Hexagonal site line scanning method and system

• US 20080117425A1
• Filed: 11/21/2006
• Published: 05/22/2008
• Est. Priority Date: 11/21/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kain, Robert
• Granted Patent: US 7,813,013 B2
• Time in Patent Office: Days
• US Class Current: 356/455
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 2021/6484 Optical fibres
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G02B 13/22 Telecentric objectives or lens systems
• CPC Class Codes: G02B 6/4204 the coupling comprising intermediate optical elements, e.g. lenses, holograms encapsulated active devices H01S5/02208, H01L33/52

Abstract

A scanning technique for imaging sites in an array includes illuminating or irradiating sites in lines of the array, and collecting returned radiation from the sites for imaging. The sites are sequentially scanned by means of confocally directed radiation lines from source optics. The orientation of the radiation lines with respect to the lines of sites in the array is such that the distance between nearest edges of sites in adjacent lines is greater than lines through those edges in a direction parallel to the radiation lines used for scanning. The resulting system experiences less crosstalk and a greater ability to distinguish between neighboring sites in resulting images.

Claims

1. A method for analyzing an array of discrete sites, comprising:

simultaneously detecting a first plurality of sites in a first line of the array; and

simultaneously detecting a second plurality of sites in a second line of the array;

wherein the second line is generally parallel to the first line,

wherein a distance D separates the first line and the second line when passing through nearest edges of the first and second plurality of sites, and

wherein the distance between the nearest edges of adjacent sites within each of the plurality of sites is greater than D.

2. The method of claim 1, wherein the array comprises a biological microarray.

3. The method of claim 1, wherein the array comprises discrete sites on a surface.

4. The method of claim 1, wherein the first plurality of sites is simultaneously irradiated with a radiation line.

5. The method of claim 4, wherein the radiation line is moved across the array to sequentially irradiate the first plurality of sites and the second plurality of sites.

6. The method of claim 4, wherein the first plurality of sites is sequentially irradiated with radiation, and wherein return radiation from the sites forms a line at a detector.

7. The method of claim 4, wherein the radiation line has a width less than D.

8. The method of claim 4, wherein the radiation line is confocally directed to the sites along the first line and the second line.

9. The method of claim 4, wherein the radiation line is substantially continuous along a desired length extending over the plurality of sites.

10. The method of claim 1, wherein the sites have a generally symmetric shape.

11. The method of claim 1, wherein the sites are arranged in a generally hexagonal grid, and wherein the first and second lines are parallel to lines of the grid.

12. The method of claim 1 further comprising returning radiation from the sites to a detector that generates signals for analysis of the sites.

13. A method for analyzing an array of discrete sites comprising:

sequentially irradiating a series of lines of the sites, each line being irradiated with a radiation line;

wherein the distance between the nearest edges of adjacent sites in each of the adjacent lines of sites is greater than the distance between parallel lines passing through the nearest edges of the sites in the adjacent lines of sites.

14. The method of claim 13, wherein the array comprises a biological microarray.

15. The method of claim 13, wherein the array comprises discrete sites on a surface.

16. The method of claim 13, wherein each line is simultaneously irradiated with the radiation line.

17. The method of claim 13, wherein each line is sequentially irradiated with radiation, and wherein return radiation from the sites forms a line at a detector.

18. The method of claim 13, wherein the sites have a generally symmetric shape.

19. The method of claim 13, wherein the sites are arranged in a non-rectilinear grid.

20. The method of claim 19, wherein the sites are arranged in a generally hexagonal grid.

21. The method of claim 13, wherein the radiation line is confocally directed to the sites along the adjacent lines of sites.

22. The method of claim 13, wherein the radiation line is substantially continuous along a desired length extending over the plurality of sites.

23. The method of claim 13 further comprising returning radiation from the sites to a detector that generates signals for analysis of the sites.

24. A method for analyzing an array having discrete sites comprising:

(a) irradiating a line of the sites with radiation;

(b) repeating step (a) for a plurality of lines of sites; and

(c) returning radiation from each of the lines of sites to a detector that generates signals for analysis of the sites;

wherein the sites are disposed in a non-rectilinear grid on the array surface, whereby the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between parallel lines passing through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, and

wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines.

25. The method of claim 24, wherein step (a) comprises simultaneously irradiating the line of the sites with a radiation line.

26. The method of claim 25, wherein the radiation line has a width less than the distance between parallel lines passing through the nearest edges of the sites in adjacent lines of the plurality of lines of sites.

27. The method of claim 24, wherein step (a) comprises sequentially irradiating the line of the sites with radiation, wherein the return radiation from the sites forms a line at a detector.

28. The method of claim 24, wherein the array comprises a biological microarray.

29. The method of claim 24, wherein the array comprises discrete sites on a surface.

30. The method of claim 24, wherein the sites have a generally symmetric shape.

31. The method of claim 24, wherein the sites are disposed in a generally hexagonal grid on the array surface.

32. A system for analyzing an array of discrete sites, the system configured to:

simultaneously detect a first plurality of sites in a first line of the array; and

simultaneously detect a second plurality of sites in a second line of the array,

wherein the second line is generally parallel to the first line,

wherein a distance D separates the first line and the second line when passing through the nearest edges of the first and second plurality of sites, and

wherein the distance between the nearest edges of adjacent sites within each of the plurality of sites is greater than D.

33. A system for analyzing an array of discrete sites, the system configured to:

sequentially irradiate a series of lines of the sites, each line being irradiated with a radiation line;

wherein the distance between the nearest edges of adjacent sites in each of the adjacent lines of sites is greater than the distance between parallel lines passing through the nearest edges of the sites in the adjacent lines of sites.

34. A system for analyzing an array of discrete sites, the system configured to:

(a) simultaneously irradiate a plurality of sites with a line of radiation;

(b) repeat step (a) for a plurality of lines of sites; and

(c) return radiation from each of the pluralities of sites to a detector that generates signals for analysis of the sites;

wherein the sites are disposed in a non-rectilinear grid on the array surface,

wherein the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between parallel lines passing through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, and

wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines.

35. A system for analyzing an array of discrete sites, the system configured to:

(a) sequentially irradiate a plurality of sites with radiation, wherein said sites are disposed along a line,

wherein the return radiation from the plurality of sites forms a line at a detector;

(b) repeat step (a) for a plurality of lines of the sites; and

(c) return radiation from each of the pluralities of sites to a detector that generates signals for analysis of the sites;

wherein the sites are disposed in a non-rectilinear grid on the array surface,

wherein the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between parallel lines passing through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, and

wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines.