Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2007-08-07
2007-08-07
Brusca, John S. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S004000, C435S006120, C435S069100, C514S002600, C514S04400A, C702S020000
Reexamination Certificate
active
09823322
ABSTRACT:
This invention provides methods for determining drug specificity, therapeutic index and effective doses for individual patients. According to the methods of the invention, graded levels of drug are applied to a biological sample or a patient. A plurality of cellular constituents are measured to determine the activity of the drug on a target pathway and at least one off-target pathway. A drug specificity is determined by comparing the target and off target activities of the drug. A therapeutic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the target pathway. A toxic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the off target pathway. Therapeutic index is the ratio of the toxic concentration over therapeutic concentration. Methods are also provided to determine an effective dose of a drug for a patient by measuring the activity of the drug on the particular patient.
REFERENCES:
patent: 4946778 (1990-08-01), Ladner et al.
patent: 5137877 (1992-08-01), Kaneko et al.
patent: 5258453 (1993-11-01), Kopecek et al.
patent: 5332567 (1994-07-01), Goldenberg
patent: 5445934 (1995-08-01), Fodor et al.
patent: 5510270 (1996-04-01), Fodor et al.
patent: 5539083 (1996-07-01), Cook et al.
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 5569588 (1996-10-01), Ashby et al.
patent: 5578832 (1996-11-01), Trulson et al.
patent: 5645988 (1997-07-01), Vande Woude et al.
patent: 5744305 (1998-04-01), Fodor et al.
patent: 5777888 (1998-07-01), Rine et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5811231 (1998-09-01), Farr et al.
patent: 5965352 (1999-10-01), Stoughton et al.
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6165709 (2000-12-01), Friend et al.
patent: 6203987 (2001-03-01), Friend et al.
patent: 6222093 (2001-04-01), Marton et al.
patent: 6370478 (2002-04-01), Stoughton et al.
patent: 0 534 858 (1992-09-01), None
patent: 0816 511 (1996-01-01), None
patent: WO 88/09810 (1988-12-01), None
patent: WO 90/11364 (1990-10-01), None
patent: WO 94/17208 (1994-08-01), None
patent: WO 97/10365 (1997-03-01), None
patent: WO 97/27317 (1997-07-01), None
patent: WO 98/06874 (1998-02-01), None
U.S. Appl. No. 60/090,046, filed Jun. 19, 1998, Friend and Stoughton.
U.S. Appl. No. 60/090,004, filed Jun. 19, 1998, Friend and Stoughton.
U.S. Appl. No. 60/084,742, filed May 8, 1998, Friend and Stoughton.
U.S. Appl. No. 60/056,109, filed Aug. 20, 1997, Friend and Hartwell.
U.S. Appl. No. 60/039,134, filed Feb. 28, 1997, Friend and Hartwell.
Alberts, DS et al., 1976 “Rubidazone vs adriamycin: an evaluation of their differential toxicity in the spleen colony assay system”,British Journal of Cancer, 34: 64-8.
Blanchard et al., 1996, “Sequence to array: Probing the genome's secrets,”Nature Biotechnology 14:1649.
Blanchard et al., 1996, “High-density oligonucelotide arrays,”Biosensors&Bioelectronics 11:687-690.
Bryant et al., (1998), “Gene Expression and Genetic Networks,”Pacific Symposium on Biocomputing 3:3-5. Available Web Site: http://www-smi.stanford.edu/projects/helix/psb98/ Accessed on: Nov. 24, 1998 3:48 p.m.
Bulmer MG,Principles of Statistics, M.I.T. Press, Cambridge, Massachusetts, 1967. pp. 117, 221-224.
Carr et al., 1997, “Templates for Looking at Gene Expression Clustering,”Statistical Computing&Statistical Graphics Newsletterpp. 20-29.
Chee et al., 1996, “Accessing genetic information with high-density DNA arrays,”Science 274:610-614.
