Methods for Screening, Predicting and Monitoring Prostate Cancer
First Claim
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1. A method for screening or monitoring a patient for prostate cancer, comprising:
- obtaining a biological sample for the patient;
detecting within each of the biological sample and a control an expression level of a product of each of from one to four genes consisting of PDZ and LIM5 (SEQ ID NO.
1), UAP1/AgX1 antigen (SEQ ID NO.
2), HSPD1/chaperonin (SEQ ID NO.
3), IMPDH2 (SEQ ID NO.
5);
detecting within the biological sample and the control an expression level of a product of a reference gene;
normalizing the expression level of the product of each of the from one to four genes using the expression level of the product of the reference gene;
classifying the biological sample as “
cancer”
or “
normal”
by generating a binary prediction score by combining the normalized expression level of all of the from one to four genes with a bias.
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Abstract
Biomarkers are identified by analyzing gene expression data using support vector machines (SVM) to rank genes according to their ability to separate prostate cancer from normal tissue. Expression products of identified genes are detected in patient samples, including prostate tissue, serum, semen and urine, to screen, predict and monitor prostate cancer.
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Citations
20 Claims
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1. A method for screening or monitoring a patient for prostate cancer, comprising:
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obtaining a biological sample for the patient; detecting within each of the biological sample and a control an expression level of a product of each of from one to four genes consisting of PDZ and LIM5 (SEQ ID NO.
1), UAP1/AgX1 antigen (SEQ ID NO.
2), HSPD1/chaperonin (SEQ ID NO.
3), IMPDH2 (SEQ ID NO.
5);detecting within the biological sample and the control an expression level of a product of a reference gene; normalizing the expression level of the product of each of the from one to four genes using the expression level of the product of the reference gene; classifying the biological sample as “
cancer”
or “
normal”
by generating a binary prediction score by combining the normalized expression level of all of the from one to four genes with a bias. - View Dependent Claims (2, 3, 4, 5, 6, 7)
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8. A method for predicting a clinical outcome in response to a treatment of a prostate cancer, the method comprising the steps of:
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(1) measuring expression levels of expression products of from one to four prognostic genes selected from the group consisting of PDZ and LIM5 (SEQ ID NO.
1), UAP1/AgX1 antigen (SEQ ID NO.
2), HSPD1/chaperonin (SEQ ID NO.
3), F5 (SEQ ID NO.
4), IMPDH2 (SEQ ID NO.
5), PPIB (SEQ ID NO.
6), RGS10 (SEQ ID NO.
9) and PYCR1 (SEQ ID NO.
10) in tissue, serum, semen or urine from a patient; and(2) comparing each of the expression levels to a corresponding control level, wherein the result of the comparison is predictive of a clinical outcome. - View Dependent Claims (9, 10, 11, 12, 13, 14)
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15. A method of detecting the presence or absence of prostate cancer in a subject, comprising:
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a) providing a biological sample from the subject; b) providing a reagent for detecting from one to four expression products selected from a group of genes consisting of PDZ and LIM5 (SEQ ID NO.
1), UAP1/AgX1 antigen (SEQ ID NO.
2), HSPD1/chaperonin (SEQ ID NO.
3), F5 (SEQ ID NO.
4), IMPDH2 (SEQ ID NO.
5), PPIB (SEQ ID NO.
6), RGS10 (SEQ ID NO.
9) and PYCR1 (SEQ ID NO.
10);c) contacting the biological sample with the reagent under conditions such that said reagent detects the presence or absence of the from one to four expression products in the biological sample; d) determining the presence or absence of prostate cancer in said subject based on the presence or absence of the from one to four expression products in the biological sample. - View Dependent Claims (16, 17, 18, 19, 20)
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Specification