Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-12-06
2005-12-06
Marschel, Ardin H. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S006120, C435S069100, C703S011000
Reexamination Certificate
active
06973388
ABSTRACT:
The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject to obtain a diagnostic profile, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects to obtain perturbation response profiles which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profile or profiles which best fit the diagnostic profile. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, databases comprising perturbation response profiles for one or more diseases and/or therapies, and kits for determining levels of disease states and/or therapeutic effects according to the methods of the invention.
REFERENCES:
patent: 5464742 (1995-11-01), Swift et al.
patent: 5510270 (1996-04-01), Fodor 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: 5633161 (1997-05-01), Shyjan
patent: 5663071 (1997-09-01), Zetter et al.
patent: 5674739 (1997-10-01), Shyjan
patent: 5677125 (1997-10-01), Holt et al.
patent: 5695937 (1997-12-01), Kinzler et al.
patent: 5702902 (1997-12-01), Tartaglia
patent: 5707807 (1998-01-01), Kato
patent: 5721337 (1998-02-01), Zetter et al.
patent: 5721351 (1998-02-01), Levinson
patent: 5723290 (1998-03-01), Eberwine et al.
patent: 5738998 (1998-04-01), Deth
patent: 5741666 (1998-04-01), Tartaglia
patent: 5746204 (1998-05-01), Schauss
patent: 5756310 (1998-05-01), Bandman et al.
patent: 5759776 (1998-06-01), Smith et al.
patent: 5935060 (1999-08-01), Iliff
patent: 5965352 (1999-10-01), Stoughton et al.
patent: 6132969 (2000-10-01), Stoughton et al.
patent: 6146830 (2000-11-01), Friend et al.
patent: 6165709 (2000-12-01), Friend et al.
patent: 6218122 (2001-04-01), Friend et al.
patent: 6222093 (2001-04-01), Marton et al.
patent: 6267722 (2001-07-01), Anderson et al.
patent: 6324479 (2001-11-01), Friend et al.
patent: 0 534 858 (1992-09-01), None
patent: WO 97/10365 (1997-03-01), None
patent: WO 98/07888 (1998-02-01), None
patent: WO 98/24935 (1998-06-01), None
patent: WO 98/41531 (1998-09-01), None
“Tumor Markers”, National Cancer Institute, accessed Jun. 5, 1998, modified 4/98. http://cancernet.nci.nih.gov/clinpdq/detection/Tumor_Markers. html.
“Adult Primary Liver Cancer”, National Cancer Institute, accessed Jun. 5, 1998, modified 6/98, http://cancernet.nci.nih.gov/clinpdq/soa/Adult_primary_liver_cancer_Physician.html.
“Ovarian Germ Cell Tumor”, National Cancer Institute, accessed Jun. 5, 1998, modified 10/97, http://cancernet.nci.nih.gov/clinpdq/soa/Ovarian_germ_cell_tumor_Physician.html.
“Huntington's Disease: Hope through Rersearch”, National Institute of Neurological Disorders and Stroke, accessed Jun. 19, 1998; updated Apr. 7, 1998; http://www.intelihealth . . . /ihtlH?d=dmtJHE&c=36290&p=˜br, IHW . . . .
“The Neurofibromatoses”, National Institute of Neurological Disorders and Stroke, accessed Jun. 19, 1998; updated May, 1997, http://www.intelihealth . . . /ihtlH?d=dmtJHE&c=36296&p=˜br, IHW . . . .
“Tay-Sachs Disease”, National Institute of Neurological Disorders and Stroke, accessed Jun. 19, 1998; updated Apr. 4, 1997; http://www.intelihealth . . . /ihtlH?d=dmtJHE&c=36308&p=˜br, IHW . . . .
“Polycystic Kidney Disease”, National Institute of Diabetes and Digestive and Kidney Diseases, accessed Jun. 19, 1998, updated Mar. 11, 1998, www.niddk.nih.gov/health/kidney/pubs/polycyst/polycyst.htm.
Blanchard et al., 1996, “High-density oligonucleotide arrays”, Biosensors & Bioelectronics 11:687-690.
Blanchard and Hood, 1996, “Sequence to array: probing the genome's secrets”, Nature Biotechnol. 14:1649.
