Phase-protecting reagent flow orderings for use in sequencing-by-synthesis

• US 10,597,711 B2
• Filed: 04/09/2013
• Issued: 03/24/2020
• Est. Priority Date: 04/08/2011
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hubbell, Earl, Schultz, Jonathan
• Primary Examiner(s): Chunduru, Suryaprabha
• Application Number:
  US13/859,360
• Publication Number:
  US 20130288904A1
• Time in Patent Office: 2,541 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 2533/101 Primer extension
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

A method for nucleic acid sequencing includes: disposing a plurality of template polynucleotide strands, sequencing primers, and polymerases in a plurality of defined spaces of a sensor array; exposing template polynucleotide strands to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtaining, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

Claims

1. A method for nucleic acid sequencing, comprising:

disposing a plurality of template polynucleotide strands, sequencing primers, and polymerases in a plurality of defined spaces of a sensor array;

exposing the plurality of template polynucleotide strands to a series of flows of nucleotide species, the series comprising a combinatorial ordering of flows comprising a plurality of different adjacent 4-flow permutations of different nucleotide species A, C, G, and T, wherein adjacent 4-flow permutations in the combinatorial ordering of flows differ by a single transposition of two nucleotide species; and

obtaining, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the plurality of template polynucleotide strands.

2. The method of claim 1, wherein the combinatorial ordering of flows comprises all 24 possible 4-flow permutations of different nucleotide species A, C, G, and T.

3. The method of claim 2, wherein the combinatorial ordering of flows comprises all 24 possible 4-flow permutations of different nucleotide species A, C, G, and T once followed by the first permutation in the combinatorial ordering.

4. The method of claim 1, wherein the sensor array is configured to detect hydrogen ions released by incorporation of nucleotides.

5. The method of claim 1, wherein the sensor array is configured to detect inorganic pyrophosphate released by incorporation of nucleotides.