46 results about "Biomarker discovery" patented technology

The present invention provides users with cloud-based high throughput computing system for integrative analyses of next generation sequencing genomic data, such that human cancer biomarkers and drug targets can be accurately and quickly identified. Advantageously, the present invention harness a comprehensive systematic analysis pipelines for all types of next generation sequencing genomic data, advanced genomic variants calling algorithms and modeling, variant data correlation and integration, and identification of cancer specific biomarkers and therapeutic targets. Thus, the present invention will aid users so that less of their time and efforts are required in order to obtain precisely the desired information for which they are analyzing.

An analytic apparatus and method is provided for diagnosis, prognosis and biomarker discovery using transcriptome data such as mRNA expression levels from microarrays, proteomic data, and metabolomic data. The invention provides for model-based analysis, especially using kernel-based models, and more particularly similarity-based models. Model-derived residuals advantageously provide a unique new tool for insights into disease mechanisms. Localization of models provides for improved model efficacy. The invention is capable of extracting useful information heretofore unavailable by other methods, relating to dynamics in cellular gene regulation, regulatory networks, biological pathways and metabolism.

The invention discloses application for analyzing micromolecules with irradiating nanometer carbon spots serving as a matrix assisted laser desorption ionization (MALDI) matrix. The carbon spots serve as an analysis method of the MALDI matrix and are suitable to mass spectrum analysis for the micromolecules with the m/z between 150-1000. Suitable molecule types comprise amino acid, polypeptide, beta-exhilarant, fatty acid, polymer and the like. When the method is used for detecting the molecule with the m/z between 150-1000, background peaks hardly exist to produce background interference. The method can be effectively used in the fields of organic and biomass spectrometry, spectrometry imaging, protein spectroscopy, metabonomics, biomarker discovery, environment analysis and the like.

The present application discloses an epigenetic marker for lung cancer.

The present application discloses a method for discovering a methylation marker gene for the conversion of a cell comprising: (i) comparing converted and unconverted cell gene expression content to identify a gene that is present in greater abundance in the unconverted cell; (ii) treating a converted cell with a demethylating agent and comparing its gene expression content with gene expression content of an untreated converted cell to identify a gene that is present in greater abundance in the cell treated with the demethylating agent; and (iii) identifying a gene that is common to the identified genes in steps (i) and (ii), wherein the common identified gene is the methylation marker gene.

Described herein are methods, devices, and compositions for fractionation and processing of microparticles from biological samples, and to methods for obtaining and using the microparticles for biomarker discovery. Biological samples include cell-free fluids, for example blood plasma, blood serum, cerebrospinal fluid, urine, and saliva, as well as conditioned media. Conditioned media is the liquid growth media used to propagate cells in vitro. Purification of microparticles from cell-free fluids is challenging, typically accomplished by prolonged ultracentrifugation. Described herein is an alternative method for efficiently harvesting and processing microparticles from cell-free fluids and from conditioned media. Embodiments described herein relate to use of the microparticles and their contents recovered from conditioned media derived from propagation of human and animal cells, as a source of biomarkers for diagnosis and prognosis of diseases and pathological conditions.

A method or platform for monoclonal antibody based biomarker discovery is disclosed. The method according to the invention provides for the integration of analyte collection, hybridoma screening and nanovolume integrated mass spectrometry (NVIMS) to achieve a robust screening system that is capable, for example, of cutting 4-6 years off of the classical biomarker discovery and development process. The invention provides a platform for the rapid, high-throughput production, isolation and characterization of, e.g., disease specific biomarkers together with highly specific monoclonal antibodies. The method of the invention has a variety of applications such as, but not limited to, drug testing, biohazard applications, ecological applications, physiological applications and/or pathology screening applications. The method of the invention is also capable of being performed or used as or with a high-throughput screening process or system of the invention.

The invention relates to the technical field of biological separation and extraction, in particular to an extracting method of extracellular vesicles. The method comprises the steps that a biologicalsample is provided; the biological sample is in contact with a capturing surface at least twice on the condition that impurities in the biological sample are partially or wholly reserved on the capturing surface, wherein the impurities are partial or whole other substances except the extracellular vesicles in the biological sample, and the capturing surface comprises an inner surface and/or outersurface of a spherical-particle porous material; when the impurities are partially or wholly reserved on the surface of a capture, breakthrough liquid is extracted liquid containing the extracellularvesicles; or the breakthrough liquid is further concentrated. By means of the method, the epicyte vesicles can be quickly separated and purified, the separation operation is simple, the single use cost is low, the separated sample in high in purity, the bioactivity of the sample is kept good, and the extracting method is applied to fundamental research in the aspects of biomarker discovery, biotherapy and the like and industrial production.

