COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS
First Claim
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1. A method of identifying a nucleotide in a candidate sequence, said method comprising the steps of:
- a) providing an array substrate comprising a surface having a first subpopulation and a second subpopulation of identifier probes distributed thereon, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation comprise a primer sequence adjacent to a candidate sequence, the primer sequence of the first subpopulation of identifier probes having the same sequence as the primer sequence of the second subpopulation of identifier probes and the candidate sequence of the first subpopulation of identifier probes being different from the candidate sequence of the second subpopulation of identifier probes, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation are hybridized to a set of decoding probes, said decoding probes comprising a priming sequence complementary to a portion of the primer sequence and a variable region adjacent to said priming sequence, wherein said variable region comprises at least one detection nucleotide at a detection position, said detection nucleotide being able to basepair with a nucleotide of at least one of said different candidate sequences, wherein said set of decoding probes comprises different subsets, and wherein decoding probes from different subsets comprise a different detection nucleotide at the same detection position and a label that distinguishes the detection nucleotide;
b) detecting the presence of said label;
c) dehybridizing said decoding probes from said identifier probes; and
d) associating the label with the identity of a nucleotide in the candidate sequence.
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Abstract
Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
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Citations
51 Claims
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1. A method of identifying a nucleotide in a candidate sequence, said method comprising the steps of:
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a) providing an array substrate comprising a surface having a first subpopulation and a second subpopulation of identifier probes distributed thereon, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation comprise a primer sequence adjacent to a candidate sequence, the primer sequence of the first subpopulation of identifier probes having the same sequence as the primer sequence of the second subpopulation of identifier probes and the candidate sequence of the first subpopulation of identifier probes being different from the candidate sequence of the second subpopulation of identifier probes, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation are hybridized to a set of decoding probes, said decoding probes comprising a priming sequence complementary to a portion of the primer sequence and a variable region adjacent to said priming sequence, wherein said variable region comprises at least one detection nucleotide at a detection position, said detection nucleotide being able to basepair with a nucleotide of at least one of said different candidate sequences, wherein said set of decoding probes comprises different subsets, and wherein decoding probes from different subsets comprise a different detection nucleotide at the same detection position and a label that distinguishes the detection nucleotide; b) detecting the presence of said label; c) dehybridizing said decoding probes from said identifier probes; and d) associating the label with the identity of a nucleotide in the candidate sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
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27. A method of identifying a nucleotide in a candidate sequence, said method comprising the steps of:
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a) providing an array substrate comprising a surface having a first subpopulation and a second subpopulation of identifier probes distributed thereon, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation comprise a primer sequence adjacent to a candidate sequence, the primer sequence of the first subpopulation of identifier probes having the same sequence as the primer sequence of the second subpopulation of identifier probes and the candidate sequence of the first subpopulation of identifier probes being different from the candidate sequence of the second subpopulation of identifier probes, wherein an identifier probe of the first subpopulation is hybridized to a first decoding probe and an identifier probe of the second subpopulation is hybridized to a second decoding probe, each decoding probe comprising a priming sequence complementary to a portion of the primer sequence and a variable region adjacent to said priming sequence, each variable region comprising at least one detection nucleotide that will basepair with a nucleotide of at least one of said different candidate sequences, wherein the first decoding probe and the second decoding probe have a different detection nucleotide at the same position and a label that distinguishes the detection nucleotide; b) detecting the presence of said label; c) dehybridizing said first and second decoding probes from said identifier probes; and d) associating the label with the identity of a nucleotide in the candidate sequence. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51)
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Specification