Methods and systems for dynamic gene expression profiling
First Claim
Patent Images
1. A method for comparing gene expression profiles of two or more samples, said method comprising:
- (a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag is GC rich at its 5′
terminal and At rich at its 3′
terminal;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(d) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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Abstract
The invention provides compositions, methods and systems for dynamic transcription profiling of two or more samples. The method of the invention comprises the uses of sample-specific primers for cDNA synthesis and for subsequent amplification of the synthesized cDNAs. The levels of abundance of genes are compared between samples for the identification of differentially expressed genes.
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Citations
73 Claims
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1. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag is GC rich at its 5′
terminal and At rich at its 3′
terminal;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(d) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples. - 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50)
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- 24. The method of 4, wherein said amplifying further comprises using a fourth oligonucleotide primer which comprises said first arbitrary sequence tag of said second oligonucleotide primer.
- 40. The method of 1, wherein said method further comprises separating said one or more amplified products before detecting the abundance of said one or more amplified products.
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51. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said first oligonucleotide primer comprises at least one degenerate nucleotide;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(d) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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52. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag comprises at least one artificial nucleotide;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(d) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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53. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag is GC rich at its 5′
terminal and AT rich at its 3′
terminal;
(b) selectively synthesizing one or more second strand cDNAs complementary to said first strand cDNAs using a second oligonucleotide primer comprising a first arbitrary sequence tag;
(c) amplifying said one or more second strand cDNA so as to generate one or more sample-specific amplified products;
(d) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(e) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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54. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said first oligonucleotide primer comprises at least one degenerate nucleotide;
(b) selectively synthesizing one or more second strand cDNAs complementary to said first strand cDNAs using a second oligonucleotide primer comprising a first arbitrary sequence tag;
(c) amplifying said one or more second strand cDNA so as to generate one or more sample-specific amplified products;
(d) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(e) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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55. A method for comparing gene expression profiles of two or more samples, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs from a first sample using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag comprises at least one artificial nucleotide;
(b) selectively synthesizing one or more second strand cDNAs complementary to said first strand cDNAs using a second oligonucleotide primer comprising a first arbitrary sequence tag;
(c) amplifying said one or more second strand cDNA so as to generate one or more sample-specific amplified products;
(d) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said first sample; and
(e) comparing the expression profile of said one or more genes in said first sample with an expression profile of said one or more genes in a second sample, wherein a difference in the expression profile indicates differential expression of said one or more genes in the two samples.
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56. A method of identifying a modulator which regulates one or more gene expression in a sample, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs, before contacting said sample with said modulator, using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag is GC rich at its 5′
terminal and At rich at its 3′
terminal;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said sample; and
(d) comparing the expression profile of said one or more genes in said sample before contacting with said modulator with an expression profile of said one or more genes in said sample after contacting said modulator, wherein a difference in the expression profile indicates said modulator regulating one or more gene expression in said sample.
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57. A method of identifying a modulator which regulates one or more gene expression in a sample, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs, before contacting said sample with said modulator, using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said first oligonucleotide primer comprises at least one degenerate nucleotide;
(b) selectively amplifying at least a subset of said cDNA so as to generate one or more sample-specific amplified products;
(c) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said sample; and
(d) comparing the expression profile of said one or more genes in said sample before contacting with said modulator with an expression profile of said one or more genes in said sample after contacting said modulator, wherein a difference in the expression profile indicates said modulator regulating one or more gene expression in said sample.
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58. A method of identifying a modulator which regulates one or more gene expression in a sample, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs, before contacting said sample with said modulator, using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said sample-specific sequence tag is GC rich at its 5′
terminal and At rich at its 3′
terminal;
(b) synthesizing one or more second strand cDNAs using a second oligonucleotide primer comprising a first arbitrary sequence tag;
(c) amplifying said second strand cDNAs so as to generate one or more sample-specific amplified products;
(d) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said sample; and
(e) comparing the expression profile of said one or more genes in said sample before contacting with said modulator with an expression profile of said one or more genes in said sample after contacting said modulator, wherein a difference in the expression profile indicates said modulator regulating one or more gene expression in said sample.
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59. A method of identifying a modulator which regulates one or more gene expression in a sample, said method comprising:
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(a) synthesizing a plurality of first strand cDNAs, before contacting said sample with said modulator, using a first oligonucleotide primer comprising a sample-specific sequence tag, wherein said first oligonucleotide primer comprises at least one degenerate nucleotide;
(b) synthesizing one or more second strand cDNAs using a second oligonucleotide primer comprising a first arbitrary sequence tag;
(c) amplifying said second strand cDNAs so as to generate one or more sample-specific amplified products;
(d) detecting the abundance of one or more said sample-specific amplified products, wherein said abundance determines an expression profile of one or more genes in said sample; and
(e) comparing the expression profile of said one or more genes in said sample before contacting with said modulator with an expression profile of said one or more genes in said sample after contacting said modulator, wherein a difference in the expression profile indicates said modulator regulating one or more gene expression in said sample.
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60. A composition for detecting the level of gene expression, comprising a first oligonucleotide primer, wherein said first oligonucleotide primer comprises a sample-specific sequence tag and wherein said sample-specific sequence tag is GC rich at its 5′
- terminal and AT rich at its 3′
terminal. - View Dependent Claims (61, 62, 63, 64, 65)
- terminal and AT rich at its 3′
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66. A composition for detecting the level of gene expression, comprising a first oligonucleotide primer, wherein said first oligonucleotide primer comprises a sample-specific sequence tag and wherein said first oligonucleotide primer comprises at least one degenerate nucleotide.
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67. A kit for detecting the level of gene expression, comprising a first oligonucleotide primer, wherein said first oligonucleotide primer comprises a sample-specific sequence tag and wherein said sample-specific sequence tag is GC rich at its 5′
- terminal and AT rich at its 3′
terminal, and packaging material thereof. - View Dependent Claims (68, 69, 70, 71, 72)
- terminal and AT rich at its 3′
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73. A kit for detecting the level of gene expression, comprising a first oligonucleotide primer, wherein said first oligonucleotide primer comprises a sample-specific sequence tag and wherein said first oligonucleotide primer comprises at least one degenerate nucleotide, and packaging material thereof.
Specification