The invention discloses a preparation method of saliva extracellular vesicles and application of the saliva extracellular vesicles to molecular diagnosis.The preparation method includes the steps of removing high-abundance proteins from saliva samples, filtering out mucoproteins, separating and extracting the extracellular vesicles, characterizing the obtained extracellular vesicles, extracting extracellular vesicle proteins, identifying the extracellular vesicle proteins and applying the extracellular vesicle proteins to lung cancer biomarker discovery.Currently, a normalized saliva extracellular vesicle preparation technology is absent, and high-abundance protein interference and background impurity interference, existing in existing preparation technologies, result in shortcomings of low extracellular vesicle recovery rate, fewer identified proteins and the like, so that true extracellular vesicle proteomics information can be reflected difficultly.The preparation method of the saliva extracellular vesicles and application of the saliva extracellular vesicles to molecular diagnosis have the advantages that saliva of healthy adult volunteers and lung cancer patients is taken as the samples, and an affinity chromatography and membrane separation combined technology is adopted, so that after the high-abundance proteins and the mucoproteins of the saliva are removed, the extracellular vesicles in the saliva are extracted centrifugally, proteomes of the extracellular vesicles are analyzed and more extracellular vesicle proteins are identified.

A new fractionation device shows desirable features for exploratory screening and biomarker discovery. The constituent MSCs may be tailored for desired pore sizes and surface properties and for the sequestration and enrichment of extremely low abundant protein and peptides in desired ranges of the mass/charge spectrum. The MSCs are effective in yielding reproducible extracts from complex biological samples as small as 10 μl in a time as short as 30 minutes. They are inexpensive to manufacture, and allow for scaled up production to attain the simultaneous processing of a large number of samples. The MSCs are multiplexed, label-free diagnostic tools with the potential of biological recognition moiety modification for enhanced specificity. The MSCs may store, protect and stabilize biological fluids, enabling the simplified and cost-effective collection and transportation of clinical samples. The MSC-based device may serve as a diagnostic tool to complement histopathology, imaging, and other conventional clinical techniques. The MSCs mediated identification of disease-specific protein signatures may help in the selection of personalized therapeutic combinations, in the real-time assessment of therapeutic efficacy and toxicity, and in the rational modulation of therapy based on the changes in the protein networks associated with the prognosis and the drug resistance of the disease.

The invention discloses 2,3,4,5,-tetra(3',4'-dihydroxyl phenyl)thiophene and application of 2,3,4,5,-tetra(3',4'-dihydroxyl phenyl)thiophene as an MALDI (matrix assisted laser desorption ionization) matrix in analyzing small molecules. The analysis method using 2,3,4,5,-tetra(3',4'-dihydroxyl phenyl)thiophene as the MALDI matrix is suitable for performing mass spectrum analysis on the small molecules with m/z being less than 1000. And adaptive molecule varieties comprise amine matters such as amino acids, vitamins, excitants, caffeine, urea, dopamine, melamine, aniline, purines and pyrimidines, etc., wherein background interference is not produced because of only a few fixed background peaks when the method is used for detecting the molecules with m/z being less than 1000. The method for preparing 2,3,4,5,-tetra(3',4'-dihydroxyl phenyl)thiophene provided by the invention can be effectively applied to fields such as the organic and biological mass spectrum, the mass spectrum imaging, the protein spectroscopy, the metabonomics, the biomarker discovery, the environment analysis and the like.

A method of determining disease diagnosis, progression and response to therapy through the use of xenograft animal models for determining cancer biomarkers is presented. In use, a tumor from a patient is transplanted into an animal model such as a mouse. Expression levels of biomarkers for a disease are assessed in the serum of the animal model. A personalized gene expression profile or biomarker gene signature may be obtained from the expression levels of the biomarkers which can be used to determine disease recurrence, progression and response to therapy.

An isogenic murine animal model for liver disease resulting from a Western (high fat, high sugar) diet is provided. This phenotypically and genotypically stable model sequentially develops steatosis (4-8 weeks), steatohepatitis (12-16 weeks), progressive fibrosis (16 week onwards) and spontaneous HCC (32-52 weeks), but only when fed a diet high in fat and sugar. The mice also develop obesity, insulin resistance and dyslipidemia, and the mouse hepatic transcriptome is concordant with the human NASH transcriptome at early and late time points, including activation of lipogenic, inflammatory and apoptotic signaling. The mouse HCC gene signature resembles S1 and S2 human HCC subclasses. This simple model of NASH and HCC that mirrors the development of human disease in terms of its triggers, serology, phenotype, histology, transcriptome and outcomes has utility in new target discovery, biomarker discovery, diagnostic test development, and screening and development of drugs for the corresponding liver conditions.

The present invention relates to the field of proteomics and more specifically to a method for analyzing a sample possible containing peptides or modified peptides; in particular useful for biomarker discovery or validation of biomarkers. The method uses isoelectric focusing and mass spectrometry (MS) and enables identification of modified peptides with high resolution and predictability.