Novel Methods and Devices for Evaluating Poisons

• US 20060253262A1
• Filed: 04/26/2006
• Published: 11/09/2006
• Est. Priority Date: 04/27/2005
• Status: Abandoned Application

• Current Assignee: Emiliem
• Original Assignee: Emiliem
• Inventors: Johnson, Dale E., Sudarsanam, Sucha, Ching, Edwin P.
• Application Number:
  US11/380,388
• Publication Number:
  US 20060253262A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/142 Toxicological screening, e.g. expression profiles which identify toxicity
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/172 Haplotypes
• CPC Class Codes: G06Q 30/0601 Electronic shopping [e-shopping]
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 40/20 Supervised data analysis
• CPC Class Codes: G16B 40/30 Unsupervised data analysis

Abstract

Methods and devices useful for evaluating poisons or other chemical entities, and for using such methods to forecast unfavorable drug effects.

Claims

1. A method for inferring a 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).

2. The method of claim 1 further comprising identifying in said nucleic acid sample one or more additional haplotypes, wherein expression of said one or more haplotypes and said at least one diploid pair of haplotype alleles indicative of said clinical outcome define an expression profile and wherein identifying said expression profile increases the statistical accuracy of inferring said clinical outcome compared to identifying said at least one diploid pair of haplotype alleles alone.

3. The method of claim 2 wherein said expression profile comprises changes in the expression of said haplotypes in the same individual over a predetermined period of time.

4. The method of claim 2 wherein said one or more additional haplotypes (1) are identified in an interaction database to interact physically with said at least one diploid pair of haplotype alleles indicative of said clinical outcome;

(2) are commonly referred to in a scientific literature reference with said at least one diploid pair of haplotype alleles indicative of said clinical outcome;

(3) are expressed with profiles that match the expression profile of said at least one diploid pair of haplotype alleles indicative of said clinical outcome in similar tissues;

(4) are co-localized in expression analyses in similar tissues as said at least one diploid pair of haplotype alleles indicative of said clinical outcome;

or (5) are located physically on a chromosome close to said at least one diploid pair of haplotype alleles indicative of said clinical outcome.

5. The method of claim 2 wherein said one or more additional haplotypes play a role in a biological pathway upstream or downstream from said diploid pair of haplotype alleles indicative of said clinical outcome.

6. The method of claim 1 wherein step (a) comprises identifying a gene from a non-human species and mapping said gene to a human counterpart which is a member of a diploid pair of haplotype alleles analyzed in step (a).

10. The method of claim 1 wherein analyzing diploid pairs of haplotype alleles of individuals selected from a homogeneous population comprises analyzing diploid data based on heterozygote models.

11. The method of claim 1 wherein analyzing diploid pairs of haplotype alleles of individuals selected from a homogeneous population comprises separating the alleles in diploid pairs and comparing results of the analysis of the separated pairs to the analysis of diploid pairs.

12. The method of claim 1 wherein analyzing diploid pairs of haplotype alleles of individuals selected from a homogeneous population comprises RNA analysis, postranslational analysis, or immunoassay based analysis.

21. A method according to claim 1, wherein said clinical outcome comprises an adverse reaction, a favorable therapeutic result, an unfavorable therapeutic result, an efficacy result or an absence of therapeutic response to the administration of said medicament or therapeutic treatment.

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.

22. A method according to claim 7, wherein said clinical outcome comprises an adverse reaction, a favorable therapeutic result, an unfavorable therapeutic result, an efficacy result or an absence of therapeutic response to the administration of said medicament or therapeutic treatment.

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.

23. A method according to claim 8, wherein said clinical outcome comprises an adverse reaction, a favorable therapeutic result, an unfavorable therapeutic result, an efficacy result or an absence of therapeutic response to the administration of said medicament or therapeutic treatment.

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.

24. A method according to claim 9, wherein said clinical outcome comprises an adverse reaction, a favorable therapeutic result, an unfavorable therapeutic result, an efficacy result or an absence of therapeutic response to the administration of said medicament or therapeutic treatment.

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.

14. The method of claim 13, wherein:

a) said toxicity pathway is expressed in liver;

cardiovascular tissue, neural tissue, kidney, PBMC (peripheral blood mononuclear cell), skin, and/or lung

b) said form of evaluating is a protein evaluation, including an immunoassay, modification, quantitation, mass spectroscopy, NMR, imaging, or characteristic temporal pattern determination;

c) said evaluating is from a blood, hair, skin, saliva, oral mucosa, tears, mucus, or other accessible body fluid sample;

d) said discriminatory biomarker is from a subset 1 of Tables 3A, 5A or 6A;

e) said discriminatory biomarker is from a subset 2 or 3 of Tables 3A, 5A or 6A; and

/or

f) said discriminatory biomarker is derived from two or more datasets from Tables 3A, 4A, 5A and 6A.

15. A toxicology pathway evaluation kit comprising instructions for use and a diagnostic means directed to an evaluating discriminatory biomarker for use in a method according to claim 14.

16. A biological system to test candidate compounds for inducing a liver or other toxicity pathway, wherein said system comprises multiple biological samples exhibiting common combinations of alleles corresponding to biomarkers for use in the method of claim 14, thereby representing response among individuals represented by said combinations.

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 3 of Tables 3A, 5A and 6A.

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, 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, 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 in similar tissues;

4) which have been co-localized in expression analyses in similar tissues;

or

5) which are closely located physically on a chromosome.

19. The method of claim 18, wherein said toxicity is evaluated in a mammal, and said method comprising evaluating a plurality of features at multiple time points with use of an extended primate group whose members are selected based on their propensity to be phenotypically homogeneous, as indicated by medical record or other selection criteria, or are genetically homogeneous.

20. The method of claim 29, wherein list 1 and/or list 2 contain 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 75, 100, 200, 500, 1000 or more genes.