Method for pair-wise sequencing a plurity of target polynucleotides

• US 7,754,429 B2
• Filed: 10/05/2007
• Issued: 07/13/2010
• Est. Priority Date: 10/06/2006
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Ost, Tobias William Barr, Rigatti, Roberto
• Primary Examiner(s): Horlick; Kenneth R.
• Application Number:
  US11/973,321
• Publication Number:
  US 20090088327A1
• Time in Patent Office: 1,012 Days
• Field of Search: 435/6, 435/91.1
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/119 Double strand sequencing
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

The invention relates to 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. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template.

Claims

1. A method for pairwise sequencing of first and second regions in each of a plurality of target polynucleotides, the method comprising:

(a) providing a solid support having immobilised thereon a plurality of first template polynucleotides linked to the solid support at their 5′

ends, wherein a 5′

-end immobilised primer is hybridised to the 3′

end of each of the first template polynucleotides;

(b) obtaining sequence data from a first region of the first template polynucleotides;

(c) extending the 5′

-end immobilised primers to copy the first template polynucleotides to generate a plurality of second immobilised template polynucleotides;

(d) removing the plurality of first template polynucleotides from the solid support; and

(e) obtaining sequence data for a second region of each of the second immobilised template polynucleotides, wherein determining the sequences of the first and second regions of the first and second template polynucleotides achieves pairwise sequencing of said first and second regions of said target polynucleotides.

2. The method according to claim 1, wherein the sequences of the first and second region are determined using labelled nucleotides or oligonucleotides.

3. The method according to claim 1, wherein the template polynucleotides are immobilised on a single pianar solid support or on a plurality of microspheres.

4. The method according to claim 3, wherein the microspheres are immobilised on a single solid support.

5. The method according to claim 1, wherein the removal of the plurality of first template polynucleotides comprises nicking the immobilised template polynucleotides with an endonuclease.

6. The method according to claim 1, wherein the removal of the plurality of first template polynucleotides comprises formation and cleavage of an abasic site in the immobilised template polynucleotides.

7. The method according to claim 6, wherein said abasic site is generated from a uracil base or from an 8-oxo-guanine base.

8. The method according to claim 7, wherein the uracil base is removed by treatment with Uracil DNA glycosylase (UDG) and DNA glycosylase-lyase Endonuclease VIII or FPG glycosylase.

9. The method according to claim 1, wherein step (b) comprises obtaining sequence data from a first region of the first template polynucleotides using a polymerase with strand displacing activity, wherein the first template polynucleotide is double stranded.

10. The method according to claim 1, further comprising an additional step prior to step 1(b) of making the immobilised template polynucleotides single stranded.

11. The method according to claim 10, wherein the additional step comprises treating the immobilised template polynucleotides with a 5′

-3′

exonuclease to digest strands not immobilised at their 5′

-ends or treating the immobilised template polynucleotides with a chemical denaturant.

12. The method according to claim 1, wherein step (b) comprises obtaining sequence data from a first region of the first template polynucleotides by hybridising an immobilised primer to the immobilised template polynucleotides.

13. The method according to claim 1, wherein step (b) comprises obtaining sequence data from a first region of the first template polynucleotides by hybridising a non immobilised sequencing primer to the immobilised template polynucleotides.

14. The method according to claim 1, wherein the first template polynucleotide strands are attached via a diol linkage which is cleaved by treatment with a chemical cleavage agent comprising periodate, and the duplex is subsequently denatured.

15. The method according to claim 8, wherein the immobilised template polynucleotide is treated with a phosphatase to remove a 3′

-phosphate group left by the action of Uracil DNA glycosylase.

16. The method according to claim 1, further comprising a step of treating said 5′

-end immobilised primer with a restriction enzyme prior to step 1(c).

17. The method according to claim 1, wherein step 1c is repeated through multiple cycles of extension and denaturation.

18. The method according to claim 1, wherein at least one of the immobilised primers comprises a block at the 3′

end, and the block is removed prior to step 1(c).

19. The method of claim 18, wherein said block is a phosphate moiety, a 3′

-deoxynucleotide or wherein the 5′

-end immobilised primer comprises a self complementary hairpin with a sequence that binds to a restriction enzyme that can be cleaved using said restriction enzyme.

20. The method according to claim 1, wherein the target polynucleotides each comprise a specific nucleotide sequence tag to identify the source of the polynucleotide.