Novel Methods and Devices for Evaluating Poisons
First Claim
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1. A method for inferring clinical outcome to the administration of a medicament to a human or animal subject from a nucleic acid sample of the subject, the method comprising identifying, in the nucleic acid sample, at least one diploid pair of haplotype alleles indicative of said clinical outcome, wherein the diploid pair of haplotype alleles is identified by (a) analyzing diploid pairs of haplotype alleles of individuals selected from a homogeneous population and (b) correlating clinical outcomes from medical data of said population to the analysis in step (a).
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Abstract
Methods and devices useful for evaluating poisons or other chemical entities, and for using such methods to forecast unfavorable drug effects.
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Citations
24 Claims
- 1. A method for inferring clinical outcome to the administration of a medicament to a human or animal subject from a nucleic acid sample of the subject, the method comprising identifying, in the nucleic acid sample, at least one diploid pair of haplotype alleles indicative of said clinical outcome, wherein the diploid pair of haplotype alleles is identified by (a) analyzing diploid pairs of haplotype alleles of individuals selected from a homogeneous population and (b) correlating clinical outcomes from medical data of said population to the analysis in step (a).
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7. A computer-implemented method of identifying diploid pairs of haplotype alleles useful for predicting clinical outcome of an individual to therapeutic treatment, comprising:
- (a) obtaining gene expression profile data from a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
(b) analyzing diploid pairs of haplotype alleles of individuals selected from said homogeneous population (c) correlating clinical outcomes from medical data of said population to identify diploid pairs of haplotype alleles which correlate with said clinical outcome, and (d) viewing the results of step (c) to facilitate the identification of said diploid pairs of haplotype alleles indicative of said clinical outcome. - View Dependent Claims (22)
- (a) obtaining gene expression profile data from a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
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8. A method for generating a database of biomarkers useful for predicting a clinical outcome of an individual to therapeutic treatment, comprising:
- (a) collecting a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
(b) analyzing diploid pairs of haplotype alleles of individuals selected from said homogeneous population (c) correlating clinical outcomes from medical data of said population to identify diploid pairs of haplotype alleles which correlate with said clinical outcome, and (d) recording diploid pairs of haplotype alleles from step (c) in a computer readable database. - View Dependent Claims (23)
- (a) collecting a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
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9. A business method for commercializing a database of biomarkers useful for predicting a clinical outcome of an individual to therapeutic treatment, comprising:
- (a) collecting a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
(b) analyzing diploid pairs of haplotype alleles of individuals selected from said homogeneous population (c) correlating clinical outcomes from medical data of said population to identify diploid pairs of haplotype alleles which correlate with said clinical outcome, (d) recording diploid pairs of haplotype alleles from step (c) in a computer readable database; and
(e) marketing said database. - View Dependent Claims (24)
- (a) collecting a homogeneous population of individuals having received the treatment with a recorded result from the treatment;
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13. A method for detecting the state of a toxicity pathway in a primate, said method comprising evaluating the form or function of one or more discriminatory biomarker selected from Table 2A subset 1, subset 2 or subset 3;
- Table 3A subset 1, subset 2 or subset 3 Table 4, subset 1 or subset 2;
Table 5A subset 1, subset 2 or subset 3;
or Table 6A subset 1, subset 2 or subset 3. - View Dependent Claims (14, 15, 16)
- Table 3A subset 1, subset 2 or subset 3 Table 4, subset 1 or subset 2;
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17. A method for detecting the state of a toxicity pathway in a primate, said method comprising evaluating the form or function of at least 3 or more discriminatory biomarkers selected from the subsets 3of Tables 3A, 5A and 6A.
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18. A method of identifying additional relevant genes as candidate test targets for toxicity pathway evaluation, comprising providing a first list of candidate targets and identifying a second list of additional candidate targets:
- 1) which in an interaction database have been reported to interact physically with said targets of list 1 and/or list 2, including a physical interaction or 2-hybrid physical interaction;
2) which have been commonly referred to in a reference with a target of list 1 and/or list 2, said reference being in the abstract of a paper contained in a literature database;
3) whose gene expression profiles match the expression profiles of those members of list 1 and/or list 2 in similar tissues;
4) which have been co-localized in expression analyses in similar tissues;
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5) which are closely located physically on a chromosome. - View Dependent Claims (19, 20)
- 1) which in an interaction database have been reported to interact physically with said targets of list 1 and/or list 2, including a physical interaction or 2-hybrid physical interaction;
Specification