Sequencing methods, compositions and systems using terminator nucleotides

• US 10,544,455 B2
• Filed: 09/16/2015
• Issued: 01/28/2020
• Est. Priority Date: 10/03/2014
• Status: Active Grant

• Current Assignee: Life Technologies GmbH (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hinz, Wolfgang, Vander Horn, Peter, Hubbell, Earl, Woehler, Christian
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US14/856,220
• Publication Number:
  US 20160097091A1
• Time in Patent Office: 1,595 Days
• Field of Search: None
• 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 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide

Abstract

In some embodiments, the disclosure relates generally to methods, as well as compositions, systems, kits and apparatuses, for performing nucleotide incorporation, comprising: (a) providing a surface including one or more reaction sites containing a polymerase and a nucleic acid template that has, or is hybridized to, an extendible end; (b) performing a first nucleotide flow by contacting one or more of the reaction sites with a first solution including one or more types of terminator nucleotide; (c) incorporating at least one type of terminator nucleotide at the extendible end of the nucleic acid template contained within at least one of the reaction sites using the polymerase; and (d) detecting a non-optical signal indicating the nucleotide incorporation using a sensor that is attached or operatively linked to the at least one reaction site.

Claims

1. A method for performing nucleotide incorporation, comprising:

a) providing a surface including one or more reaction sites, each site operatively linked to an ion-sensitive field effect transistor (ISFET), wherein one or more reaction sites contain a polymerase and a nucleic acid template that has, or is hybridized to, an extendible end;

b) performing a first nucleotide flow of a first series of nucleotide flows at one or more reaction sites wherein in the first nucleotide flow the one or more reaction sites is contacted with a first solution containing one or more types of terminator nucleotides;

c) incorporating a first terminator nucleotide at the extendible end contained within one or more reaction sites using the polymerase;

d) detecting using the ISFET a non-optical signal indicating the nucleotide incorporation of the first terminator nucleotide;

e) deblocking the first incorporated terminator nucleotide to generate a second extendible end;

f) performing one or more subsequent nucleotide flows by contacting the one or more reaction sites with subsequent solutions containing one or more types of terminator nucleotides, thereby incorporating terminator nucleotides from the subsequent solutions and synthesizing an extension product which is annealed to the nucleic acid template, and after each subsequent nucleotide flow (i) detecting the presence or absence of a non-optical signal, and (ii) deblocking an incorporated subsequent terminator nucleotide to generate a subsequent extendible end, wherein steps (b)-(f) are conducted in the one or more reaction sites;

g) identifying contiguous nucleotides in the nucleic acid template contained within the one or more reaction sites using for each template in the one or more reaction sites only the non-optical signals from that reaction site; and

h) obtaining a first sequencing read from the extension product.

2. The method of claim 1, further including analyzing the non-optical signal from the first incorporated terminator nucleotide.

3. The method of claim 1, further including identifying the first incorporated terminator nucleotide.

4. The method of claim 1, wherein the deblocking includes removing a terminator moiety from the terminator nucleotide.

5. The method of claim 1, wherein the first and/or the subsequent solutions include only a single type of nucleotide.

6. The method of claim 1, wherein the subsequent solutions of the first series of nucleotide flows include a non-terminator nucleotide.

7. The method of claim 1, wherein the first series of nucleotide flows includes at least two flows containing one or more terminator nucleotides.

8. The method of claim 1, wherein the only nucleotides in all the flows in the first series of nucleotide flows are terminator nucleotides.

9. The method of claim 1, wherein the first series of nucleotide flows includes at least one flow containing a non-terminator nucleotide.

10. The method of claim 3, further including identifying the first incorporated terminator nucleotide with an error rate of less than 0.1%.

11. The method of claim 10, further including identifying the first incorporated terminator nucleotide with an error rate of less than 0.001%.

12. The method of claim 1, wherein the polymerase is not linked to the reaction site.

13. The method of claim 1, further comprising:

i) denaturing the extension product from the nucleic acid template contained within the one or more reaction sites;

j) performing a second series of nucleotide flows by contacting the one or more reaction sites with subsequent solutions containing one or more types of non-terminator nucleotides, thereby incorporating the subsequent non-terminator nucleotides and synthesizing a second extension product which is annealed to the nucleic acid template, and after each subsequent nucleotide flow in the second series detecting the presence or absence of a non-optical signal wherein the presence of a non-optical signal indicates incorporation of a subsequent non-terminator nucleotide; and

k) obtaining a second sequencing read from the second extension product, and aligning the first and second sequencing reads to reconstruct the sequence of the nucleic acid template.

14. The method of claim 13, wherein the first nucleotide flow and the one or more subsequent nucleotide flows of step (f) comprise the first series of nucleotide flows, and wherein the subsequent nucleotide flows of step (j) comprise the second series of nucleotide flows.

15. The method of claim 14, further including determining the identity and number of nucleotides incorporated following each nucleotide flow in the first series.

16. The method of claim 14, wherein the second series of nucleotide flows includes at least one flow containing a terminator nucleotide.

17. The method of claim 14, wherein the first series of nucleotide flows consists only of flows containing a terminator nucleotide and the second series of nucleotide flows consists only of flows containing a non-terminator nucleotide.