Brecher et al., 1996, “Coagulation protein function. IV. Effect of acetaldehyde upon factor X and factor Xa, the proteins at the gateway to the common coagulation pathway”, Alcohol 13:539-545.
Burnette, 1981, “Western blotting: electrophoretic transfer of proteins from sodium dodecyl sulphate-polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A”, Anal. Biochem. 112:195-203.
Chang et al., 1998, “Cloning, expression, and characterization of mouse tissue factor pathway inhibitor (TFPI)”, Thromb. Haemost. 79:306-309.
Csendes, 1989, “An interval method for bounding level sets of parameter estimation problems”, Computing 41:75-86.
Cyert and Thorner, 1992, “Regulatory subunit (gene product) of yeast Ca2+/calmodulin-dependent phosphoprotein phosphatases is required for adaptation to pheromone”, Mol. Cell. Biol. 12:3460-3469.
Dackiw et al., 1996, “Integrin engagement induces monocyte procoagulant activity and tumor necrosis factor production via induction of tyrosine phosphorylation”, J. Surg. Res. 64:210-215.
D'Ambra, 1997, “Restoration of the normal coagulation process: advances in therapies to antagonize heparin”, J. Cardiovasc. Pharmacol. 27(Suppl 1):S58-62.
DeRisi et al., 1996, “Use of a cDNA microarray to analyse gene expression patterns in human cancer”, Nature Genet. 14:457-460.
Deshaies et al., 1988, “A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides”, Nature 332:800-805.
DiGuiseppi, “Screening for neural tube defects—including folic acid prophylaxis”, Ch. 42 in NIH on-line publication entitledGuide to Clinical Preventive Services,accessed on Jun. 5, 1998. http://text.nlm.nih.gov/cps/www/cps.48.html.
El Harrouni et al. 1996, Boundary and parameter identification using genetic algorithms and boundary element method, Proceedings of the International Conference on Computer Methods and Water Resources, Computational Mechanics, Inc., Bellerica, MA, pp. 487-495.
Elisen et al., 1998, “Protein C acts as a procoagulant by inhibiting the thrombomodulin-induced activation of protein C in human plasma”, Blood 91:1542-1547.
Esmon, 1995, “Thrombomodulin as a model of molecular mechanisms that modulate protease specificity and function at the vessel surface”, FASEB J. 9:946-955.
Ferguson et al., 1996, “A fiber-optic DNA biosensor microarray for the analysis of gene expression”, Nature Biotechnol. 14:1681-1684.
Fodor et al., 1991, “Light-directed, spatially addressable parallel chemical synthesis”, Science 251:767-773.
Goffeau et al., 1996, “Life with 6000 genes”, Science 274:546, 563-567.
Heller et al., 1997, “Discovery and analysis of inflammatory disease-related genes using cDNA microarrays”, Proc. Natl. Acad. Sci. USA 94:2150-2155.
Izumi, et al., 1992, “Alpha-fetoprotein production by hepatocellular carcinoma is prognostic of poor patient survival”, J. Surg. Oncol. 49:151-155.
Kalafatis et al., 1997, “The regulation of clotting factors”, Crit. Rev. Eukaryot. Gene Expr. 7:241-280.
Lander, 1996, “The new genomics: global views of biology”, Science 274:536-539.
Lockhart et al., 1996, “Expression monitoring by hybridization to high-density oligonucleotide arrays”, Nature Biotechnol. 14:1675-1680.
Marubini and Resele, 1971, “Computer program for fitting the logistic and the Gompertz function to growth data”, Computer Programs in Biomedicine 2:16-23.
Marx, “Familial Multiple Endocrine Neoplasia Type 1”, National Institute of Diabetes and Digestive and Kidney Diseases, accessed Jun. 19, 1998, updated Mar. 11, 1998, www.niddk.nih.gov/health/wndo/pubs/fmen1/fmen1.htm.
Maskos and Southern, 1992, “Oligonucleotide hybridizations
Friend Stephen H.
Stoughton Roland
Jones Day
Marschel Ardin H.
Rosetta Inpharmatics LLC
LandOfFree
Methods of diagnosing disease states using gene expression... 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 of diagnosing disease states using gene expression..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods of diagnosing disease states using gene expression... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3518667