Simultaneous measurement of gene expression and genomic abnormalities using nucleic acid microarrays
First Claim
1. A method for simultaneous detection of gene expression and chromosomal abnormality in a tissue sample comprising:
- (a) providing an array of nucleic acid target elements attached to a solid support wherein the nucleic acid target elements comprise polynucleotide sequences substantially complementary under preselected hybridization conditions to nucleic acids indicative of gene expression and indicative of chromosomal sequence of a tissue sample;
(b) providing at least three labeled nucleic acid populations;
(i) a mRNA or cDNA population labeled with a first marker and derived from the tissue sample, (ii) a chromosomal DNA population labeled with a second marker and derived from the tissue sample, and (iii) at least one reference nucleic acid population labeled with a third marker;
(c) contacting the array with the labeled nucleic acid populations under hybridization conditions; and
(d) detecting presence and intensity of each of the first, second and third markers on at least two target elements.
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Abstract
The invention comprises a multi-color, comparative hybridization assay method using an array of nucleic acid target elements attached to a solid support for the simultaneous detection of both gene expression and chromosomal abnormalities in a tissue sample. The method of the invention employs a comparative hybridization of a tissue mRNA or cDNA sample labeled in a first fluorescent color, a tissue chromosomal DNA sample labeled in a second fluorescent color, and at least one reference nucleic acid labeled in a third fluorescent color, to the array. The fluorescent color presence and intensity at each of at least two target elements are detected and the fluorescent ratios (i) of the first and third colors and (ii) the second and third colors determined. Gene expression and chromosomal abnormalities are thus simultaneously detected.
227 Citations
78 Claims
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1. A method for simultaneous detection of gene expression and chromosomal abnormality in a tissue sample comprising:
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(a) providing an array of nucleic acid target elements attached to a solid support wherein the nucleic acid target elements comprise polynucleotide sequences substantially complementary under preselected hybridization conditions to nucleic acids indicative of gene expression and indicative of chromosomal sequence of a tissue sample;
(b) providing at least three labeled nucleic acid populations;
(i) a mRNA or cDNA population labeled with a first marker and derived from the tissue sample, (ii) a chromosomal DNA population labeled with a second marker and derived from the tissue sample, and (iii) at least one reference nucleic acid population labeled with a third marker;
(c) contacting the array with the labeled nucleic acid populations under hybridization conditions; and
(d) detecting presence and intensity of each of the first, second and third markers on at least two target elements. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 73, 76)
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20. A method for simultaneous detection of gene expression and chromosomal abnormality in a tissue sample comprising:
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(a) providing an array of nucleic acid target elements comprising genomic DNA attached to a solid support wherein the nucleic acid target elements comprise polynucleotide sequences substantially complementary under preselected hybridization conditions to nucleic acids indicative of gene expression and indicative of chromosomal sequence of a tissue sample;
(b) providing at least three labeled nucleic acid populations;
(i) a mRNA or cDNA population labeled with a first fluorescent marker and derived from the tissue sample, (ii) a chromosomal DNA population labeled with a second fluorescent marker and derived from the tissue sample, and (iii) at least one reference nucleic acid population labeled with a third fluorescent marker;
(c) contacting the array with the labeled nucleic acid populations under hybridization conditions; and
(d) detecting presence and intensity of each of the first, second and third fluorescent markers on at least two target elements. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 67, 71, 72, 77)
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34. A method for simultaneous detection of gene expression and chromosomal abnormality in a tissue sample comprising:
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(a) providing an array of nucleic acid target elements attached to a solid support wherein the nucleic acid target elements comprise polynucleotide sequences substantially complementary under preselected hybridization conditions to nucleic acids indicative of gene expression and indicative of chromosomal sequence of a tissue sample;
(b) providing at least three labeled nucleic acid populations;
(i) a mRNA or cDNA population labeled with a first fluorescent marker and derived from the tissue sample, (ii) a chromosomal DNA population labeled with a second fluorescent marker and derived from the tissue sample, and (iii) at least one reference nucleic acid population labeled with a third fluorescent marker;
(c) contacting the array with the labeled nucleic acid populations under hybridization conditions; and
(d) detecting presence and intensity of each of the first, second and third fluorescent markers on at least two target elements. - View Dependent Claims (35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 68, 74, 75, 78)
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Specification