Multibase delivery for long reads in sequencing by synthesis protocols

• US 8,236,532 B2
• Filed: 12/17/2009
• Issued: 08/07/2012
• Est. Priority Date: 12/23/2008
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Ronaghi, Mostafa, Eltoukhy, Helmy A.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US12/641,104
• Publication Number:
  US 20100173303A1
• Time in Patent Office: 964 Days
• Field of Search: 435/91.1
• US Class Current: 435/91.1
• 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 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

Methods for obtaining nucleic acid sequence information including the steps of (a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, wherein the first sequencing reagent includes at least two different nucleotide monomers and no more than three nucleotide monomers, wherein the nucleotide monomers are simultaneously in the presence of the target nucleic acid, (b) providing a second sequencing reagent to the target nucleic acid, wherein the second sequencing reagent comprises one or more nucleotide monomers, at least one of the one or more nucleotide monomers being different from the nucleotide monomers present in the first sequencing reagent, and wherein the second sequencing reagent is provided subsequent to providing the first sequencing reagent, and optionally (c) repeating (a) and (b) for said target nucleic acid, whereby sequence information for at least a portion of the target nucleic acid is obtained.

Claims

1. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, wherein the first sequencing reagent comprises at least two different nucleotide monomers and no more than three nucleotide monomers, wherein the nucleotide monomers are simultaneously in the presence of the target nucleic acid;

(b) providing a second sequencing reagent to said target nucleic acid, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent, and wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent; and

(c) repeating (a) and (b) for said target nucleic acid, whereby sequence information for at least a portion of said target nucleic acid is obtained,

wherein the polymerase extends a polynucleotide strand,

further comprising detecting the incorporation of at least one nucleotide monomer into said polynucleotide strand, wherein said detecting comprises detecting pyrophosphate.

2. The method of claim 1, wherein the at least two different nucleotide monomers of the first sequencing reagent are separately provided to said target nucleic acid.

7. The method of claim 1 or 3, wherein said first sequencing reagent and said second sequencing reagent comprise nucleotide monomers selected from the group consisting of deoxyribonucleotides, modified deoxyribonucleotides, ribonucleotides, modified ribonucleotides, peptide nucleotides, modified peptide nucleotides, modified phosphate sugar backbone nucleotides and mixtures thereof.

8. The method of claim 1 or 3, wherein said first sequencing reagent is provided to a single target nucleic acid.

9. The method of claim 1 or 3, wherein said first sequencing reagent is provided simultaneously to a plurality of target nucleic acids.

10. The method of claim 9, wherein said plurality of target nucleic acids comprise target nucleic acids having different nucleotide sequences.

11. The method of claim 1 or 3, wherein said polymerase comprises a polymerase selected from the group consisting of a DNA polymerase, an RNA polymerase, a reverse transcriptase, and mixtures thereof.

12. The method of claim 1 or 3, wherein said polymerase is a thermostable polymerase.

14. The method of claim 1 or 3, further comprising a step of removing at least a portion of said first sequencing reagent.

19. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) providing a first low resolution sequence representation for a target nucleic acid, wherein said first low resolution sequence representation is degenerate with respect to two or more nucleotide types, wherein the first low resolution sequence representation is obtained using the method of claim 1, 3, 13, 15, 16, 17 or 18,

(b) providing a second low resolution sequence representation for said target nucleic acid, wherein said second low resolution sequence representation is degenerate with respect to two or more nucleotide types, wherein at least one of said two or more nucleotide types in the first low resolution sequence representation is different from at least one of said two or more nucleotide types in said second low resolution sequence representation; and

(c) comparing said first low resolution sequence representation and said second low resolution sequence representation to determine the actual sequence of said target nucleic acid at single nucleotide resolution.

20. A method for determining the presence or absence of a target nucleic acid, said method comprising the steps of:

(a) providing a first low resolution sequence representation for a target nucleic acid, wherein said target nucleic acid is obtained from a target sample, wherein said first low resolution sequence representation is degenerate with respect to two or more nucleotide types, wherein the first low resolution sequence representation is obtained using the method of claim 1, 3, 13, 15, 16, 17 or 18,

(b) providing a second low resolution sequence representation for said target nucleic acid, wherein said target nucleic acid is obtained from a reference sample, wherein the second low resolution sequence representation is degenerate with respect to two or more nucleotide types; and

(c) comparing said first low resolution sequence representation and said second low resolution sequence representation to determine the presence or absence of said target nucleic acid in said target sample.

21. The method of claim 1 or 3, wherein said second sequencing reagent comprises one nucleotide monomer and no more than one nucleotide monomer, said one nucleotide monomer being different from said nucleotide monomers of the first sequencing reagent.

22. The method of claim 1 or 3, wherein said polymerase is a thermodegradable polymerase.

27. The method of claim 1, 3, 13, 15, 16, 17 or 18, wherein said first sequencing reagent comprises no more than two nucleotide monomers.

28. The method of claim 27, wherein said second sequencing reagent comprises two different nucleotide monomers and no more than two nucleotide monomers that are simultaneously in the presence of the target nucleic acid, said two different nucleotide monomers both being different from the two nucleotide monomers of the first sequencing reagent.

31. The method of claim 1, 3, 13, 15, 16, 17 or 18, wherein said first sequencing reagent comprises a nucleotide monomer comprising a reversibly terminating moiety.

