the at least one sample by the controller using the stitched data representations is performed after comparing a number of reaction sites within the data representation of the microarray to an expected number of reaction sites.

15. The method of claim 1 , wherein the reaction sites of the microarray have a known size and shape and a known order or arrangement with respect to one another within the microarray.

16. The method of claim 1 , wherein each of the reaction sites of the microarray correspond to a plurality of pixels in a corresponding image of the series of images.

17. The method of claim 1 , wherein the substrate is an open-face substrate.

18. The method of claim 1 , wherein the capturing the series of images comprising step-and-shooting by the optical system of the microarray.

19. The method of claim 1 , wherein the optical system comprises at least one objective lens.

20. The method of claim 19 , wherein the at least one objective lens has a numerical aperture of at least 0.6.

Assignees

• Illumina Cambridge Ltd

Inventors

• Rawlings Stephen
• Rao Venkatesh Mysore Nagaraja
• Ang Beng Keong
• Udpa Nitin

Classifications

• G01N21/253

  for batch operation, i.e. multisample apparatus (analytical automats G01N35/00) · CPC title

• G01N21/6452

  Individual samples arranged in a regular 2D-array, e.g. multiwell plates · CPC title

• B01L9/527 Primary

  for microfluidic devices, e.g. used for lab-on-a-chip · CPC title

• B01L2300/0877

  Flow chambers · CPC title

• G01N2201/025

  Mechanical control of operations · CPC title