Methods, systems, and computer readable media for repeat sequencing

• US 10,329,608 B2
• Filed: 10/08/2013
• Issued: 06/25/2019
• Est. Priority Date: 10/10/2012
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hubbell, Earl, Koller, Christian, Homer, Nils
• Primary Examiner(s): Brusca, John S
• Application Number:
  US14/048,843
• Publication Number:
  US 20140113281A1
• Time in Patent Office: 2,086 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2535/119 Double strand sequencing
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Claims

1. A method for sequencing a nucleic acid template, comprising:

(a) performing a first sequencing process on a first portion of the nucleic acid template to obtain a first sequencing result using a sequencing instrument configured to sequence a given sample two or more times, wherein the first sequencing process includes delivering first reagents including a first polymerase and first primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a first order comprising a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set; and

(b) after the first sequencing process, performing a second sequencing process on a second portion of the nucleic acid template to obtain a second sequencing result using the sequencing instrument, wherein the second sequencing process includes delivering second reagents including a second polymerase and second primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a second order different from the first order, wherein the first and second portions of the nucleic acid template may overlap at least partially, completely, or not at all.

2. The method of claim 1, wherein at least one of the first and second orders comprises a combination of Kautz sequences generated using all possible dimers of A, C, G, and T.

3. The method of claim 1, wherein at least one of the first and second orders comprises a combination of loops through a Kautz graph of possible dimers of A, C, G, and T.

4. The method of claim 1, wherein at least one of the first and second orders comprises a series of a predetermined number of predetermined permutations of a combination of at least three loops through a Kautz graph of possible dimers of A, C, G, and T.

5. The method of claim 4, wherein the series of a predetermined number of predetermined permutations of a combination of at least three loops comprises a first loop, followed by a second loop, followed by a third loop, followed by the first loop, followed by the third loop, followed by the second loop.

6. The method of claim 1, wherein, in the first order, the isolated flow of the nucleotide not in the first set is followed by a second 4-flow permutation of flows A, C, G, and T different than the first 4-flow permutation, followed by a second predetermined number of repeats of a second 3-flow permutation of a second set of three flows selected from A, C, G, and T different than the first set, followed by an isolated flow of the nucleotide not in the second set.

7. The method of claim 6, wherein, in the first order, the isolated flow of the nucleotide not in the second set is followed by a third 4-flow permutation of flows A, C, G, and T different than the first and second 4-flow permutations, followed by a third predetermined number of repeats of a third 3-flow permutation of a third set of three flows selected from A, C, G, and T different than the first and second sets, followed by an isolated flow of the nucleotide not in the third set.

8. The method of claim 7, wherein, in the first order, the isolated flow of the nucleotide not in the third set is followed by a fourth 4-flow permutation of flows A, C, G, and T different than the first, second, and third 4-flow permutations, followed by a fourth predetermined number of repeats of a fourth 3-flow permutation of a fourth set of three flows selected from A, C, G, and T different than the first, second, and third sets, followed by an isolated flow of the nucleotide not in the fourth set.

9. The method of claim 1, wherein the second order comprises a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set.

12. The method of claim 1, wherein the first predetermined number of repeats is equal to three.

13. The method of claim 8, wherein the first, second, third, and fourth predetermined numbers of repeats are each equal to three.

14. The method of claim 1, wherein the second reagents differ from the first reagents in at least one property selected from the group comprising:

nucleotide fidelity, rate of nucleotide incorporation, and kinetics of nucleotide binding.

15. The method of claim 1, wherein the second reagents differ from the first reagents in at least one property selected from the group comprising:

processivity, catalysis, polymerase translocation, and exonuclease activity.

10. A system for sequencing a nucleic acid template, comprising:

a machine-readable memory; and

a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform a method comprising;

(a) performing a first sequencing process on a first portion of the nucleic acid template to obtain a first sequencing result using a sequencing instrument configured to sequence a given sample two or more times, wherein the first sequencing process includes delivering first reagents including a first polymerase and first primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a first order comprising a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set; and

(b) after the first sequencing process, performing a second sequencing process on a second portion of the nucleic acid template to obtain a second sequencing result using the sequencing instrument, wherein the second sequencing process includes delivering second reagents including a second polymerase and second primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a second order different from the first order, wherein the first and second portions of the nucleic acid template may overlap at least partially, completely, or not at all.

16. The system of claim 10, wherein the first predetermined number of repeats is equal to three.

17. The system of claim 10, wherein the second reagents differ from the first reagents in at least one property selected from the group comprising:

nucleotide fidelity, rate of nucleotide incorporation, and kinetics of nucleotide binding.

18. The system of claim 10, wherein the second reagents differ from the first reagents in at least one property selected from the group comprising:

processivity, catalysis, polymerase translocation, and exonuclease activity.

11. A non-transitory machine-readable storage medium comprising instructions which, when executed by a processor, cause the processor to perform a method for nucleic acid sequencing comprising:

(a) performing a first sequencing process on a first portion of the nucleic acid template to obtain a first sequencing result using a sequencing instrument configured to sequence a given sample two or more times, wherein the first sequencing process includes delivering first reagents including a first polymerase and first primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a first order comprising a first 4-flow block of flows comprising a first 4-flow permutation of flows A, C, G, and T, followed by a first predetermined number of repeats of a first 3-flow permutation of a first set of three flows selected from A, C, G, and T, followed by an isolated flow of the nucleotide not in the first set, followed by a second 4-flow permutation of flows A, C, G, and T different than the first 4-flow permutation, followed by a second predetermined number of repeats of a second 3-flow permutation of a second set of three flows selected from A, C, G, and T different than the first set, followed by an isolated flow of the nucleotide not in the second set; and

(b) after the first sequencing process, performing a second sequencing process on a second portion of the nucleic acid template to obtain a second sequencing result using the sequencing instrument, wherein the second sequencing process includes delivering second reagents including a second polymerase and second primers to the nucleic acid template and further includes flowing nucleotides to the nucleic acid template according to a second order different from the first order, wherein the first and second portions of the nucleic acid template may overlap at least partially, completely, or not at all.

19. The non-transitory machine-readable storage medium of claim 11, wherein the first predetermined number of repeats is equal to three.

20. The non-transitory machine-readable storage medium of claim 11, wherein the first and second predetermined numbers of repeats are each equal to three.