DNA sequencing from high density DNA arrays using asynchronous reactions

Patent metadata

Field	Value
Publication number	US-10351909-B2
Application number	US-201715442659-A
Country	US
Kind code	B2
Filing date	Feb 25, 2017
Priority date	Jun 15, 2005
Publication date	Jul 16, 2019
Grant date	Jul 16, 2019

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.

First claim

What is claimed is:

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 10 5 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 10 5 per mm 2 ,
more than 50% of the DNA binding regions in the array have multiple copies of one single DNA of said more than 10 5 different DNAs,
the sequence of the single DNA at each DNA binding region is not known, and
the array is not a bead array.

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 10 5 DNA binding regions per mm 2 , 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 10 5 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 10 5 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.

3. The method of claim 1 , wherein the more than 10 5 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.

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 mm 2 .

Assignees

• Complete Genomics Inc

Inventors

• Drmanac Radoje
• Callow Matthew J
• Drmanac Snezana
• Hauser Brian K
• Yeung George

Classifications

• C12Q1/6837

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• Y10S977/882

  Assembling of separate components, e.g. by attaching · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• G01N15/1404

  Handling flow, e.g. hydrodynamic focusing · CPC title

• C12Q1/682

  Signal amplification · CPC title