66 results about "Genomic Profile" patented technology

A variety of methods and systems related to genomic profile information and related participants are described. Participants can be encouraged to allow access to their genomic profile information in a variety of ways. A peer-to-peer genomic profile information network can be implemented. A collection of genomic profile information for a large number of participants can be built, and anonymity of the participants can be maintained. Participants can maintain custodial control over their genomic profile information. Comparative tools and groups can help participants identify and communicate with other participants having similar information.

The present invention is in the field of plant biochemistry and genetics. More specifically the invention relates to nucleic acid molecules from plant cells, in particular, genomic DNA sequences from rice plants and nucleic acid molecules that contain markers, in particular, single nucleotide polymorphism (SNP) and repetitive element markers. In addition, the present invention provides nucleic acid molecules having regulatory elements or encoding proteins or fragments thereof. The invention also relates to proteins and fragments of proteins so encoded and antibodies capable of binding the proteins. The invention also relates to methods of using the nucleic acid molecules, markers, repetitive elements and fragments of repetitive elements, regulatory elements, proteins and fragments of proteins, and antibodies, for example for genome mapping, gene identification and analysis, plant breeding, preparation of constructs for use in plant gene expression, and transgenic plants.

The present disclosure provides methods and systems for incorporating multiple environmental and genetic risk factors into an individual's genomic profile. Methods include assessing the association between an individual's genotype and at least one disease or condition by incorporating multiple genetic risk factors, environmental risk factors, or a combination of both.

Disclosed are methods for analyzing reactions involving nucleic acids. The invention utilizes nucleic acids immobilized on a defined substrate in such a manner that the nucleic acid can participate in enzymatic and chemical reactions. These reactions are carried out in the presence of labeled reagents, thereby enabling the progress of the reactions to be analyzed using various techniques, such a fluorescent microscopy. The invention is particularly well suited for investigating transcription phenomena and generating genome-wide maps based upon reactions of individual nucleic acid molecules.

A method for preparing a food composition for animals comprising (a) accessing at least one database that comprises a first data set relating functional genomic profile of a biofluid or tissue sample from an animal to physiological condition and optionally genotype of the animal; (b) accessing at least one database that comprises a second data set relating to effects of bioactive dietary components on functional genomic profile; (c) by use of an algorithm drawing on these data sets, processing input data defining physiological condition and optionally genotype of a subpopulation of animals to derive a nutritional formula promoting wellness of one or more animals of the subpopulation; and (d) preparing a food composition based on the nutritional formula.

The invention enables multimodal cognitive communications, collaboration, consultation and instruction between and among heterogeneous networked teams of persons, machines, devices, neural networks, robots and algorithms during various stages of medical disease management, including detection, diagnosis, prognosis, treatment, measurement, monitoring and reporting. The invention enables both synchronous and asynchronous multiparty collaboration with multichannel, multiplexed streaming imagery data, including interactive curation, multisensory annotation and metadata tagging, as well as multi-formatted encapsulation, saving and sharing of collaborated imagery data as packetized augmented intelligence. The invention acquires both live stream and archived medical modality imagery from network-connected medical devices, cameras, signals and sensors, as well as multiomic data [phenotypic, genomic, metabolomic, pathomic, radiomic, radiopathomic and radiogenomic] maps and clinical data sets from structured reports and clinical documents, including biometric maps and movies, hapmaps, heat maps and data stream visualizations. The invention also acquires both medical and non-medical streaming imagery data from image data repositories, documents and structured reports, workstations and mobile devices, as well as from wearable computing, signals and sensors. The invention enables networked teams to interactively communicate, concurrently collaborate and bi-directionally exchange multichannel multiplexed imagery data streams, singly or together, in real time or asynchronously, generally by curating, annotating and tagging imagery information objects. The invention encapsulates and saves collaborated imagery data, together with multisensory annotations and metadata tags, in standard file formats as packetized augmented intelligence. The invention enables recursive cognitive enrichment of clinical cognitive vismemes, and saves packetized imagery information objects, multisensory annotations and metadata tags in native file formats [PDF, MPEG, JPEG, XML, XMPP, QR,TIFF, RDF, RDF / XML, SVG and DAE] as well as in formats compliant with standards for digital communications in medicine [DICOM]. The invention enables live stream multicasting of multimodal cognitive instruction and collaborative knowledge exchange with multisensory [visual, auditory, haptic] annotation of streaming imagery data, as well as secure, encrypted transmission of streaming augmented intelligence across file sharing data networks for informatics-enabled learning, specialist skills acquisition and accelerated knowledge exchange.