DeRisi et al., 1996, “Use of a cDNA microarray to analyze gene expression patterns in human cancer,”Nature Genetics 14:457-460.
DeRisi et al., 1997, “Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale,”Science 278:680-686.
D'haeseleer et al., (1998), “Mining the Gene Expression Matrix: Inferring Gene Relationships From Large Scale Gene Expression Data” Available Web Site: www.cs.unm.edu/˜patrik
etworks/IPCAT/ipcat.html Accessed on: Nov. 18, 1998 6:16 p.m.
“Experts gather to discuss technologies being developed for functional genomic analysis,”Genetic Engineering Newsvol. 16, Nov. 15, 1996.
Fingl E and Woodbury DM, 1975, “Chapter 1: General Principles”In: The Pharmacological Basis of Therapeutics, Ch. 1, p. 1.
Fodor et al., 1991, “Light-directed spatially addressable parallel chemical synthesis,”Science 251:767-773.
Fuhrman et al., (1997), “Genetic Network Inference,”Proceedings of the International Conference on Complex Systems, Nashua, NH, 21-26. Available Web Site: http://rsb.info.nih.gov/mol-physiol/ICCS/inference/ICCS.html. Accessed on: Nov. 18, 1998 6:14 p.m.
Goffeau et al., 1996, “Life with 6000 genes,”Science 274:546-567.
Herskowitz, 1987, “Functional inactivation of genes by dominant negative mutations,”Nature 329:219-222.
Lennon and Lehrach, 1991, “Hybridization analyses of arrayed cDNA libraries”Trends Genet. 7:314-317.
Lockhart et al., 1996, Expression monitoring by hybridization to high-density oligonucleotide arrays,Nature Biotechnology 14:1675-1680.
Marnellos et al., (1998) “A Gene Network Approach to Modeling Early Neurogenesis in Drosophila,”Pacific Symposium on Biocomputing3:30-41. Available Web Site: http://www-smi.stanford.edu/projects/helix/psb98/Accessed on: Nov. 24, 1998 3:48 p.m.
Marton et al., 1998 “drug target validation and identification of secondary drug target effects using DNA microarrays”, Nature Medicine, 4: 1293-1301.
Michaels et al., (1998), “Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data,”Pacific Symposium on Biocomputing3:42-53. Available Web Site: http://www-smi.stanford.edu/projects/helix/psb98/ Accessed on: Nov. 24, 1998 3:48 p.m.
Nguyen et al., 1995, “Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones,”Genomics 29:207-216.
Stormo et al., 1998 “drug target validation and identification of secondary drug target effects using DNA microarrays”,Nature Medicine, 4: 1293-1301.
Thomas et al., 1995, “Dynamical behavior of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state,”Bull. Math. Biol. 57:247-276.
van der Krol et al., 1988 “Modulation of Eukaryotic Gene Expression by Complementary RNA or DNA Sequences,”Biotechniques, 6: 958-676.
Weinstein, JN et al., 1997 “An information-intensive approach to the molecular pharmacology of cancer”,Science, 275: 343-349.
Wen et al., (1998), “Large-Scale Temporal Gene Expression Mapping of Central Nervous System Development,”Proc. Natl. Acad. Sci. USA 95:334-339.
Yatscoff, R.W. et al., 1996, “Pharmacodynamic Monitoring of Immunosuppressive Drugs,”Transplantation Proceedings 28:3013-3015.
Zhao et al., 1995, “High-density cDNA filer analysis: a novel approach for large-scale, quantitative analysis of gene expression,”Gene 156:207-213.
Stewart, 1998, “Yeast arrays join the search for specific drugs” Molecular Medicine Today 4:48.
Marton Matthew
Stoughton Roland
Brusca John S.
DeJong Eric S.
Jones Day
Rosetta Inpharmatics LLC
LandOfFree
Methods for determining therapeutic index from gene... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods for determining therapeutic index from gene..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods for determining therapeutic index from gene... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3899914