598 results about "Gene expression profiling" patented technology

The present invention relates to compositions and methods for treating, characterizing, and diagnosing cancer. In particular, the present invention provides gene expression profiles associated with solid tumor stem cells, as well as novel stem cell cancer markers useful for the diagnosis, characterization, and treatment of solid tumor stem cells.

The present invention relates to compositions and methods for treating, characterizing, and diagnosing cancer. In particular, the present invention provides gene expression profiles and signatures associated with solid tumor stem cells, as well as novel stem cell cancer markers useful for the diagnosis, characterization, prognosis and treatment of solid tumor stem cells. More particularly, the present invention identifies two profiles of cancer stem cells useful for the diagnosis, characterization, and treatment of cancer and cancer metastases. The invention also provides a variety of reagents such as stem cell gene signatures for use in the diagnosis and management of cancer.

The present invention relates to compositions and methods for treating, characterizing, and diagnosing cancer. In particular, the present invention provides gene expression profiles associated with solid tumor stem cells, as well as novel stem cell cancer gene signatures useful for the diagnosis, characterization, prognosis and treatment of solid tumor stem cells.

A method of providing a prognosis of lung cancer is conducted by analyzing the expression-of a group of genes. Gene expression profiles in a variety of medium such as microarrays are included as are kits that contain them.

The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provide methods for the sensitive and specific detection of target gene sequences and gene expression profiles.

The present invention is directed to providing sensitive and accurate assays for gene detection, genome-wide gene expression profiling and alternative splice monitoring with a minimum or absence of target-specific amplification.

Methods are provided for modulating the expression of genes involved in lipid metabolism, useful in the treatment of conditions associated with cardiovascular risk. Antisense oligonucleotides targeted to apolipoprotein B reduce the level of apolipoprotein B mRNA, lower serum cholesterol and shift liver gene expression profiles from those of an obese animal towards those of a lean animal. Further provided are methods for improving the cardiovascular risk of a subject through antisense inhibition of apolipoprotein B. Also provided are methods for employing antisense oligonucleotides targeted to apolipoprotein B to modulate a cellular pathway or metabolic process.

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.

The present invention comprises a method to identify granulocytic cell genes that are differentially expressed upon exposure to a pathogen or in a sterile inflammatory disease by preparing a gene expression profile of a granulocytic cell population exposed to a pathogen or isolated from a subject having a sterile inflammatory disease and comparing that profile to a profile prepared from quiescent granulocytic cells. The present invention is particularly useful for identifying cytokine genes, genes encoding cell surface receptors and genes encoding intermediary signaling molecules. The invention also includes methods to identify a therapeutic agent that modulates the expression of at least one gene in a granulocytic population. Genes which are differentially expressed during neutrophil contact with a pathogen, such as a virulent bacteria, or that are differentially expressed in a subject having a sterile inflammatory disease are of particular importance.

The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, cancer markers. In particular, the present invention provides gene expression profiles associated with prostate cancers. Genes identified as cancer markers using the methods of the present invention find use in the diagnosis and characterization of prostate cancer. In addition, the genes provide targets for cancer drug screens and therapeutic applications.

A method of providing predicting relapse of breast cancer in bone is conducted by analyzing the expression of a group of genes. Gene expression profiles in a variety of medium such as microarrays are included as are kits that contain them.

Genes and gene expression profiles useful for predicting outcome, risk classification, cytogenetics and / or etiology in pediatric acute lymphoblastic leukemia (ALL). OPAL1 is a novel gene associated with outcome and, along with other newly identified genes, represent a novel therapeutic targets.

The present invention provides methods of designing PCR primers that allow the efficient and simultaneous amplification of a large number of different desired DNA fragments in a single multiplex PCR and minimize the formation of nonspecific extensions of undesired DNA fragments. The present invention allows a multiplex PCR to use at least 50 pairs of primers and produce at least 50 DNA fragments of interest. The present invention significantly broadens the application of multiplex PCR in the identification of multiple genes related to multifactorial diseases, the genome-scale detection of genetic alterations, the studies in large-scale pharmacogenetic reactions, the genotyping genetic polymorphism in a large population, the gene expression profiling in various samples, and high throughput genotyping technologies.

The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, cancer markers. In particular, the present invention provides gene expression profiles associated with thyroid cancers. Genes identified as cancer markers using the methods of the present invention find use in the diagnosis and characterization of thyroid cancer. In addition, the genes provide targets for cancer drug screens and therapeutic applications.

The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provides methods for the sensitive and specific detection of target gene sequences and gene expression profiles.