The present invention provides, inter alia, a method for generating a genome-wide epigenomic map, comprising a correlation between methylation variable CpG positions (MVP) and genomic DNA sample types. MVP are those CpG positions that show a variable quantitative level of methylation between sample types. Particular genomic regions of interest (ROI) provide preferred marker sequences that comprise multiple, and preferably proximate MVP, and that have novel utility for distinguishing sample types. The epigenic maps have broad utility, for example, in identifying sample types, or for distinguishing between and among sample types. In a preferred embodiment the epigenomic map is based on methylation variable regions (MVP) within the major histocompatibility complex (MHC), and has utility, for example, in identifying the cell or tissue source of a genomic DNA sample, or for distinguishing one or more particular cell or tissue types among other cell or tissue types. Analysis of epigenetic characteristics of one, or of a set of nucleic acid sequences, in the context of an inventive epigenomic map, allows for the determination of an origin of the nucleic acids.

The present invention provides for certain polynucleotide sequences that have been correlated to AMD. These polynucleotides are useful as diagnostics, and are preferably used to fabricate an array, useful for screening patient samples. The array is used as part of a laboratory information management system, to store and process additional patient information in addition to the patient's genomic profile. As described herein, the system provides an assessment of the patient's risk for developing AMD, risk for disease progression, and the likelihood of disease prevention based on patient controllable factors.

A method for preparing a food composition for animals comprising (a) accessing at least one database that comprises a first data set relating functional genomic profile of a biofluid or tissue sample from an animal to physiological condition and optionally genotype of the animal; (b) accessing at least one database that comprises a second data set relating to effects of bioactive dietary components on functional genomic profile; (c) by use of an algorithm drawing on these data sets, processing input data defining physiological condition and optionally genotype of a subpopulation of animals to derive a nutritional formula promoting wellness of one or more animals of the subpopulation; and (d) preparing a food composition based on the nutritional formula.

The present invention is in the field of plant biochemistry and genetics. More specifically the invention relates to nucleic acid sequences from plant cells, in particular, genomic DNA sequences from Arabidopsis thaliana plants. The invention encompasses nucleic acid molecules present in non-coding regions as well as nucleic acid molecules that encode proteins and fragments of proteins. In addition, the invention also encompasses proteins and fragments of proteins so encoded and antibodies capable of binding these proteins or fragments. The invention also relates to methods of using the nucleic acid molecules, proteins and fragments of proteins, and antibodies, for example for genome mapping, gene identification and analysis, plant breeding, preparation of constructs for use in plant gene expression, and transgenic plants.

The invention discloses a heterozygous genome processing method. The method comprises the following steps: carrying out at least 200 times ultrahigh deep sequencing on target species by using a whole genome shotgun process to obtain an effective read length sequence Reads; carrying out scaffold sequence Scaffold assembling and construction on the effective Reads to obtain a genome map with a redundant sequence; and carrying out heterozygous recognition processing on the genome map with a redundant sequence to remove redundant Scaffold in a heterozygous region and reserve heterozygous region information in order to obtain a whole genome map. The method realizes the rapid assembling of the whole high-quality heterozygous genome map, and shortens the drafting cycle and cost.

The invention is directed to methods and kits that allow for classification of colorectal cancer cells according to genomic profiles, and methods of diagnosing, predicting clinical outcomes, and stratifying patient populations for clinical testing and treatment using the same.

This invention relates to methods and compositions for determining the prognosis of cancer in a patient, particularly for gastrointestinal cancer, such as gastric or colorectal cancer. Specifically, this invention relates to the use of genetic markers for the prediction of the prognosis of cancer, such as gastric or colorectal cancer, based on cell proliferation signatures. In various aspects, the invention relates to a method of predicting the likelihood of long-term survival of a cancer patient, a method of determining a treatment regime for a cancer patient, a method of preparing a personalized genomics profile for a cancer patient, among other methods as well as kits and devices for carrying out these methods.

The invention relates to a method for predicting the localization of a primary tumour, wherein said method comprises the use of genomic profile data, and wherein the method is capable of predicting the type of cancer by a classification score ranking among a variety of the possible tumour types.

The invention is directed to methods and kits that allow for classification of non-small cell lung carcinoma tumors and cell lines according to genomic profiles, and methods of diagnosing, predicting clinical outcomes, and stratifying patient populations for clinical testing and treatment using the same.

The present invention relates to a method for diagnosing Alzheimer's Disease (AD) using PKC-elicited gene expression profiles PKC-activation elicits different genomic profiles in AD cells, as compared with control cells, which can he used to diagnose AD and individuals at risk for developing AD.

The invention is directed to methods and kits that allow for classification of malignant melanoma cells according to genomic profiles, and methods of diagnosing, predicting clinical outcomes, and stratifying patient populations for clinical testing and treatment using the same.

The present invention provides methods and compositions related to genomic profiling, and in particular, to assigning probabilistic measure of clinical outcome for a patient having a disease or a tumor using segmented genomic profiles such as those produced by representational oligonucleotide microarray analysis (ROMA).

