Patents by Inventor Janet A. Warrington
Janet A. Warrington has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 6884578Abstract: The present invention compares expression profiles from matched samples to identify differential gene expression. Samples are matched according to physiological, pharmacological and/or disease state. Comparison of matched samples eliminates gene expression differences that are the result of changes in variables that are not of interest. The gene expression differences that remain can be attributed with a high degree of confidence to the unmatched variation. The gene expression differences thus identified can be used for example to diagnose disease, identify physiological state, design drugs, and monitor therapies.Type: GrantFiled: December 11, 2000Date of Patent: April 26, 2005Assignee: Affymetrix, Inc.Inventors: Janet A. Warrington, Mamatha Mahadevappa
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Publication number: 20050064472Abstract: The disclosed methods relate to the use of an amplification product generated from RNA to validate an expression measurement obtained by microarray analysis. RNA may be amplified as cRNA or cDNA and an aliquot of the amplified sample, cRNA or cDNA, may be analyzed for the amount of selected RNAs using an analysis method such as quantitative RT-PCR. Microarry measurements for selected RNAs may be compared to measurements obtained for the same RNAs using an independent analysis method.Type: ApplicationFiled: July 20, 2004Publication date: March 24, 2005Applicant: Affymetrix, INC.Inventors: Mamatha Shekar, Liu Chunmei, Janet Warrington
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Publication number: 20050053998Abstract: This invention provides methods for discovering maintenance genes and for using maintenance genes. In one embodiment, the expression of at least three maintenance genes are measured and used as reference (or control) for comparing the expression of target genes in two or more biological samples.Type: ApplicationFiled: October 18, 2004Publication date: March 10, 2005Applicant: Affymetrix, INC.Inventors: Janet Warrington, Mamatha Mahadevappa, Archana Nair
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Publication number: 20050042622Abstract: A computer based method and computer program product are presented for evaluating information concerning candidate genes and experiments used to identify the candidate genes, wherein the candidate genes are identified via examining expression levels of a plurality of genes, wherein the expression levels are measured by conducting hybridization experiments with nucleic acid microarray chips.Type: ApplicationFiled: October 15, 2003Publication date: February 24, 2005Applicant: Affymetrix, INC.Inventor: Janet Warrington
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Publication number: 20050032074Abstract: A method is described that receives user-selected sequence and provides a custom array designed for resequencing the user-selected sequence. The system determines probes corresponding to the sequence and to possible variants of the sequence and generates a custom probe array design. The system then displays the custom probe array design to the user via a graphical user interface and receives a user acceptance of the design. The system provides the user with the accepted custom probe array. The system may also enable a number of users to share space on a custom probe array. Another optional feature is to enable a number of users to share in ordering portions of a lot of catalog probe arrays to take advantage of economies of scale from lot-size purchases.Type: ApplicationFiled: September 9, 2003Publication date: February 10, 2005Applicant: Affymetrix, INC.Inventors: Nila Shah, Janet Warrington, Xue Zhou, Michael Mittmann, Rui Mei
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Patent number: 6841348Abstract: This invention provides methods for discovering maintenance genes and for using maintenance genes. In one embodiment, the expression of at least three maintenance genes are measured and used as reference (or control) for comparing the expression of target genes in two or more biological samples.Type: GrantFiled: October 19, 2000Date of Patent: January 11, 2005Assignee: Affymetrix, Inc.Inventors: Janet A. Warrington, Mamatha Mahadevappa, Archana Nair
