Gene specific arrays, preparation and use
First Claim
1. An array comprising a plurality of polynucleotide probes immobilized on a solid support, wherein:
- (a) the plurality of polynucleotide probes corresponds to a multiplicity of gene transcripts and comprises at least 100 polynucleotides that are each complementary to a distinct gene transcript;
(b) each polynucleotide probe of the plurality is localized to a predetermined region on the solid support;
(c) each polynucleotide probe of the plurality is from about 50 to 500 nucleotides in length;
(d) each polynucleotide probe of the plurality is complementary to 3′
untranslated sequence of a gene transcript, the untranslated sequence having a defined chromosomal location; and
(e) each polynucleotide probe of the plurality is prepared by amplification of genomic DNA or cDNA using a primer pair selected from the group consisting of SEQ ID NOs. 1-2, 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, 41-42, 43-44, 45-46, 47-48, 49-50, 51-52, 53-54, 55-56, 57-58, 59-60, 61-62, 63-64, 65-66, and 67-68.
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Accused Products
Abstract
The present invention provides arrays comprising a plurality of polynucleotide probes having sequences complementary to the 3′ untranslated region of a gene transcript, whose chromosomal location has been defined. The arrays are particularly useful for conducting comparative gene expression analyses. The present invention also includes a method of preparing these arrays and various methods of using these arrays for detecting differential expression of multiple gene transcripts amongst multiple subjects. Further provided by the invention are computer readable media recorded thereon an array of polynucleotide probes as specified herein, a computer-based system, and kits for detecting differential expression of a multiplicity of gene transcripts.
9 Citations
24 Claims
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1. An array comprising a plurality of polynucleotide probes immobilized on a solid support, wherein:
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(a) the plurality of polynucleotide probes corresponds to a multiplicity of gene transcripts and comprises at least 100 polynucleotides that are each complementary to a distinct gene transcript;
(b) each polynucleotide probe of the plurality is localized to a predetermined region on the solid support;
(c) each polynucleotide probe of the plurality is from about 50 to 500 nucleotides in length;
(d) each polynucleotide probe of the plurality is complementary to 3′
untranslated sequence of a gene transcript, the untranslated sequence having a defined chromosomal location; and
(e) each polynucleotide probe of the plurality is prepared by amplification of genomic DNA or cDNA using a primer pair selected from the group consisting of SEQ ID NOs. 1-2, 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, 41-42, 43-44, 45-46, 47-48, 49-50, 51-52, 53-54, 55-56, 57-58, 59-60, 61-62, 63-64, 65-66, and 67-68. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24)
(a) contacting the polynucleotide probes of the array of claim 1 with labeled target polynucleotides from the sample under conditions to form stable target-probe complexes; and
(b) detecting complex formation, thereby detecting gene expression in the sample.
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23. A method of preparing an array of polynucleotide probes corresponding to a multiplicity of gene transcripts, the method comprising:
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(a) generating a plurality of gene-specific polynucleotides by amplification of genomic DNA or cDNA using a primer pair selected from the group consisting of SEQ ID NOs. 1-2, 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, 41-42, 43-44, 45-46, 47-48, 49-50, 51-52, 53-54, 55-56, 57-58, 59-60, 61-62, 63-64, 65-66, and 67-68, wherein each polynucleotide of the plurality is from about 50 to about 500 nucleotides in length, and wherein each polynucleotide is complementary to 3′
untranslated sequence of a gene transcript, the untranslated sequence having a defined chromosomal location;
(b) immobilizing the plurality of polynucleotides in a predetermined region on a solid support; and
(c) repeating steps (a) and (b) to yield an array of polynucleotide probes corresponding to a multiplicity of gene transcripts.
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Specification