Random array DNA analysis by hybridization

• US 7,910,304 B2
• Filed: 10/31/2007
• Issued: 03/22/2011
• 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:
  US11/981,730
• Publication Number:
  US 20090005259A1
• Time in Patent Office: 1,238 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 sequencing target nucleic acids, said method comprising:

(a) providing a random array of said target nucleic acids;

(b) hybridizing a first and second population of oligonucleotide probes to said array;

(c) ligating oligonucleotide probes from said first and second populations that are hybridized to adjacent positions on said target nucleic acids to produce ligated probes;

(d) collecting a signal produced by said ligated probes;

(e) analyzing said signal to identify at least one nucleotide of said target nucleic acids;

(f) repeating steps (b)-(e) to provide multiple cycles of sequence information for said target nucleic acids, such that at least one nucleotide of said target nucleic acids is identified in more than one cycle;

(g) assembling said multiple cycles of sequence information to provide sequences of all or a portion of said target nucleic acids.

2. The method of claim 1, wherein each repetition of steps (b)-(e) utilizes a first and second population of oligonucleotide probes that are overlapping with first and second population of oligonucleotide probes used in a previous cycle.

3. The method of claim 1, wherein each repetition of steps (b)-(e) utilizes first and second populations of oligonucleotide probes that are different than first and second populations of oligonucleotide probes used in previous cycles.

4. The method of claim 3, wherein at least one of said first and second populations of oligonucleotide probes across said multiple cycles together comprises a universal probe set.

5. The method of claim 1, wherein at least one of said first and second population of oligonucleotide probes is detectably labelled.

6. The method of claim 1, wherein said analyzing step (e) identifies at least two nucleotides of said target nucleic acids.

7. The method of claim 1, wherein said target nucleic acids together represent an entire genome.

8. The method of claim 1, wherein said target nucleic acids together represent 10-100 copies of a genome.

9. The method of claim 1, wherein said target nucleic acids comprise an adapter of known sequence.

10. The method of claim 9, wherein said adapter further comprises a tag sequence identifying a sample from which said target nucleic acids are derived.

11. The method of claim 10, wherein said target nucleic acids represent sequences of multiple genomes, and wherein said tag sequence identifies from which genome a target sequence is derived.

12. The method of claim 1, wherein said target nucleic acids are not identical to each other and represent sequences from different parts of said genome, such that together said target nucleic acids represent said entire genome.

13. The method of claim 12, wherein sequence information from different target nucleic acids is assembled into an assembled sequence of all or part of said genome.

14. The method of claim 1, wherein probes within the same population cannot ligate to each other.