Method for quantitative measurement of gene expression using multiplex competitive reverse transcriptase-polymerase chain reaction
First Claim
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1. Method for quantitative measurement of expression of a target gene comprising:
- a) isolating at least a portion of a RNA sequence which encodes the RNA for the target gene and a portion of an RNA for a housekeeping gene, which RNA has been isolated from a sample cell;
b) subjecting the RNA sequence of step a) and two internal mutated standards comprising single base routants of the target gene and the housekeeping gene cDNA that cause either a loss or gain of an EcoRI restriction endonuclease recognition site to reverse transcription to obtain at least one native cDNA which encodes the DNA for both the target gene and at least one native cDNA which encodes the DNA for the housekeeping gene;
c) conducting polymerase chain reaction amplification of the native cDNA in the presence of target gene and housekeeping gene primers and a predetermined quantified amount of the routate internal standards;
d) conducting a quantification step of products of the polymerase chain reaction amplification of step c) byi) maximizing heterodimer formation,ii) calculating the quantities of the products, andiii) comparing samples of the products simultaneously using a master mixture which is the same for each product and having the same dilution of internal standards;
e) subjecting the amplified cDNA of step c) to enzyme restriction by digesting with EcoRI;
f) subjecting the digested cDNA of step e) to electrophoresis to separate wild type from mutated products; and
f) measuring the expression of the target gene relative to the housekeeping gene to provide the quantitative measurement of expression of the target gene.
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Abstract
A method for quantitative measurement of gene expression through multiplex competitive reverse transcriptase polymerase chain reaction amplification has been established which comprises isolating cellular mRNA of a target gene and a housekeeping gene which are then reverse transcribed and specifically amplified in the presence of competitive templates such that a ratio of target to housekeeping gene is obtained and used to assess the amount of gene expression. This method is useful for analysis of the small specimens (cells and tissues) available from human subjects and will allow improved understanding of mechanisms of disease.
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Citations
22 Claims
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1. Method for quantitative measurement of expression of a target gene comprising:
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a) isolating at least a portion of a RNA sequence which encodes the RNA for the target gene and a portion of an RNA for a housekeeping gene, which RNA has been isolated from a sample cell; b) subjecting the RNA sequence of step a) and two internal mutated standards comprising single base routants of the target gene and the housekeeping gene cDNA that cause either a loss or gain of an EcoRI restriction endonuclease recognition site to reverse transcription to obtain at least one native cDNA which encodes the DNA for both the target gene and at least one native cDNA which encodes the DNA for the housekeeping gene; c) conducting polymerase chain reaction amplification of the native cDNA in the presence of target gene and housekeeping gene primers and a predetermined quantified amount of the routate internal standards; d) conducting a quantification step of products of the polymerase chain reaction amplification of step c) by i) maximizing heterodimer formation, ii) calculating the quantities of the products, and iii) comparing samples of the products simultaneously using a master mixture which is the same for each product and having the same dilution of internal standards; e) subjecting the amplified cDNA of step c) to enzyme restriction by digesting with EcoRI; f) subjecting the digested cDNA of step e) to electrophoresis to separate wild type from mutated products; and f) measuring the expression of the target gene relative to the housekeeping gene to provide the quantitative measurement of expression of the target gene. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method for quantitative measurement of gene expression of a target gene comprising:
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a) isolating cellular mRNA of a target gene and a housekeeping gene which are reverse transcribed and specifically amplified in the presence of competitive template such that a ratio of the target gene to the housekeeping gene is obtained and that ratio is used to assess the amount of gene expression of the target gene by conducting simultaneous polymerase chain reaction amplification of a mixture of the following; i) at least one oligonucleotide primer pair of at least one target gene, ii) at least one oligonucleotide primer pair of at least one housekeeping gene, iii) at least one mutated competitive template of the target gene, iv) at least one mutated competitive template of the housekeeping gene, and v) native cDNA which contains at least one copy of the target gene cDNA and at least one copy of the housekeeping gene cDNA;
to form polymerase chain reaction cDNA products comprising;
native cDNA of the target gene and the housekeeping gene, and mutated cDNA of the target gene and the housekeeping gene;(b) isolating the cDNA products; and
,(c) detecting the relative presence of the native cDNA products and mutated cDNA products by comparing the amount of native cDNA coding for the target gene and the amount of mutated cDNA coding for the competitive template of the target gene to the amount of native cDNA coding for the housekeeping gene and the amount of mutated cDNA coding for the competitive template of the housekeeping gene;
wherein comparison of the relative presence of the amounts of native cDNA products and mutated cDNA products of the target gene and the housekeeping gene provide the quantitative measurement of the expression of the target gene. - View Dependent Claims (8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A method for quantitative measurement of gene expression of a target gene in tissue samples comprising:
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a) synthesizing at least one oligonucleotide primer pair of at lest one housekeeping gene, b) synthesizing at least one oligonucleotide primer pair of at least one target gene, c) synthesizing at least one competitive template of the housekeeping gene, d) synthesizing at least one competitive template of the target gene, e) isolating at least a portion of an RNA sequence from said tissue samples, subjecting the RNA sequence to reverse transcription to obtain at least one native cDNA, g) conducting polymerase chain reaction amplification of the native cDNA in the presence of the target gene oligonucleotide primers, the housekeeping gene oligonucleotide primers, and predetermined quantities of the housekeeping gene competitive template and the target gene competitive template, h) subjecting amplified cDNA products of step "g" above to digestion with at least one restriction enzyme, i) subjecting the digested cDNA to electrophoresis to separate the amplified target gene and the amplified housekeeping gene from the amplified target gene competitive template and the amplified housekeeping gene competitive template, and j) measuring the relative expression of the target gene in at least one tissue sample by dividing a ratio of the target gene to a known amount of the competitive template of the target gene by a ratio of housekeeping gene to a known amount of the competitive template of the housekeeping gene to provide the quantitative measurement of expression of the target gene. - View Dependent Claims (21, 22)
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Specification