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Patent number: 6806047Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent.Type: GrantFiled: February 6, 2001Date of Patent: October 19, 2004Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Publication number: 20040146894Abstract: The invention disclosed in this application provides methods of diagnosing and treating stress urinary incontinence and predisposition to stress urinary incontinence. These methods are based on the identification of significant differences in gene expression in the pelvic supporting tissues of premenopausal women afflicted with SUI as compared with continent, control women, using microarray-based techniques. The identified differences in gene expression may contribute to altered ECM metabolism and ECM remodeling in pelvic tissue from SUI women. The invention also provides candidate genes for use in diagnosing disorders characterized by pelvic floor dysfunction, including SUI, identification of therapeutic gene targets, evaluation of treatment regimens, prediction of treatment outcome, design of therapeutic agents, and identification of individuals at risk for developing these disorders. Various embodiments of the present invention are disclosed which relate to the above-described uses of candidate genes.Type: ApplicationFiled: October 14, 2003Publication date: July 29, 2004Inventors: Janet A. Warrington, Zhaomei Zhang, Bertha Chen, Yan Wen, Mary Lake Polan
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Publication number: 20040137493Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent.Type: ApplicationFiled: January 7, 2004Publication date: July 15, 2004Applicant: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Publication number: 20040029151Abstract: Many genes are affected in prostate cancers which have not been previously identified. This includes genes that have been up-regulated or down-regulated. Monitoring the expression levels of these genes is useful to identify the existence of prostate cancer. Also, monitoring the expression levels of these genes is useful to predict the effectiveness of treatment, outcome, use of therapeutics, and screening drugs useful for the treatment of prostate cancer.Type: ApplicationFiled: April 9, 2003Publication date: February 12, 2004Applicant: Affymetrix, INC.Inventors: Mamatha Mahadevappa, Zhaomei Zhang, Janet A. Warrington, John F. Palma, Mitchell C. Caldwell, Zuxiong Chen, Zhenbin Fan, John E. McNeal, Rosalie Nolley, Thomas A. Stamey
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Publication number: 20030124539Abstract: In one embodiment of the invention, methods and systems are provided for high thoughput genotyping. The system includes an automated sample preparation system, a sample tracking system, automated array processing and system for data analysis.Type: ApplicationFiled: December 21, 2001Publication date: July 3, 2003Applicant: Affymetrix, Inc. A corporation organized under the laws of the State of DelawareInventors: Janet A. Warrington, Nila A. Shah
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Publication number: 20030113762Abstract: Sixty-four down regulated and 22 up regulated genes have been indentified in Gleason grade 4/5 cancer, using the gene profile from benign prostatic hyperplasia as control tissue. Hepsin appears to be the most promising of the up regulated genes. PSMA is also highly overexpressed at the transcript level in grade 4/5 cancer, re-emphasizing its potential importance as a target for chemotherapy. The regulated genes can be used diagnostically, prognostically, and therapeutically. They can be used to form prostate specific expression monitoring tools.Type: ApplicationFiled: August 16, 2002Publication date: June 19, 2003Inventor: Janet A. Warrington
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Publication number: 20010044104Abstract: The present invention compares expression profiles from matched samples to identify differential gene expression. Samples are matched according to physiological, pharmacological and/or disease state. Comparison of matched samples eliminates gene expression differences that are the result of changes in variables that are not of interest. The gene expression differences that remain can be attributed with a high degree of confidence to the unmatched variation. The gene expression differences thus identified can be used for example to diagnose disease, identify physiological state, design drugs, and monitor therapies.Type: ApplicationFiled: December 11, 2000Publication date: November 22, 2001Inventors: Janet A. Warrington, Mamatha Mahadevappa
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Publication number: 20010041335Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent.Type: ApplicationFiled: February 6, 2001Publication date: November 15, 2001Applicant: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Patent number: 6203989Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent.Type: GrantFiled: March 25, 1999Date of Patent: March 20, 2001Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Patent number: 6033860Abstract: Expression profiles have been constructed for liver and brain, in adult and fetal and adolescent tissue. These provide the art with probes which are highly differentially expressed among stages and organs. The profiles and probes can be used to prioritize potential drug targets, to monitor disease progression and remission, and to assess drug metabolism. Solid supports are also provided which facilitate these uses.Type: GrantFiled: October 30, 1998Date of Patent: March 7, 2000Assignee: Affymetrix, Inc.Inventors: David J. Lockhart, Janet A. Warrington, Archana Nair