Expression monitoring for gene function identification
First Claim
1. A method for detecting a functional mutation in a target up-stream regulatory gene comprising:
- preparing a reference sample from reference cells having a wild-type up-stream regulatory gene corresponding to said target up-stream regulatory gene;
preparing a target sample from target cells suspected of having a mutation in said target up-stream regulatory gene, said target cells being otherwise substantially similar to said reference cells;
detecting the expression of a plurality of down-stream genes in said reference sample to obtain a reference expression pattern, said down-stream genes being up or down regulated by said wild-type up-stream regulatory gene;
detecting the expression of said plurality of down-stream genes in said target sample to obtain a target expression pattern; and
comparing said reference expression pattern with said target expression pattern to detect functional mutation in or inactivation of said target gene.
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Abstract
This invention provides methods, compositions and apparatus for mapping the regulatory relationship among genes by massive parallel monitoring gene expression. In some embodiments, mutations in the up-stream regulatory genes are detected by monitoring the change in down-stream gene expression. Similarly, the function of a specific mutation in a up-stream gene is determined by monitoring the down-stream gene expression. In addition, regulatory function of a target gene can be determined by monitoring the expression of a large number of down-stream genes. The invention also provides specific embodiments for detecting p53 functional homozygous and heterozygous mutations and for determining the function of p53 mutations.
17 Citations
15 Claims
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1. A method for detecting a functional mutation in a target up-stream regulatory gene comprising:
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preparing a reference sample from reference cells having a wild-type up-stream regulatory gene corresponding to said target up-stream regulatory gene;
preparing a target sample from target cells suspected of having a mutation in said target up-stream regulatory gene, said target cells being otherwise substantially similar to said reference cells;
detecting the expression of a plurality of down-stream genes in said reference sample to obtain a reference expression pattern, said down-stream genes being up or down regulated by said wild-type up-stream regulatory gene;
detecting the expression of said plurality of down-stream genes in said target sample to obtain a target expression pattern; and
comparing said reference expression pattern with said target expression pattern to detect functional mutation in or inactivation of said target gene. - View Dependent Claims (2, 3, 4, 5, 6, 7)
detecting expression of a plurality of control genes in said reference and target samples, said control genes being unresponsive to the function of said up-stream regulatory gene; and
comparing reference and target expression patterns of control genes to provide a baseline for detecting a significant difference in expression patterns.
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6. The method of claim 1 further comprising the step of:
indicating a loss of wild-type function in said target gene if a significant number of said down regulated genes are expressed relatively higher in said target sample than in said reference sample or if a significant number of said up-regulated genes are expressed lower in said target sample than in said reference sample.
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7. The method of claim 1 further comprising the step of:
indicating a gain of function mutation in said target gene if a significant portion of said down regulated genes are expressed lower in said target sample than in said reference sample or if a significant portion of said up-regulated genes are expressed higher in said target sample than in said reference sample.
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8. A method for detecting a p53 gene functional mutation in target cells comprising the steps of:
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preparing a reference sample from reference cells having a wild-type p53 gene, said reference cells being otherwise substantially similar to said target cells;
detecting the expression of a plurality of more than 100 down-stream genes in said reference cells and said target cells to obtain a target expression pattern and a reference expression pattern, said down-stream genes being up- or down-regulated by said wild-type p53 gene; and
comparing said reference expression pattern with said target expression pattern to detect said p53 functional mutation. - View Dependent Claims (9, 10, 11)
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12. An in-cell functional assay for a p53 sequence alteration comprising the steps of:
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preparing a target sample from target cells having said p53 sequence alteration;
preparing a reference sample from reference cells having a wild-type p53 gene, said reference cells being otherwise substantially similar to said target cells;
detecting the expression of a plurality of more than 100 down-stream genes in said reference cells to obtain a reference expression pattern and in said target cells to obtain a target expression pattern, said down-stream genes being selected from the group consisting of p53 up-regulated genes and p53 down-regulated genes; and
comparing said reference expression pattern with said target expression pattern to determine the function of said p53 sequence alteration. - View Dependent Claims (13, 14, 15)
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Specification