System and method with fiducials responding to multiple excitation frequencies

Patent metadata

Field	Value
Publication number	US-2020009525-A1
Application number	US-201816482592-A
Country	US
Kind code	A1
Filing date	Jan 31, 2018
Priority date	Feb 1, 2017
Publication date	Jan 9, 2020
Grant date	—

Abstract

Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.

First claim

1 . An array, comprising:
a support having a plurality of areas, each of the plurality of areas having locations that, in operation, receive biological samples differing from one another to respond differently in successive cycles of fluorescent imaging; and a fiducial feature on the support in each of the plurality of areas, each of the fiducial features having a fluorescent material that responds by producing a detectable signal in the successive cycles of fluorescent imaging.

2 . The array of claim 1 , wherein in performing the successive cycles of fluorescent imaging only some of the biological samples appear in successive images to the exclusion of other of the biological samples, but in which the fiducial features appear in all images.

3 . The array of claim 1 , wherein the successive cycles of fluorescent imaging are performed utilizing light at at least two different wavelengths, and wherein the fluorescent material of the fiducial features is responsive to both of the at least two different wavelengths.

4 . The array of claim 1 , wherein the fiducial features comprise at least one depression and objects disposed in the at least one depression, the objects comprising the fluorescent material.

5 . The array of claim 4 , wherein the objects disposed in the at least one depression are too large to be received in the locations of the support that receive the biological samples.

6 . The array of claim 1 , wherein the locations are disposed in a regular repeating pattern on the support.

7 . (canceled)

8 . The array of claim 1 , wherein the biological samples comprise nucleic acid sequences.

9 . The array of claim 1 , wherein the fiducial features comprise adjacent but non-concentric shapes.

10 . The array of claim 1 , wherein the fiducial features comprise a non-closed shape.

11 . The array of claim 1 , wherein the fiducial features are disposed on the support in a non-rectilinear layout.

12 . The array of claim 1 , wherein the fiducial features are structured to produce image data encoding information.

13 . The array of claim 1 , further comprising at least one additional fiducial feature that is formed in or on the support and is optically reflective to, during imaging, return at least a portion of incident radiation for locating, adjusting the location of, or registering the support or the locations.

14 . The array of claim 1 , wherein the fiducial features comprise a plurality of autofluorescent elements disposed in wells or a trench.

15 . The array of claim 1 , wherein the fiducial features comprise a plurality of elements having a diameter of between about 5 μm and about 10 μm.

16 . The array of claim 1 , wherein the fiducial features comprise a plurality of elements comprising polystyrene, silica, or a combination thereof.

17 . A method, comprising:
disposing reaction sites at locations on a support including a plurality of areas, each of the plurality of areas having some of the locations, the reaction sites to attach biological samples differing from one another to respond differently in successive cycles of fluorescent imaging; and disposing a fiducial feature on the support in each of the plurality of areas, the fiducial feature comprising fluorescent material that responds by producing a detectable signal in the successive cycles of fluorescent imaging.

18 . The method of claim 17 , further comprising:
introducing the biological samples to the support to attach the biological samples to the reaction sites; imaging the biological samples and the fiducial features in the successive cycles of fluorescent imaging at different wavelengths of light to produce image data that encodes fluorescent signals produced by the biological samples and the fiducial feature.

19 . The method of claim 17 , further comprising introducing the biological samples to the support to attach the biological samples to the reaction sites; wherein between each successive cycle of fluorescent imaging, a tag is removed from the biological sample at each location, and an additional biological component is added to each biological sample at each location, the additional biological components having tags that respond to the successive cycle of fluorescent imaging.

20 . A method, comprising:
accessing image data encoding successive images of biological samples disposed at locations in a plurality of areas on a support, the biological samples differing from one another to respond differently in successive cycles of fluorescent imaging, the image data further encoding images of fiducial features in each of the plurality of areas on the support, each of the fiducial features having fluorescent material that responds by producing a detectable signal in successive cycles of fluorescent imaging; registering, for the successive images, the locations on the support by reference to the fiducial features; and processing the registered successive images to transform data derived from the registered successive images to sequence data.

21 . (canceled)

22 . The array of claim 9 , wherein the adjacent but non-concentric shapes comprise circles.

23 . (canceled)

24 . The array of claim 1 , further comprising an auto-centering fiducial located outside of the plurality of areas on the support where the locations of the support that receive the biological samples are disposed.

25 .- 38 . (canceled)

39 . The method of claim 20 , further comprising characterizing molecules having tags at locations in each of the registered successive images, wherein the molecules comprise nucleic acids.

40 . The method of claim 20 , further comprising imaging the biological samples and the fiducial features in the successive cycles of fluorescent imaging at different wavelengths of light to produce the image data that encodes fluorescent signals produced by the biological samples and the fiducial feature.

41 . (canceled)

42 . The array of claim 12 , wherein the information is encoded by alternate signal-producing areas and non-signal producing areas detectable in the image data, and wherein the alternate signal-producing areas and non-signal-producing areas are detectable as unchanged through the successive cycles of fluorescent imaging.

43 . (canceled)

44 . The array of claim 42 , wherein the alternate signal-producing areas and non-signal-producing areas comprise dash-like areas, dot-like areas, or combinations thereof.

45 . The array of claim 12 , wherein the information is encoded by a shape of at least a portion of the fiducial features, or an orientation of at least a portion of the fiducial features.

46 . (canceled)

47 . The array of claim 12 , wherein each of the fiducial features comprises a plurality of elements, and wherein the information is encoded by a relative orientation or positioning of the elements.

48 . The array of claim 12 , wherein each of the fiducial features comprises machine-readable indicia comprising discrete regions arranged to define binary data having an interpretable meaning.

49 .- 53 . (canceled)

54 . The array of claim 48 , wherein the machine-readable indicia comprise a bar-code indicia.

55 . The array of claim 12 , wherein the

Assignees

• Illumina Inc

Inventors

• Vieceli John S
• Nemiroski Alex
• Belitz Paul
• Langlois Robert
• Bowen M Shane
• Chan Danny Yuan
• Venkatesan Bala Murali K
• Han Hui
• Samiee Kevan
• Tanner Stephen

Classifications

• B01J2219/00722

  Nucleotides · CPC title

• B01J2219/00648

  by the use of solid beads · CPC title

• B01J2219/00693

  Means for quality control · CPC title

• G01N21/6456

  Spatial resolved fluorescence measurements; Imaging · CPC title

• B01J2219/00608

  DNA chips · CPC title