Nucleic acid sequencing by selective excitation of microparticles

• US 8,222,040 B2
• Filed: 08/28/2007
• Issued: 07/17/2012
• Est. Priority Date: 08/28/2007
• Status: Active Grant

• Current Assignee: Rebus Biosystems, Inc.
• Original Assignee: LightSpeed Genomics, Inc.
• Inventors: Hong, Stanley S., Ryu, Jekwan, Park, Jong Buhm
• Primary Examiner(s): Gakh, Yelena G
• Assistant Examiner(s): Adams, Michelle
• Application Number:
  US11/846,049
• Publication Number:
  US 20090061526A1
• Time in Patent Office: 1,785 Days
• Field of Search: None
• US Class Current: 436/94
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G06F 18/00 Pattern recognition
• CPC Class Codes: G06V 2201/04 Recognition of patterns in DNA microarrays
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Nucleic acid microparticles are sequenced by performing a sequencing reaction on the microparticles using one or more reagents, selectively exciting the microparticles in an excitation pattern, optically imaging the microparticles at a resolution insufficient to resolve individual microparticles, and processing the optical images of the microparticles using information on the excitation pattern to determine the presence or absence of the optical signature, which indicates the sequence information of the nucleic acid. An apparatus for optical excitation of the microparticles comprises an optical fiber delivering a first laser beam, and an interference pattern generation module coupled to the optical fiber. The interference pattern generation module splits the first laser beam into second and third laser beams and generates the excitation pattern for selectively exciting the microparticles by interference between the second and third laser beams.

Claims

1. A method for sequencing nucleic acid microparticles, the method comprising the steps of:

selectively exciting a calibration target by interference of a plurality of illumination beams;

obtaining optical images of the excited calibration target;

processing the optical images of the excited calibration target to generate a first optical image of the excited calibration target;

predicting a second optical image of the excited calibration target based on first calibration parameters;

generating second calibration parameters based on a difference between the first optical image and the second optical image;

performing a sequencing reaction on the nucleic acid microparticles using one or more sequencing reagents, the nucleic acid particles being different from the calibration target;

selectively exciting the nucleic acid microparticles in an excitation pattern using the second calibration parameters;

obtaining optical images of the nucleic acid microparticles at a resolution insufficient to resolve individual microparticles; and

processing the optical images of the nucleic acid microparticles using information on the excitation pattern to determine a presence or absence of at least one optical signature, the presence or absence of said at least one optical signature indicating sequence information of the nucleic acid microparticles.

2. The method of claim 1, wherein the nucleic acid microparticles are selectively excited at a resolution sufficient to resolve the individual microparticles.

3. The method of claim 1, wherein the excitation pattern is generated by interference of a plurality of illumination beams.

4. The method of claim 3, wherein the plurality of illumination beams undergo total internal reflection off a substrate on which the microparticles are placed.

5. The method of claim 3, wherein the excitation pattern generated by interference of the plurality of illumination beams produces sampling of a frequency domain in which an extent of the distribution of frequency samples is matched to a feature size of the microparticles.

6. The method of claim 3, wherein the excitation pattern generated by interference of the plurality of illumination beams produces a rectangle-like sampling of a frequency domain.

7. The method of claim 3, wherein the excitation pattern generated by interference of the plurality of illumination beams produces a non-rectilinear sampling of a frequency domain.

8. The method of claim 3, wherein selectively exciting the nucleic acid microparticles comprises:

selectively exciting the nucleic acid microparticles in a first excitation pattern generated by interference of the illumination beams; and

selectively exciting the nucleic acid microparticles in a second excitation pattern different from the first pattern generated by a different interference of the illumination beams.

9. The method of claim 8, wherein a phase of at least one of the illumination beams is modulated to generate the different interference of the illumination beams.

10. The method of claim 1, further comprising:

performing another sequencing reaction on the nucleic acid microparticles;

selectively exciting the nucleic acid microparticles in another excitation pattern;

obtaining additional optical images of the nucleic acid microparticles at a resolution insufficient to resolve the individual microparticles; and

processing the additional optical images of the nucleic acid microparticles using information on said another excitation pattern to determine a presence or absence of another optical signature, the presence or absence of said another optical signature indicating different sequence information of the nucleic acid microparticles.

11. The method of claim 1, wherein determining the presence or absence of at least an optical signature comprises determining that at least one of the microparticles exhibits an optical signature brighter or with a different spectral characteristic than other microparticles.

12. The method of claim 1, wherein processing the optical images of the nucleic acid microparticles comprises:

generating a synthetic image of the microparticles with a higher resolution than the optical images based on the information on the excitation pattern;

applying a microparticle signature identification algorithm to the synthetic image to generate microparticle optical signature data; and

applying a base calling algorithm to determine the presence or absence of said at least one optical signature corresponding to the sequence information of the nucleic acid microparticles.

13. The method of claim 1, further comprising repeating the steps of selectively exciting the nucleic acid microparticles, obtaining optical images of the nucleic acid microparticles, and processing the optical images of the nucleic acid microparticles for a different field of view.

14. A method for sequencing nucleic acid microparticles, the method comprising the steps of:

performing a sequencing reaction on the nucleic acid microparticles using one or more sequencing reagents;

selectively exciting the nucleic acid microparticles with excitation patterns generated by interference of a plurality of illumination beams, at least one of the illumination beams being modulated in only two or three phases with respect to a period of an interference pattern to generate different sinusoidal interference patterns for use as the excitation patterns;

obtaining optical images of the nucleic acid microparticles at a resolution insufficient to resolve individual microparticles; and

processing the optical images of the nucleic acid microparticles using information on the excitation patterns to determine a presence or absence of at least one optical signature, the presence or absence of said at least one optical signature indicating sequence information of the nucleic acid microparticles.

15. The method of claim 14, wherein the excitation patterns generated by interference of the plurality of illumination beams produces a rectangle-like sampling of a frequency domain.

16. The method of claim 14, wherein the excitation pattern generated by interference of the plurality of illumination beams produces a non-rectilinear sampling of a frequency domain.