Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same
First Claim
1. A method for nucleic acid sequencing, comprising:
- (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence, whereinthe test or control sequence is generated by combining sequences corresponding to at least two loci that meet a systematic error criteria, andthe at least two loci are determined to meet the systematic error criteria based on a training set of sequencing runs in which each of the at least two loci is determined to cause a plurality of sequencing errors;
(b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and
(c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands.
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Abstract
A method for nucleic acid sequencing includes (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence; (b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands, wherein the test or control sequence comprises a sequence determined by identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs.
95 Citations
20 Claims
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1. A method for nucleic acid sequencing, comprising:
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(a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence, wherein the test or control sequence is generated by combining sequences corresponding to at least two loci that meet a systematic error criteria, and the at least two loci are determined to meet the systematic error criteria based on a training set of sequencing runs in which each of the at least two loci is determined to cause a plurality of sequencing errors; (b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
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19. A system, including:
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a plurality of template polynucleotide strands disposed in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence, wherein the test or control sequence is generated by combining sequences corresponding to at least two loci that meet a systematic error criteria, and the at least two loci are determined to meet the systematic error criteria based on a training set of sequencing runs in which each of the at least two loci is determined to cause a plurality of sequencing errors; 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 for nucleic acid sequencing, comprising; (a) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (b) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands. - View Dependent Claims (20)
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Specification