Method for sequencing a polynucleotide template

• US 9,297,043 B2
• Filed: 03/31/2015
• Issued: 03/29/2016
• Est. Priority Date: 07/20/2005
• Status: Active Grant

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Smith, Geoffrey Paul
• Primary Examiner(s): Kim, Young J
• Application Number:
  US14/674,392
• Publication Number:
  US 20150203911A1
• Time in Patent Office: 364 Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/119 Double strand sequencing

Abstract

The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.

Claims

1. A method for pairwise sequencing of first and second strands of target polynucleotides, wherein the first and second strands of each target polynucleotide have complementary sequences to each other, the method comprising:

(a) forming a plurality of nucleic acid colonies by solid phase nucleic acid amplification on a solid support, wherein each of the nucleic acid colonies comprises multiple copies of a first strand and a complementary second strand formed by amplification of a single originating target polynucleotide;

(b) forming a single-stranded region in first strands of the colonies and hybridizing first sequencing primers to the single-stranded region;

(c) carrying out a first sequencing reaction by sequential addition of nucleotides to the first sequencing primers to determine sequences from the first strands;

whereby after said sequencing reaction, the colonies comprise a plurality of intact duplexes on the solid support, the intact duplexes comprising a portion of the multiple copies of the first strand and a complementary second strand;

(d) cleaving the first strands;

(e) removing at least a portion of the first strands from the colonies, whereby a single-stranded region is formed in each of the complementary second strands;

(f) carrying out a second sequencing reaction by sequential addition of nucleotides to determine sequences from the complementary second strands, wherein the first sequencing reaction and the second sequencing reaction permit pairwise sequencing of the target polynucleotides.

2. The method of claim 1, wherein the nucleic acid colonies are attached to beads.

3. The method of claim 1, wherein the nucleic acid colonies are attached to a planar surface.

4. The method of claim 1, wherein the nucleotides that are added in the first sequencing reaction and in the second sequencing reaction comprise reversible blocking groups.

5. The method of claim 1, wherein the nucleotides that are added in the first sequencing reaction and in the second sequencing reaction comprise labels.

6. The method of claim 1, wherein the first sequencing reaction and the second sequencing reaction comprise pyrosequencing.

7. The method of claim 1, wherein the first sequencing reaction and the second sequencing reaction comprise sequencing-by-synthesis.

8. The method of claim 1, wherein the cleaving of the first strands comprises enzymatic cleavage.

9. The method of claim 1, wherein the cleaving of the first strands comprises chemical cleavage.

10. The method of claim 1, wherein the cleaving of the first strands comprises photochemical cleavage.

11. The method of claim 1, wherein the cleaving of the first strands comprises cleaving an abasic site.

12. The method of claim 1, wherein the cleaving of the first strands comprises nicking the first strands.

13. The method of claim 1, wherein the sequencing is carried out using a sequencing primer in solution.

14. The method of claim 1, wherein the target polynucleotides comprise known adaptor sequences on the 5′

and 3′

ends of the first and second strands.

15. The method of claim 1, wherein the first sequencing reaction and the second sequencing reaction permit pairwise sequencing of separate and distinct regions on the complementary strands of each of the target polynucleotides.

16. The method of claim 1, wherein the first sequencing reaction determines sequences of regions of the first strands, wherein the second sequencing reaction determines sequences of regions of the second strands, and wherein the regions of the first strands are not complementary to the regions of the second strands.

17. The method of claim 1, wherein the first sequencing reaction determines sequences of regions of the first strands, wherein the second sequencing reaction determines sequences of regions of the second strands, and wherein the regions of the first strands are complementary to the regions of the second strands.