Genetically elite ungulate mammals are identified on the basis of gene expression profiles from biological samples such as liver and blood. Methods and compositions are presented to select genetically elite animals with a desired phenotype such as high milk production for breeding to improve production levels. A method to select an animal with a specific phenotype, e.g. milk production and health traits, includes creating a Gene Expression Index for a specific phenotype and using the index to identify candidate animals for breeding by comparing the index to gene expression profiles of the animals.

A method for the diagnosis, prognosis and treatment of lung cancer by detecting at least one microRNA in peripheral blood is disclosed.

Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.

The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.

The present invention provides methods and compositions for isolating and detecting rare cells from a biological sample containing other types of cells. In particular, the present invention includes a debulking step that uses a microfabricated filters for filtering fluid samples and the enriched rare cells can be used in a downstream process such as identifies, characterizes or even grown in culture or used in other ways. The invention also include a method of determining the aggressiveness of the tumor or of the number or proportion of cancer cells in the enriched sample by detecting the presence or amount of telomerase activity or telomerase nucleic acid or telomerase expression after enrichment of rare cells. This invention further provides an efficient and rapid method to specifically remove red blood cells as well as white blood cells from a biological sample containing at least one of each of red blood cells and white blood cells, resulting in the enrichment of rare target cells including circulating tumor cells (CTC), stromal cells, mesenchymal cells, endothelial cells, fetal cells, stem cells, non-hematopoietic cells etc from a blood sample. The method is based upon combination of immuno-microparticles (antibody coated microparticles) and density-based separation. The final enriched target cells can be subjected to a variety of analysis and manipulations, such as flowcytometry, PCR, immunofluorescence, immunocytochemistry, image analysis, enzymatic assays, gene expression profiling analysis, efficacy tests of therapeutics, culturing of enriched rare cells, and therapeutic use of enriched rare cells. In addition, depleted plasma protein and white blood cells can be optionally recovered, and subjected to other analysis such as inflammation studies, gene expression profiling, etc.

A method of providing a prognosis of colorectal cancer is conducted by analyzing the expression of a group of genes. Gene expression profiles in a variety of medium such as microarrays are included as are kits that contain them.

Provided herein are methods for diagnosing and treating multiple myeloma based on statistical analysis of and subsequent increasing / inhibiting expression of subgroups of plasma cells and B cell genes. Also provided are methods for a developmental stage-based classification for multiple myeloma using hierarchical clustering analysis of plasma cell and B cell nucleic acids and for discriminating among normal, hyperplastic and malignant using gene expression array data and statistical analysis thereof. In addition methods for determining the risk of developing bone disease in a test individual by examining expression levels of a WNT signaling antagonist, such as DKK1, are provided. A kit comprising anti-DKK1 antibodies and detection reagents for measuring DKK1 protein levels also is provided.

A method of diagnosing cancer by identifying differential modulation of each gene (relative to the expression of the same genes in a normal population) in a combination of genes selected from two groups of genes.Gene expression portfolios and kits for employing the method are further aspects of the invention.

The invention concerns an integrated, qRT-PCR-based system for analyzing and reporting RNA expression profiles of biological samples. In particular, the invention concerns a fully optimized and integrated multiplex, multi-analyte method for expression profiling of RNA in biological samples, including fixed, paraffin-embedded tissue samples. The gene expression profiles obtained can be used for the clinical diagnosis, classification and prognosis of various pathological conditions, including cancer.

A method of developing a gene expression profile indicative of the presence or stage of a selected a disease, disorder or genetic pathology in a mammalian subject employs penalized discriminant analysis with recursive feature elimination. A method of diagnosing a cancer in a mammalian subject includes the steps of examining a sample containing the subject's immune cells and detecting a variance in the expression of a statistically significant number of genes, e.g., at least 10 non-tumor genes from those same genes in a characteristic disease or healthy gene expression profile. A significant variance in expression of these genes when compared to a gene expression profile, preferably an average gene expression profile of a normal control, or significant similarities to an average gene profile of subjects with cancer, correlates with a specific type of cancer and / or location of tumor.

The present invention concerns prognostic markers associated with EGFR positive cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed tissue samples of EGFR-expressing cancer, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.

The present invention provides a new method for producing amplified RNA from a selected set of cells. This method combines and utilizes known methods in a novel way to produce the gene expression profiles. The methods of the present invention utilize thermostable DNA polymerases and RNase H to produce high fidelity second strand synthesis of nucleic acids from selected cells in a highly efficient mariner and in substantially reduced time.