Random array DNA analysis by hybridization

• US 8,785,127 B2
• Filed: 10/01/2012
• Issued: 07/22/2014
• Est. Priority Date: 02/26/2003
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Callida Genomics, Inc. (SBH Genomics, Inc.)
• Inventors: Drmanac, Radoje T.
• Primary Examiner(s): Kim, Young J
• Application Number:
  US13/633,034
• Publication Number:
  US 20140024544A1
• Time in Patent Office: 659 Days
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00479 Means for mixing reactants or products in the reaction vessels
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 20/00 Nanooptics, e.g. quantum optics or photonic crystals
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: C12Q 2565/619 being a video camera
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• 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: G01N 2201/06113 Coherent sources; lasers
• CPC Class Codes: G01N 2223/413 sensor array [CCD]

Abstract

The invention relates to methods and devices for analyzing single molecules, i.e., nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air, and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.

Claims

1. A method for determining sequence information for a polynucleotide, comprising:

(a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;

(b) contacting the array with a set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula N_xB_yN_z, wherein;

(i) each N is independently a degenerate base;

(ii) each B is independently an informative base;

(iii) x and z are each at least one; and

(iv) y is 2 to 20;

(c) detecting labeled probes once the probes have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule; and

(d) processing the data to obtain said sequence information for the polynucleotide.

2. The method of claim 1, wherein each DNA molecule comprises multiple copies of the respective fragment.

3. The method of claim 1, wherein y is 2 to 8.

4. The method of claim 1, wherein the labels are fluorescent labels.

5. The method of claim 1, wherein the DNA molecules on the array comprise overlapping fragments of an entire human genome.

6. A method for determining sequence information for a polynucleotide, comprising:

(a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;

(b) contacting the array with a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula N_xB_y or the formula B_yN_z, wherein;

(i) each N is independently a degenerate base;

(ii) each B is independently an informative base;

(iii) x and z are each at least one; and

(iv) y is 2 to 20;

(c) detecting labeled probes from said first set once the probes have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule; and

(d) processing the data to obtain said sequence information for the polynucleotide.

7. The method of claim 6, wherein each probe of the set comprises the formula N_xB_y.

8. The method of claim 6, wherein each probe of the set comprises the formula B_yN_z.

9. The method of claim 6, further comprising:

(e) contacting the array with a second set of oligonucleotides; and

(f) ligating oligonucleotide probes from the first set to oligonucleotides from the second set that are hybridized to adjacent sites on the DNA molecules on the array.

10. The method of claim 9, wherein the first set of probes is a universal probe set.

11. The method of claim 6, wherein x is 1 to 4.

12. The method of claim 6, wherein y is 2 to 8.

13. The method of claim 6, wherein y is 4 to 5.

14. The method of claim 6, wherein z is 1 to 4.

15. The method of claim 6, wherein the labels are fluorescent labels.

16. The method of claim 6, wherein each DNA molecule comprises multiple copies of the respective fragment.

17. The method of claim 6, wherein the DNA molecules on the array comprise overlapping fragments of an entire human genome.

18. A method for determining sequence information for a polynucleotide, comprising:

(a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;

(b) contacting the array with a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula N_xB_y or the formula B_yN_z, wherein;

(i) each N is independently a degenerate base;

(ii) each B is independently an informative base; and

(iii) x, y, and z are each at least one;

(c) contacting the array with a second set of oligonucleotide probes, each configured to bind to a site in a DNA molecule of the array adjacent to a probe from the first set;

(d) detecting labeled probes from said first set once oligonucleotide probes from both the first and the second set have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule; and

(e) processing the data to obtain said sequence information for the polynucleotide.

19. The method of claim 18, further comprising ligating an oligonucleotide probe from the first set to an oligonucleotide from the second set when hybridized to adjacent sites on a DNA molecule on the array.

20. The method of claim 18, wherein probes in the first set comprise the formula N_xB_yN_z.

21. The method of claim 18, wherein y is 2 to 8.

22. The method of claim 18, wherein the DNA molecules on the array comprise overlapping fragments of an entire human genome.