Affymetrix, Inc.

Harvard College

Aueon, Inc.

Janet A Warrington

David J Lockhart

Mamatha Mahadevappa

Martin J Goldberg

Jody E Beecher

Huu Minh Tran

Thomas B Ryder

Helin Dong

Archana Nair

Eugene Yuji Tanimoto

Govinda Rao S Yelagalawadi

Dietrich Stephan

Vern Norviel

Doug Dolginow

David T W Wong

Charles Randolph Todd

Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers.

Methods for stratifying and annotating cancer drug treatment options

Methods of monitoring the expression of genes in malignant oral cells is disclosed. Gene expression profiles are used to identify markers associated with malignant oral cells and to diagnose oral cancer.

Methods for detecting and diagnosing oral cancer

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.

Genes differentially expressed in secretory versus proliferative endometrium

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.

Methods for identifying and using maintenance genes

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. Optionally, the amplification reagent, comprising a plurality of the binding ligands, is contacted with labeled receptor molecules thereby to complex a plurality of labeled receptor molecules to the amplification reagent, and the labeled receptor molecules complexed to the amplification reagent are detected. This permits the detectable signal to be enhanced and amplified. In one embodiment, the binding ligand is biotin, the receptor is streptavidin, and the amplification reagent is an antibody or a DNA matrix. In another embodiment, an array of different nucleic acid probes immobilized on a surface, each having a defined sequence and location on the surface, may be used in the assays, thus permitting screening and detection of binding of a large number of nucleic acids.

Methods and compositions for amplifying detectable signals in specific binding assays

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.

Expression profiles in adult and fetal organs

Growing community of inventors

Los Altos, CA, United States of America

Janet A Warrington