One example embodiment includes a method of preparing a personalized genomics profile for a patient with colorectal cancer. The method includes assaying an expression level of an RNA transcript in a biological sample. The biological sample includes a colorectal cancer cell obtained from a patient. The method also includes determining a normalized expression level of the RNA transcript, wherein the normalized expression level of the RNA transcript correlates with an increased likelihood of colorectal cancer recurrence in the patient. The method further includes creating a report. The report summarizes the data obtained from the normalized expression level and includes an estimate of likelihood of long-term survival without colorectal cancer recurrence in said patient.

The present invention is directed to a method of assembling genomic maps of an organism's DNA or portions thereof. A library of an organism's DNA is provided where the individual genomic segments or sequences are found on more than one clone in the library. Representations of the genome are created, and nucleic acid sequence information is generated from the representations. The sequence information is analyzed to determine clone overlap from a representation. The clone overlap and sequence information from different representations is combined to assemble a genomic map of the organism. Once the genomic map is obtained, genomic sequence information from multiple individuals can be applied to the map and compared with one another to identify single nucleotide polymorphisms. These single nucleotide polymorphisms can be detected, and alleles quantified, by conducting (1) a global PCR amplification which creates a genome representation, and (2) a ligation detection reaction process whose ligation products are captured by hybridization to a support.

The disclosure provides a method of detecting heterogeneity of disease in a cancer patient comprising (a) performing a direct analysis comprising immunofluorescent staining and morphological characteristization of nucleated cells in a blood sample obtained from the patient to identify and enumerate circulating tumor cells (CTC); (b) isolating the CTCs from the sample; (c) individually characterizing genomic parameters to generate a genomic profile for each of the CTCs, and (d) determining heterogeneity of disease in the cancer patient based on the profile. In some embodiments, the cancer is prostate cancer. In some embodiments, the prostate cancer is hormone refractory.

Disclosed are methods for analyzing reactions involving nucleic acids. The invention utilizes nucleic acids immobilized on a defined substrate in such a manner that the nucleic acid can participate in enzymatic and chemical reactions. These reactions are carried out in the presence of labeled reagents, thereby enabling the progress of the reactions to be analyzed using various techniques, such a fluorescent microscopy. The invention is particularly well suited for investigating transcription phenomena and generating genome-wide maps based upon reactions of individual nucleic acid molecules.

The present disclosure provides methods and systems for assessing an individual's genotype correlations to a phenotype by analyzing the individual's genomic profile and using ancestral data to determine the correlations between genotypes and phenotypes.

The present invention provides substrates having a plurality of micro-locations on its surface. Each micro-location has an effective dose of an ion beam treatment such that the plurality of the micro-locations exhibit an affinity to a compound that is different from the affinity of the remainder of the substrate surface to that compound. The substrates of the invention can be utilized to form microarrays of biological molecules, such as oligonucleotides or peptides. Such microarrays can find a variety of applications. For example, they can be employed in large scale hybridization assays in many genetic applications, such as mapping of genomes, monitoring of gene expression, DNA sequencing, genetic diagnosis, and genotyping of organisms.

The present disclosure provides methods and systems for incorporating multiple environmental and genetic risk factors into an individual's genomic profile. Methods include assessing the association between an individual's genotype and at least one disease or condition by incorporating multiple genetic risk factors, environmental risk factors, or a combination of both.

Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization that includes tethering crosslinked protein:DNA complexes and / or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay. In general, the method includes flash freezing a cell such that the structural organization of the chromatin or other protein:DNA complexes is preserved, cryomilling the cell, producing cross-linked protein:DNA complexes by cutting the chromatin using a chemical, physical or enzymatic method, substantially immobilizing the cross-linked protein:DNA complexes, ligating the cross-linked protein:DNA complexes intramolecularly such that the ligated protein:DNA complexes represent structural organization of the chromatin; characterizing the ligated DNA by sequencing or other methods; and identifying any structural organization of the chromatin. The structural organization preferably includes information relating to interacting loci of the chromatin.

The present invention relates to genomic maps comprising biallelic markers, new biallelic markers, and methods of using biallelic markers. Primers hybridizing to regions flanking these biallelic markers are also provided. This invention provides polynucleotides and methods suitable for genotyping a nucleic acid containing sample for one or more biallelic markers of the invention. Further, the invention provides a number of methods utilizing the biallelic markers of the invention including methods to detect a statistical correlation between a biallelic marker allele and a phenotype and / or between a biallelic marker haplotype and a phenotype.

The disclosure provides a method of detecting heterogeneity of disease in a cancer patient comprising (a) performing a direct analysis comprising immunofluorescent staining and morphological characteristization of nucleated cells in a blood sample obtained from the patient to identify and enumerate circulating tumor cells (CTC); (b) isolating the CTCs from the sample; (c) individually characterizing genomic parameters to generate a genomic profile for each of the CTCs, and (c) determining heterogeneity of disease in the cancer patient based on the profile. In some embodiments, the cancer is prostate cancer. In some embodiments, the prostate cancer is hormone refractory.