Compositions and methods for the analysis of degraded nucleic acids
First Claim
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1. A method for amplifying members of a population of degraded nucleic acids in a sample, the method comprising:
- a) providing a sample comprising said population of degraded nucleic acids;
b) providing target primer pairs, wherein i) each target primer pair comprises a forward target primer and a reverse target primer;
ii) said forward and reverse target primers each comprise (A) a target-specific nucleotide sequence that is complementary to a nucleotide subsequence of at least one member of the population of degraded nucleic acids, and (B) at least one universal priming sequence, wherein the universal priming sequence is 5′
relative to the target-specific sequence; and
c) annealing said target primer pairs to their cognate degraded nucleic acid;
d) enzymatically producing a plurality of products corresponding to subsequences of said cognate degraded nucleic acids;
e) enzymatically amplifying said plurality of products using at least one universal primer to produce a plurality of target amplicons, wherein said universal primer comprises nucleotide sequence that is complementary to said universal priming sequence, thereby amplifying members of a population of degraded nucleic acids.
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Abstract
The invention relates to compositions and methods for gene expression analysis. In some embodiments, the invention provides compositions and methods for amplifying targets in a degraded nucleic acid sample. In some embodiments, the invention provides methods for determining the quality of nucleic acids (e.g., the degree of degradation) in a nucleic acid sample. The invention also provides methods for producing a gene expression profile from a degraded RNA sample.
45 Citations
65 Claims
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1. A method for amplifying members of a population of degraded nucleic acids in a sample, the method comprising:
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a) providing a sample comprising said population of degraded nucleic acids;
b) providing target primer pairs, wherein i) each target primer pair comprises a forward target primer and a reverse target primer;
ii) said forward and reverse target primers each comprise (A) a target-specific nucleotide sequence that is complementary to a nucleotide subsequence of at least one member of the population of degraded nucleic acids, and (B) at least one universal priming sequence, wherein the universal priming sequence is 5′
relative to the target-specific sequence; and
c) annealing said target primer pairs to their cognate degraded nucleic acid;
d) enzymatically producing a plurality of products corresponding to subsequences of said cognate degraded nucleic acids;
e) enzymatically amplifying said plurality of products using at least one universal primer to produce a plurality of target amplicons, wherein said universal primer comprises nucleotide sequence that is complementary to said universal priming sequence, thereby amplifying members of a population of degraded nucleic acids. - 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41)
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42. A method for determining nucleic acid quality in a nucleic acid sample, the method comprising:
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a) providing a nucleic acid sample;
b) providing at least two target primer pairs, wherein;
i) each target primer pair comprises a forward target primer and a reverse target primer;
ii) said forward and reverse target primers each comprise a target-specific nucleotide sequence that is complementary to a subsequence of at least one nucleic acid in said sample; and
c) annealing said target primer pairs to their cognate nucleic acid;
d) enzymatically producing at least two products corresponding to nucleotide subsequences of said cognate nucleic acid, wherein each nucleotide subsequence is a different length;
e) enzymatically amplifying said products to produce at least two target amplicons;
f) quantitating said at least two target amplicons; and
g) comparing quantities of said target amplicons, thereby determining nucleic acid quality in said sample. - View Dependent Claims (43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54)
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55. A method for producing a gene expression profile from a degraded RNA sample, the method comprising the steps:
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a) providing a sample comprising degraded RNA, wherein said RNA corresponds to expressed genes;
b) providing a plurality of target primer pairs, wherein;
i) each target primer pair comprises a forward target primer and a reverse target primer;
ii) said forward and reverse target primers each comprise (A) a target-specific nucleotide sequence that is complementary to a nucleotide subsequence of at least one degraded RNA in said sample, and (B) at least one universal priming sequence, wherein the universal priming sequence is 5′
relative to the target-specific sequence; and
c) annealing said target primer pairs to their cognate degraded RNA;
d) enzymatically producing a plurality of products corresponding to subsequences of said cognate degraded RNA;
e) enzymatically amplifying said plurality of products using at least one universal primer to produce a plurality of target amplicons, wherein said universal primer comprises nucleotide sequence that is complementary to said universal priming sequence, thereby producing a gene expression profile from a degraded RNA sample. - View Dependent Claims (56, 57, 58, 59, 60, 61, 62, 63, 64)
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65. A kit for analyzing a sample, said sample comprising degraded nucleic acid, the kit comprising:
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a) a plurality of target primer pairs, wherein;
i) each target primer pair comprises a forward target primer and a reverse target primer;
ii) said forward and reverse target primers each comprise (A) a target-specific nucleotide sequence that is complementary to a nucleotide subsequence of at least one degraded nucleic acid in said sample, and (B) at least one universal priming sequence, wherein the universal priming sequence is 5′
relative to the target-specific sequence; and
iii) each primer in a target primer pair comprises a 3′
end, and wherein said 3′
end of said forward primer is not more than 20 base pairs from said 3′
end of said reverse primer when said target primers are hybridized to a cognate nucleic acid target; and
b) instructions for analyzing a sample comprising degraded nucleic acids.
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Specification