32. The method of claim 31, further comprising cleaving said reversibly terminating moiety from said nucleotide monomer.

33. The method of claim 1, 3, 13, 15, 16, 17 or 18, wherein the said first sequencing reagent is provided to a plurality of target nucleic acids on a surface of an array in parallel.

34. The method of claim 33, wherein said plurality of target nucleic acids comprise target nucleic acids having different nucleotide sequences.

3. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, wherein the first sequencing reagent comprises at least two different nucleotide monomers and no more than three nucleotide monomers, wherein the nucleotide monomers are simultaneously in the presence of the target nucleic acid, wherein said first sequencing reagent comprises a nucleotide monomer comprising a label;

(b) providing a second sequencing reagent to said target nucleic acid, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent, and wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent; and

(c) repeating (a) and (b) for said target nucleic acid, whereby sequence information for at least a portion of said target nucleic acid is obtained.

4. The method of claim 3, wherein said second sequencing reagent comprises a nucleotide monomer comprising a label.

5. The method of claim 3, wherein said label is selected from the group consisting of fluorescent moieties, chromophores, antigens, dyes, phosphorescent groups, radioactive materials, chemiluminescent moieties, scattering or fluorescent nanoparticles, Raman signal generating moieties, and electrochemical detection moieties.

6. The method of claim 3, further comprising cleaving said label from said nucleotide monomer.

23. The method of claim 3, wherein said label comprises a fluorescent moiety.

24. The method of claim 3, wherein said label comprises a chromophore.

25. The method of claim 3, wherein said label comprises a dye.

26. The method of claim 3, wherein said label comprises an electrochemical detection moiety.

13. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) providing a first sequencing reagent to a target nucleic acid, wherein said first sequencing reagent comprises at least two different nucleotide monomers that are simultaneously in the presence of the target nucleic acid;

(b) detecting the incorporation of a nucleotide monomer present in said first sequencing reagent into a polynucleotide strand complementary to at least a portion of said target nucleic acid;

(c) providing a second sequencing reagent to said target nucleic acid, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent, and wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent; and

(d) detecting the incorporation of a nucleotide monomer present in said second sequencing reagent into the polynucleotide strand, thereby obtaining sequence information for at least a portion of said target nucleic acid.

29. The method of claim 13, 15, 16, 17 or 18, wherein said first sequencing reagent comprises no more than three nucleotide monomers.

30. The method of claim 29, wherein said second sequencing reagent comprises one nucleotide monomer and no more than one nucleotide monomer, said one nucleotide monomer different from said nucleotide monomers of the first sequencing reagent.

15. A method of obtaining nucleic acid sequence information, said method comprising the step of:

(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, wherein the first sequencing reagent comprises at least two different nucleotide monomers that are simultaneously in the presence of the target nucleic acid, and wherein said polymerase incorporates at least one nucleotide monomer of said first sequencing reagent into a polynucleotide strand, thereby producing pyrophosphate;

(b) removing at least a portion of said pyrophosphate; and

(c) providing a second sequencing reagent to said target nucleic acid, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained.

16. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) detecting the incorporation of a nucleotide monomer present in a first sequencing reagent into a polynucleotide strand complementary to at least a portion of a target nucleic acid, wherein said first sequencing reagent comprises at least two different nucleotide monomers that are simultaneously in the presence of the target nucleic acid;

(b) removing at least a portion of said first sequencing reagent;

(c) detecting the incorporation of a nucleotide monomer present in a second sequencing reagent into the polynucleotide strand, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent; and

(c) repeating (a), (b) and (c) for said target nucleic acid, whereby sequence information for at least a portion of said target nucleic acid is obtained.

17. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) detecting pyrophosphate release by the incorporation of a nucleotide monomer present in a first sequencing reagent into a polynucleotide strand complementary to at least a portion of a target nucleic acid, wherein said first sequencing reagent comprises at least two different nucleotide monomers that are simultaneously in the presence of the target nucleic acid;

(b) removing at least a portion of said pyrophosphate; and

(c) detecting the incorporation of a nucleotide monomer present in a second sequencing reagent into the polynucleotide strand complementary to at least a portion of a target nucleic acid, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained.

18. A method for obtaining nucleic acid sequence information, said method comprising the steps of:

(a) detecting the incorporation of a nucleotide monomer present in a first sequencing reagent into a first polynucleotide strand complementary to at least a portion of a target nucleic acid, wherein said first sequencing reagent comprises at least two different nucleotide monomers that are simultaneously in the presence of the target nucleic acid;

(b) detecting the incorporation of a nucleotide monomer present in a second sequencing reagent into the first polynucleotide strand, wherein said second sequencing reagent comprises one or more nucleotide monomers, at least one of said one or more nucleotide monomers being different from the nucleotide monomers present in said first sequencing reagent;

(c) removing said first polynucleotide strand; and

(d) detecting the incorporation of a nucleotide monomer present in a third sequencing reagent into a second polynucleotide strand complementary to at least a portion of said target nucleic acid, wherein said third sequencing reagent comprises two or more nucleotide monomers that are simultaneously in the presence of the target nucleic acid, wherein at least one of said two or more nucleotide monomers is different from the at least two different nucleotide monomers present in said first sequencing reagent and at least one of said two or more nucleotide monomers is different from the one or more nucleotide monomers present in said second sequencing reagent.