Methods for mapping the chromosomal loci of genes expressed by a cell
First Claim
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1. An array-based method for identifying a chromosomal loci of a gene expressed by a cell, the method comprising:
- (a) providing an array comprising a plurality of cloned genomic nucleic acid segments, wherein each genomic nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array and the cloned genomic nucleic acid segments comprise a substantially complete genome or a known subset of a genome;
(b) providing a sample comprising a nucleic acid sequence comprising a detectable label, wherein the nucleic acid sequence comprises the same sequence or a sequence complementary to a sequence of a transcript expressed by a cell;
(c) contacting the sample of step (b) with the array of step (a) under conditions wherein the labeled nucleic acid can specifically hybridize to the genomic nucleic acid segments immobilized on the array; and
, (d) identifying to which discrete and known spots on the substrate surface are specifically hybridized to a labeled nucleic acid segment, wherein the identification is made by detecting a specifically hybridized nucleic acid sequence, thereby identifying a chromosomal loci of a gene expressed by a cell.
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Abstract
The invention provides novel methods to map the location and measure the expression of some or all the genes expressed by a cell using array-based nucleic acid hybridizations. The use and applicability of the invention includes identification of tissue specific genes and identifying different tissue types during growth and development. The methods also can be used to identify genes expressing abnormal types of transcripts or abnormal levels or transcripts. Thus, the invention can be used to identify genes encoding transcripts associated with disease processes, such as cancer.
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Citations
58 Claims
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1. An array-based method for identifying a chromosomal loci of a gene expressed by a cell, the method comprising:
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(a) providing an array comprising a plurality of cloned genomic nucleic acid segments, wherein each genomic nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array and the cloned genomic nucleic acid segments comprise a substantially complete genome or a known subset of a genome;
(b) providing a sample comprising a nucleic acid sequence comprising a detectable label, wherein the nucleic acid sequence comprises the same sequence or a sequence complementary to a sequence of a transcript expressed by a cell;
(c) contacting the sample of step (b) with the array of step (a) under conditions wherein the labeled nucleic acid can specifically hybridize to the genomic nucleic acid segments immobilized on the array; and
,(d) identifying to which discrete and known spots on the substrate surface are specifically hybridized to a labeled nucleic acid segment, wherein the identification is made by detecting a specifically hybridized nucleic acid sequence, thereby identifying a chromosomal loci of a gene expressed by a cell. - View Dependent Claims (2, 3, 4, 5, 6, 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)
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7. An array-based method for identifying a chromosomal loci of a gene differentially expressed by different cells or by a cell under different conditions by performing an array-based comparative genomic hybridization (CGH), comprising the following steps:
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(a) providing an array comprising a plurality of cloned genomic nucleic acid segments, wherein each genomic nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array and the cloned genomic nucleic acid segments comprise a substantially complete genome or a known subset of a genome;
(b) providing a first sample, wherein the sample comprises a plurality of nucleic acid sequences comprising a first detectable label, wherein the nucleic acid sequence comprises the same sequence or a sequence complementary to all of the transcripts expressed by a first cell or a subset of transcripts expressed by the first cell;
(c) providing a second sample, wherein the sample comprises a plurality of nucleic acid sequences comprising a second detectable label, wherein the nucleic acid sequence comprises the same sequence or a sequence complementary to all of the transcripts expressed by a second cell or a subset of transcripts expressed by the second cell;
(d) contacting the samples of step (b) and step (c) with the array of step (a) under conditions wherein the nucleic acid in the samples can specifically hybridize to the immobilized nucleic acid of step (a); and
(e) identifying to which discrete and known spots on the substrate surface are specifically hybridized to a nucleic acid sequence of step (b) and identifying to which discrete and known spots on the substrate surface are specifically hybridized to a nucleic acid sequence of step (c), wherein the identification is made by detecting a specifically hybridized first and a specifically hybridized second sample nucleic acid sequence, thereby identifying a chromosomal loci of a gene differentially expressed by a first cell compared to a second cell. - View Dependent Claims (8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification