28 results about "Epigenome" patented technology

Described herein are gene features that provide prognosis, diagnosis, treatment and molecular subtype classification of cancer by genomic and epigenomic profiling, including immune checkpoint regulators such as Programmed Death Ligand 1 (PDL-1). Using the methods and compositions described herein, specific and sensitive detection of biomarkers of interest is provided. Such biomarkers indicate disease pathogenesis, which provides opportunities for selection of treatments, including treatment regimens intended to overcome tolerance mechanisms.

Disclosed are methods for trapping and barcoding discrete biological units in a hydrogel. Also disclosed are methods for analyzing gene expression, genotype, haplotype or epigenome in discrete biological units, as well as kits for implementing the methods of the present disclosure.

The invention discloses a microneedle patch for in-vivo space-time omics analysis and a preparation method and application thereof, and belongs to the technical field of gene detection. Comprising the following steps: performing high-density modification on the surface of the microneedle for molecular binding; preparing a micro-needle base grinding tool for constructing a micro-needle patch; connecting the universal primer probe and the capture primer probe to the bar code probe; the microneedle patch captures to-be-detected molecules in a living body in situ; a probe complementary with the strand displacement region is added, polymeric strand displacement is carried out, and the obtained product can be used for constructing a sequencing library to realize spatial omics analysis of a living sample; the microneedle after strand displacement can be coupled with the bar code probe again to realize reuse of the microneedle for a new round of reaction. According to the method, the analysis of the spatial group in the living body sample is realized at extremely low cost, the operation is simple, the application field is wide, and the method can be used for detecting genomes, transcriptomes, proteomes, epigenomes, metabolomes and the like.

Provided herein are methods, compositions, systems, kits and uses for integrated, simultaneous spatial multiomic analyses of tissues and samples including chromatin accessibility epigenomic analysis, RNA expression transcriptomic analysis, cell cluster and cell lineage analysis, transcription factor motif analysis, extrachromosomal DNA analysis and mitochondrial DNA analysis.

Described herein are gene features for providing prognosis, diagnosis, treatment and molecular subtype classification of cancer by genomic and epigenomic profiling, methods and compositions for determining cancer and subtypes, including breast cancer, and provide specific and sensitive detection of biomarkers of interest. Such biomarkers indicate disease pathogenesis, which provides opportunities to select treatment, including treatment regimens intended to identify responsive candidates and overcome resistance mechanisms.

The application provides a 5mCpG high-throughput detection method TnM-seq based on TnM transposase, which adopts transposase TnM including an MBD domain to detect 5mCpG in situ, and comprises the following steps: after pretreatment of cells to be detected, the cells are incubated with transposase TnM; DNA in the target sample after transposition is recovered and purified; the purified DNA is subjected to PCR library construction; and the library construction product is subjected to high-throughput sequencing. The new transposase TnM newly designed and synthesized is used, combined with high-throughput sequencing, to realize convenient, fast, low-cost and high-sensitivity detection of 5mCpG in a sample. Based on the transposase TnM, a multi-omics technology HAM-seq for simultaneously detecting histone modification H3K9me3, chromatin accessibility and DNA methylation modification 5mCpG in the same sample is further developed, and after being combined with a commercial single-cell microfluidic platform, an epigenome and gene expression four-omics technology EpiX-seq for single-cell analysis in a complex tissue is obtained.

The present invention relates to a method for preparing a single cell multi-sample multi-body library and a use thereof. The present invention relates to a method whereby an epigenome and a transcriptome can be simultaneously analyzed at a single cell level, and the principle of regulating the epigenome and the transcriptome has been identified. Accordingly, the present invention makes it possible to reduce reagent costs by about 1 / 10 compared to the prior art and simultaneously analyze six or more samples, thus being economical and having the advantage of being able to contribute to high-tech genomic research. According to the present invention, six samples can be simultaneously analyzed, and ATAC as an epigenome and 5 prime RNA information as a transcript can be simultaneously collected and used to clearly identify the starting point of gene expression that immediately responds to epigenetic changes.

The application discloses a chip for spatial multi-omics sequencing and a preparation method and application thereof. The chip designed in the application is fixed with clusters of oligonucleotide probes, the oligonucleotide probes are double-omics probe chains, and the double-omics probe chains simultaneously include transcriptome and epigenome capture probes, so that spatial transcriptome and spatial open chromatin information can be synchronously acquired on the same tissue section, registration errors among multiple sections are avoided, and a more complete solution is provided for multi-modal spatial omics research.

The application discloses a bar code repeatable microsphere, a preparation method and application thereof, and relates to the fields of biomedical detection and high-throughput single cell sequencing.The bar code repeatable microsphere comprises a microsphere, a universal primer probe and a bar code probe, and the bar code probe comprises a Nick region, a capture region, a cell bar code region and a molecular bar code region.The method can realize preparation of the bar code microsphere and repetition of the bar code at a very low cost, is simple to operate, and is widely applied, and can be used for detection in the aspects of genomes, transcriptomes, proteomes, epigenomes and metabolomes.

Downregulated miR-99b-5p and upregulated mTOR cooperatively promotes the African American (AA) PCa aggressiveness and drug resistance. Nuclear mTOR, AR, and SMARCD1 are highly expressed in AA PCa (MDA PCa 2b) compared to EA PCa (LNCaP) cell line. miR-99b-5p inhibited protein levels of mTOR, AR / AR-V7 and SMARCD1 in cytoplasm and nuclei of EA and AA PCa. miR-99b-5p effectively inhibits cell proliferation / survival and induced cell apoptosis in EA and AA PCa cells. Moreover, combination of miR-99b-5p and enzalutamide (Enz) synergistically enhances the cytotoxicity against aggressive AA PCa and castration resistant prostate cancer (CRPC). miR-99b-5p or miR-99b-5p / Enz significantly reduces the recruitment of mTOR to the genes involved in the metabolic reprogramming in CRPC. miR-99b-5p can function as an epigenomic driver to modulate the mTOR / AR / SMARCD1 signaling axis in AA PCa and resistant CRPC. miR-99b-5p can be utilized as a biomarker for identifying the presence of prostate cancer.

The present invention relates to a method of spatially barcoding one or more biological molecules located on or within a substrate by using a transposase complex to label the biological molecule of interest with a detection probe which may then give rise to a spatial barcode. Such analysis may include determining the spatial profiling of one or more biological molecules, specifically the spatial analysis of DNA, open chromatin, chromatin features, proteins and / or RNA which may be spatially barcoded by methods of the invention, either alone or in various combinations. The invention further relates to a transposase complex for use in spatially barcoding one or more biological molecules and reagents kits for performing such methods.

The application relates to the field of biomedical technology and discloses a peripheral blood leukocyte DNA methylation gene network model for lung nodule benignity and malignancy and infiltration risk assessment and a construction method thereof. The method is based on an epigenome network medical algorithm, specific methylation characteristics are screened from whole blood leukocytes of sub-centimeter lung nodule patients, and a diagnostic model is constructed. Research proves that, by using peripheral blood leukocyte DNA methylation combined with network topology analysis, the low cfDNA content, the PBMC separation complexity and the cell heterogeneity interference can be effectively overcome, the systemic immune remodeling signal of early lung cancer can be accurately captured, benignity and malignancy classification and infiltration risk stratification can be performed, the model has good sensitivity and specificity, can be used as an important supplement of LDCT screening, can improve early risk assessment accuracy, can guide high-risk patient treatment and reduce over-treatment of low-risk patients, and realizes precise management of lung small nodules.

The invention provides herein epigenomic changes identified in old mice compared to young mice or old mice treated with Oct4, Sox2, Klf4 and c-Myc (OSKM). The invention further provides methods of identifying a compound by analyzing one or more PRC2-associated epigenomic change in a sample before and after contacting the sample with one or more compounds. Also provided herein are methods of using compounds identified using the methods described herein for improving proliferative capacity, cell and tissue regeneration, and / or reducing fibrosis.

Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, including immune checkpoint regulators such as programmed death ligand 1 (PDL-1). Using methods and compositions described herein, specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at overcoming resistance mechanisms.

The invention discloses a chip for spatial multi-omics sequencing as well as a preparation method and application of the chip. A cluster of oligonucleotide probes is fixed on the designed chip, the oligonucleotide probes are biomics probe chains and comprise transcriptome and epigenome capture probes at the same time, space transcriptome and space open chromatin information can be synchronously obtained on the same tissue slice, registration errors among multiple slices are avoided, and the detection accuracy is improved. And a more complete solution is provided for multi-modal spatial omics research.

Methods and kits for trapping and barcoding discrete biological units in a hydrogel are disclosed. The kits provide barcode units possessing unique identifiers and a moiety for binding biological units. Also included is a hydrogel solution or monomers for preparing a hydrogel solution, and reagents for molecular biology assays. In certain versions, the barcode units are beads that may be pre-bound to a support. The platform facilitates forming complexes between biological units—such as cells, nuclei, or DNA fragments—and the barcode units, then embedding these complexes within a polymerized hydrogel matrix. This enables analyzing gene expression, genotype, haplotype, or the epigenome by allowing reagent diffusion while keeping the biological units and their unique barcodes spatially associated.

The invention relates to an early disease detection device based on high-depth cell-free nucleic acid sequencing, and the device can comprise a library preparation part which is used for preparing a library set comprising a whole genome sequencing library, a whole epigenome sequencing library, a transcriptome sequencing library and an epitranscriptome sequencing library based on cell-free nucleic acid extracted from blood; the sequencing part is used for sequencing the library set to generate high-depth cell-free nucleic acid sequencing data; the signal calculation part is used for mapping the high-depth cell-free nucleic acid sequencing data to a genome reference sequence so as to determine the position of the high-depth cell-free nucleic acid sequencing data on a genome, and calculating at least one disease-specific signal value based on the mapped high-depth cell-free nucleic acid sequencing data; a prediction signal value generation section for processing the at least one disease-specific signal value to generate a disease prediction signal value; and a prediction model generation unit for generating a disease prediction model using the marker information relating to the blood and the disease prediction signal value to detect the occurrence or absence of a disease in the input blood and the type of the disease.

This specification describes diagnostic methods for selecting treatments for personalized cancer therapy by simultaneously detecting genomic and epigenomic characteristics from a single patient sample, including the quantification of promoter methylation, as well as applications for confirming methylation patterns associated with epigenetic allele status. This specification also describes methods comprising the steps of detecting methylation in one or more promoter regions of at least one of multiple genes, and generating multiple methylation calls to quantify methylation in one or more promoter regions.

The invention relates to the creation of a platform developed for use in the fields of medicine, health, biotechnology, public health, where individuals can determine their DNA methylation patterns and single nucleotide polymorphisms associated with metabolism, share the relevant epigenetic and genetic information with professionals (experts such as doctors, dietitians, psychologists) who monitor the health of individuals, and receive individual sports and dietary recommendations for their metabolism in line with their epigenomic and genomic characteristics.

Disclosed herein are methods, compositions, and devices for diagnosing and treating diseases, including cardiovascular diseases as well as such diseases and dysfunctions associated with administration of cancer therapy. Methods include sequencing a set of regions in a cell-free nucleic acid molecule and detecting one or more biomarkers indicative of cardiovascular disease and dysfunction.

Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.

The application discloses a method for analyzing epigenetic diversity based on a methylation-sensitive amplified polymorphism (MSAP) gene and a biological gene fingerprint table. The method comprises the following steps: obtaining an MSAP amplification electropherogram of a biological sample to be detected, and constructing a 01 matrix of the sample; converting the 01 matrix into an MSAP gene sequence by using a "CCGGN" replacement method; comparing the MSAP gene sequence with a reference genome, and annotating DNA methylation related gene information; based on the annotation result, constructing a gene fingerprint table based on the copy number of the methylation gene and the methylation / hemimethylation mode, and analyzing epigenetic diversity. The method can convert a traditional MSAP band fingerprint map into a gene fingerprint table with annotation function information without performing cloning and sequencing of MSAP differential fragments, can improve MSAP marker analysis to epigenome analysis, solves the problem that MSAP epigenes are difficult to clone, and improves the level of germplasm resource identification and molecular breeding.

The present invention relates to an artificially engineered CRISPR / Cas9 system. More particularly, the present invention relates to an artificially engineered CRISPR enzyme having enhanced target specificity and a use of an artificially engineered CRISPR / Cas9 system including the same enzyme in genome and / or epigenome manipulation or modification, genome targeting, genome editing, and in vitro diagnosis, etc.

The application provides a chromatin domain recognition method and system based on a hypergraph, and the method comprises the following steps: acquiring epigenome data; and pre-processing the data, fragment cutting the chromatin according to a certain base pair quantity, regarding each fragment as a node of the genome, and acquiring a Hi-C interaction matrix; calculating a feature vector of each genome node represented by spatial interaction data and epigenome data; generating an initial TADs division for the Hi-C data matrix, clustering the nodes according to the node features by using a clustering algorithm, adjusting the nodes in the cluster, and obtaining an optimized TADs structure division. The optimized TADs division is expressed as a hypergraph, a TADs node set is used as a hyperedge, and the hypergraph division is recognized. The divided chromatin region is mapped to a cell nucleus to explore the biological significance. The application is suitable for the recognition and function-related research of chromatin domains in the field of biological information calculation.

Described herein are gene features for providing prognosis, diagnosis, treatment and molecular subtype classification of cancer by genomic and epigenomic profiling, methods and compositions for determining cancer and subtypes, including breast cancer, and provide specific and sensitive detection of biomarkers of interest. Such biomarkers indicate disease pathogenesis, which provides opportunities to select treatment, including treatment regimens intended to identify responsive candidates and overcome resistance mechanisms.

Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.

The present invention relates to an artificially engineered CRISPR / Cas9 system. More particularly, the present invention relates to an artificially engineered CRISPR enzyme having enhanced target specificity and a use of an artificially engineered CRISPR / Cas9 system including the same enzyme in genome and / or epigenome manipulation or modification, genome targeting, genome editing, and in vitro diagnosis, etc.