Methods for analysis of gene expression
First Claim
Patent Images
1. A method for analyzing gene expression comprising:
- a) obtaining a plurality of target sequences, wherein the plurality of target sequences comprises cDNA;
b) multiplex amplifying said plurality of target sequences, wherein multiplex amplifying comprises combining the plurality of target sequences, a plurality of target-specific primers, and one or more universal primers, and wherein the universal primer is provided in an excess concentration relative to the target-specific primer, thereby producing a plurality of amplification products;
c) separating one or more members of the plurality of amplification products;
d) detecting one or more members of the plurality of amplification products, thereby generating a set of gene expression data;
e) storing the set of gene expression data in a database; and
f) performing a comparative analysis on the set of gene expression data, thereby analyzing the gene expression.
6 Assignments
0 Petitions
Accused Products
Abstract
This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.
-
Citations
82 Claims
-
1. A method for analyzing gene expression comprising:
-
a) obtaining a plurality of target sequences, wherein the plurality of target sequences comprises cDNA;
b) multiplex amplifying said plurality of target sequences, wherein multiplex amplifying comprises combining the plurality of target sequences, a plurality of target-specific primers, and one or more universal primers, and wherein the universal primer is provided in an excess concentration relative to the target-specific primer, thereby producing a plurality of amplification products;
c) separating one or more members of the plurality of amplification products;
d) detecting one or more members of the plurality of amplification products, thereby generating a set of gene expression data;
e) storing the set of gene expression data in a database; and
f) performing a comparative analysis on the set of gene expression data, thereby analyzing the gene expression. - View Dependent Claims (2, 3, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57)
-
-
4. A method for analyzing gene expression comprising:
-
a) obtaining a plurality of target sequences, wherein the plurality of target sequences comprises cDNA;
b) multiplex amplifying said plurality of target sequences, wherein multiplex amplifying comprises combining the plurality of target sequences, a plurality of target-specific primers, and one or more universal primers, wherein an annealing temperature of the universal primer is higher than an annealing temperature of the target-specific primer;
thereby producing a plurality of amplification products;
c) separating one or more members of the plurality of amplification products;
d) detecting one or more members of the plurality of amplification products, thereby generating a set of gene expression data;
e) storing the set of gene expression data in a database; and
f) performing a comparative analysis on the set of gene expression data, thereby analyzing the gene expression.
-
-
5. A method for analyzing gene expression comprising:
-
a) obtaining a plurality of target sequences, wherein the plurality of target sequences comprises cDNA;
b) multiplex amplifying said plurality of target sequences, wherein multiplex amplifying comprises combining the plurality of target sequences, a plurality of target-specific primers, and one or more universal primers, and wherein multiplex amplifying the cDNA further comprises attenuating an amplification of abundant target genes, thereby producing a plurality of amplification products;
c) separating one or more members of the plurality of amplification products;
d) detecting one or more members of the plurality of amplification products, thereby generating a set of gene expression data;
e) storing the set of gene expression data in a database; and
f) performing a comparative analysis on the set of gene expression data, thereby analyzing the gene expression. - View Dependent Claims (6, 7, 8, 9, 10, 11, 12)
-
-
58. A method for analyzing gene expression comprising:
-
a) obtaining cDNA from a plurality of samples for a plurality of target sequences;
b) performing a plurality of multiplexed amplifications of the target sequences, thereby producing a plurality of multiplexed amplification products, wherein performing a multiplexed amplification comprises combining a plurality of target sequences, one or more target-specific primers, and one or more universal primers to form a reaction mixture, and wherein the reaction mixture comprises one or more of i) an excess concentration of the one or more universal primers relative to a target-specific primer, ii) universal primers which have a higher annealing temperature relative to the annealing temperature of a target-specific primer, or iii) modified target-specific primer for attenuation of abundant target genes;
c) pooling the plurality of multiplexed amplification products;
d) separating the plurality of multiplexed amplification products;
e) detecting the plurality of multiplexed amplification products, thereby generating a set of gene expression data;
f) storing the set of gene expression data in a database; and
g) performing a comparative analysis of the set of gene expression data. - View Dependent Claims (59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72)
-
-
73. A method for analyzing gene expression comprising:
-
a) obtaining cDNA from multiple samples;
b) amplifying a plurality of target sequences from the cDNA, thereby producing a multiplex set of amplification products, wherein amplifying the plurality of target sequences comprises combining the plurality of target sequences, one or more target-specific primers, and one or more universal primers to form a reaction mixture, and wherein the reaction mixture comprises one or more of i) an excess concentration of the one or more universal primers relative to a target-specific primer, ii) universal primers which have a higher annealing temperature relative to the annealing temperature of a target-specific primer, or iii) modified target-specific primer for attenuation of abundant target genes;
c) separating and detecting the amplification products using a high throughput platform, wherein detecting generates a set of gene expression data; and
d) storing the set of gene expression data in a database; and
e) performing a comparative analysis of the set of gene expression data. - View Dependent Claims (74, 75, 76, 77, 78, 79, 80, 81, 82)
-
Specification