Methods of nucleic acid sequences analysis using solid supports containing identifier sequences
First Claim
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1. A method for analyzing a sample nucleic acid sequence, which comprises:
- a. preparing a mixture comprising the sample nucleic acid and a collection of solid supports under conditions in which a single molecule of the sample nucleic acid hybridizes to a nucleic acid molecule on a solid support in the collection, wherein;
(i) the nucleic acid molecules on each solid support in the collection comprise a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence;
(ii) at least one nucleic acid molecule of the solid phase nucleic acid species on each of the solid supports in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other solid supports in the collection;
(iii) the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence;
(iv) the solid phase nucleic acid species on each solid support in the collection share a unique identifier sequence with the other solid phase nucleic acid species on the solid support, wherein the unique identifier sequence is different than the identifier sequences of the solid phase nucleic acid species of the other solid supports in the collection;
b. contacting the mixture with extension reagents under conditions in which solid phase nucleic acid species hybridized to the sample nucleic acid in (iii) are extended by the reagents, whereby extended solid phase nucleic acid species comprising the unique identifier sequence of the solid support in (iii) and subsequences of the sample nucleic acid are obtained;
c. amplifying the extended solid phase nucleic acid species of (b) by linear amplification; and
d. determining the sequences of the amplification products of (c);
whereby the sample nucleic acid sequence is analyzed.
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Abstract
Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.
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17 Claims
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1. A method for analyzing a sample nucleic acid sequence, which comprises:
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a. preparing a mixture comprising the sample nucleic acid and a collection of solid supports under conditions in which a single molecule of the sample nucleic acid hybridizes to a nucleic acid molecule on a solid support in the collection, wherein; (i) the nucleic acid molecules on each solid support in the collection comprise a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence; (ii) at least one nucleic acid molecule of the solid phase nucleic acid species on each of the solid supports in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other solid supports in the collection; (iii) the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence; (iv) the solid phase nucleic acid species on each solid support in the collection share a unique identifier sequence with the other solid phase nucleic acid species on the solid support, wherein the unique identifier sequence is different than the identifier sequences of the solid phase nucleic acid species of the other solid supports in the collection; b. contacting the mixture with extension reagents under conditions in which solid phase nucleic acid species hybridized to the sample nucleic acid in (iii) are extended by the reagents, whereby extended solid phase nucleic acid species comprising the unique identifier sequence of the solid support in (iii) and subsequences of the sample nucleic acid are obtained; c. amplifying the extended solid phase nucleic acid species of (b) by linear amplification; and d. determining the sequences of the amplification products of (c);
whereby the sample nucleic acid sequence is analyzed. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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17. A method for preparing sample nucleic acid complements, which comprises:
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a. preparing a mixture comprising the sample nucleic acid and a collection of solid supports under conditions in which a single molecule of the sample nucleic acid hybridizes to a nucleic acid molecule on a solid support in the collection, wherein; (i) the nucleic acid molecules on each solid support in the collection comprising a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence; (ii) at least one nucleic acid molecule of the solid phase nucleic acid species on each of the solid supports in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other solid supports in the collection; (iii) the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence; (iv) the solid phase nucleic acid species on each solid support in the collection share a unique identifier sequence with the other solid phase nucleic acid species on the solid support, wherein the unique identifier sequence is different than the identifier sequences of the solid phase nucleic acid species of the other solid supports in the collection; and b. contacting the mixture with extension reagents under conditions in which solid phase nucleic acid species hybridized to the sample nucleic acid in (iii) are extended by the reagents, whereby sample nucleic acid complements comprising the shared, unique identifier sequence of the solid support in (iii) and subsequences of the sample nucleic acid are prepared c. amplifying the extended solid phase nucleic acid species of (b) by linear amplification.
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Specification