Method for sequencing a polynucleotide template

• US 8,192,930 B2
• Filed: 02/08/2007
• Issued: 06/05/2012
• Est. Priority Date: 02/08/2006
• Status: Active Grant

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Barnes, Colin Lloyd, Rigatti, Roberto, Gormley, Niall Anthony, Smith, Geoffrey Paul, Bentley, David, Vermaas, Eric Hans, Worsley, Graham John, Boutell, Jonathan Mark, Smith, Vincent Peter, Ost, Tobias William Barr
• Primary Examiner(s): Mummert, Stephanie K
• Application Number:
  US12/223,759
• Publication Number:
  US 20110009276A1
• Time in Patent Office: 1,944 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.

Claims

1. A method for pairwise sequencing of first and second regions of a double stranded polynucleotide wherein said first and second regions are in the same target double stranded polynucleotide, the method comprising hybridising and reading from a first primer, removing the first primer followed by hybridising and reading from a second primer at a different location in the same target double stranded polynucleotide.

2. The method according to claim 1, wherein the method comprises:

(a) providing solid support having immobilised thereon a plurality of double stranded template polynucleotides each formed from complementary first and second template strands linked to the solid support at their 5′

ends, wherein each double stranded template polynucleotide comprises a target double stranded polynucleotide;

(b) treating the plurality of double stranded template polynucleotides to denature said double stranded template polynucleotides to allow hybridisation of a sequencing primer;

(c) hybridising a first sequencing primer to one of the template polynucleotides generated in part (b);

(d) carrying out a first sequencing reaction to monitor the incorporation of labeled nucleotides one the first sequencing primer using cycles of primer extension with a polymerase and labeled nucleotides to generate a first extended sequencing primer and determine the sequence of a first region of the template polynucleotide;

(e) removing the extended sequencing primer from step (d);

(f) hybridising a second sequencing primer to the one template polynucleotide of step (c) or a complement thereof; and

(g) carrying out a second sequencing run to monitor the incorporation of labeled nucleotides onto the second sequencing primer using cycles of primer extension with a polymerase and labeled nucleotides to generate a second extended sequencing primer and determine the sequence of a second region of the template polynucleotide, wherein determining the sequences of the first and second regions of the template polynucleotide achieves pairwise sequencing of said first and second regions of said target double-stranded polynucleotide.

3. The method according to claim 1, wherein both strands are attached to a surface, and the first primer is hybridised by heating and cooling.

4. The method according to claim 1, wherein both strands are attached to a surface, and the second primer is hybridised by heating and cooling.

5. The method according to claim 1, wherein both strands are attached to a surface, and the first primer is hybridised after a step of chemical denaturing.

6. The method according to claim 1, wherein both strands are attached to a surface, and the second primer is hybridised after a step of chemical denaturing.

7. The method according to claim 5 or 6, wherein said chemical denaturing is performed using sodium hydroxide solution, formamide solution or urea solution.

8. The method according to claim 7, wherein the concentration of sodium hydroxide solution is greater than 0.05 M.

9. The method according to claim 1, wherein the target double stranded polynucleotide is attached to a surface and comprises an internal known primer region between said first and second regions of the target double stranded polynucleotide and the target double-stranded polynucleotide is denatured to allow hybridisation of a first primer.

10. The method according to claim 9, wherein the internal known primer region comprises a site recognised by a restriction enzyme, and the denaturation process comprises a step of treatment using a restriction enzyme which recognizes said site.

11. The method according to claim 9, wherein the internal known primer region comprises a site recognised by a restriction enzyme, and the denaturation process comprises the steps of using a restriction enzyme which recognizes said site and chemical denaturation to remove non-covalently attached single stranded polynucleotide regions from the surface.

12. The method according to claim 11, wherein said chemical denaturing is performed using sodium hydroxide solution, formamide solution or urea solution.

13. The method according to claim 12, wherein the concentration of sodium hydroxide solution is greater than 0.05 M.

14. The method according to claim 10, wherein said first and second regions of immobilised polynucleotides are sequenced using said first and second primers, said primers being complementary to different regions of the known internal primer at either side of said restriction site.

15. The method according to claim 9, wherein one strand of said double stranded polynucleotide is cleaved from the surface to leave a double stranded polynucleotide immobilised at one end, said double stranded polynucleotide containing two known regions capable of hybridising to a sequencing primer, and said method further comprises denaturing said double stranded polynucleotide to produce an immobilized single stranded polynucleotide.

16. The method according to claim 15, wherein said cleavage step is a chemical or photochemical treatment to cleave the 5′

-end of one of the strands of the double stranded polynucleotide.

17. The method according to claim 16, wherein the double stranded polynucleotide is attached via a diol linkage which is cleaved by treatment with a chemical agent comprising periodate.

18. The method according to claim 15, wherein said cleaving involves an enzymatic treatment that cleaves one of the immobilised strands of the polynucleotide.

19. The method according to claim 18, wherein cleavage is performed using a restriction endonuclease.

20. The method according to claim 15, wherein said double stranded polynucleotides are denatured by heating.

21. The method according to claim 15, wherein said double stranded polynucleotides are denatured by chemical denaturation.

22. The method according to claim 21, wherein said chemical denaturation is performed using sodium hydroxide solution, formamide solution or urea solution.

23. The method according to claim 22, wherein the concentration of sodium hydroxide solution is greater than 0.05 M.

24. The method according to claim 1, wherein a plurality of template double stranded polynucleotides are present on a clustered array.

25. The method according to claim 24, wherein the plurality of template double stranded polynucleotides are present within a single cluster on said clustered array.

26. The method according to claim 24, wherein the clustered array is formed by solid-phase nucleic acid amplification.