DNA sequencing from high density DNA arrays using asynchronous reactions

• US 10,351,909 B2
• Filed: 02/25/2017
• Issued: 07/16/2019
• Est. Priority Date: 06/15/2005
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Drmanac, Radoje, Callow, Matthew J., Drmanac, Snezana, Hauser, Brian K., Yeung, George
• Primary Examiner(s): Forman, Betty J
• Application Number:
  US15/442,659
• Publication Number:
  US 20170175184A1
• Time in Patent Office: 871 Days
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/307 Single strand endonuclease
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/313 Branched oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: G01N 15/1404 Handling flow, e.g. hydrodynamic focusing
• CPC Class Codes: G01N 15/1434 Optical arrangements
• CPC Class Codes: Y10S 977/778 within specified host or matrix material, e.g. nanocomposite films
• CPC Class Codes: Y10S 977/789 in array format
• CPC Class Codes: Y10S 977/792 : Nucleic acid array, e.g. human genome array
• CPC Class Codes: Y10S 977/88 : with arrangement, process, or apparatus for testing
• CPC Class Codes: Y10S 977/882 : Assembling of separate components, e.g. by attaching

Abstract

The invention relates to an automated method for high-throughput DNA sequencing from high density DNA arrays by (a) initiating a first sequencing reaction on a first high density DNA array; and imaging said first high density DNA array using a detector, and (b) initiating a first sequencing reaction on a second high density DNA array; and imaging said second high density DNA array using the detector, wherein the first sequencing reaction in (a) is initiated before the first sequencing reaction in (b) is initiated such that the sequencing reactions in (a) and (b) are staggered. By using asynchronous sequencing reactions and imaging two separate arrays using one detector, imaging can be carried out on one array while sequencing reactions are carried out on one the other, substrate, the other substrate is imaged, reducing the idle time of the imaging system.

Claims

1. A method comprising:

a) initiating a first sequencing reaction on a first high density DNA array; and

imaging said first high density DNA array using a detector, and

b) initiating a second sequencing reaction on a second high density DNA array; and

imaging said second high density DNA array using the same detector,

wherein the first sequencing reaction is initiated before the second sequencing reaction is initiated such that the first sequencing reaction and the second sequencing reaction are non-synchronous,

wherein the first and second high density DNA arrays each independently comprise;

a patterned surface, said surface comprising a pattern of DNA binding regions separated by a non-DNA binding surface, and

more than 10⁵ different DNAs comprising genomic sequences bound on the array at the DNA binding regions,

wherein the DNA binding regions comprise oligonucleotides for binding the DNAs within the DNA binding regions and all of the DNA binding regions of the array comprise the same oligonucleotides, and

wherein;

the density of the DNA binding regions on the array is more than 10⁵ per mm²,

more than 50% of the DNA binding regions in the array have multiple copies of one single DNA of said more than 10⁵ different DNAs,

the sequence of the single DNA at each DNA binding region is not known, and

the array is not a bead array.

3. The method of claim 1, wherein the more than 10⁵ different DNAs comprise human genomic DNA sequences.

4. The method DNA array of claim 1, wherein more than 80% of the DNA binding regions in the array have multiple copies of the one single DNA.

5. The method of claim 1, wherein the DNA binding regions have a center to center distance of about 250-500 nm.

6. The method of claim 1, wherein the DNA binding regions are arranged in a grid pattern.

2. A method comprising:

a) initiating a first sequencing reaction on a first high density DNA array; and

imaging said first high density DNA array using a detector, and

b) initiating a second sequencing reaction on a second high density DNA array; and

imaging said second high density DNA array using the same detector,

wherein the first sequencing reaction is initiated before the second sequencing reaction is initiated such that the first sequencing reaction and the second sequencing reaction are non-synchronous,

wherein the first and second high density DNA arrays each independently comprise;

a patterned surface, said surface comprising a pattern of DNA binding regions at a density of more than 10⁵ DNA binding regions per mm², separated by non-DNA binding regions of said surface,

wherein more than 50% of the DNA binding regions on said surface comprise multiple copies of a single genomic DNA sequence,

wherein the DNA binding regions on said surface comprise more than 10⁵ different genomic DNA sequences,

wherein the genomic DNA sequences are randomly disposed on the array such that the genomic sequence at any given DNA binding region is not known prior to sequencing,

the more than 10⁵ different genomic DNA sequences are linked to adaptor sequences,

the DNA binding regions comprise DNA capture oligonucleotides attached in the DNA binding regions and not attached to the non-DNA binding surface,

all of the DNA binding regions on the surface comprise the same attached capture oligonucleotides,

the capture oligonucleotides are complementary to the adaptors, and

wherein the array is not a bead array.

7. The method of claim 2, wherein the DNA binding regions have a diameter of 125-250 nm.

8. The method of claim 7, wherein the DNA binding regions are arranged in a grid pattern.

9. The method of claim 2, wherein the DNA binding regions have a center to center distance of about 250-500 nm.

10. The method of claim 9, in which there is 100-300 nm of non-DNA binding surface space between DNA binding sites.

11. The method of claim 10, wherein the DNA binding regions are arranged in a grid pattern.

12. The method of claim 2, wherein the DNA binding regions are arranged in a grid pattern.

13. The method of claim 2, wherein the density of the DNA binding regions on the array is more than 1 million per mm².