88 results about "Human DNA sequencing" patented technology

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids or the modification of nucleic acids or proteins, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of nucleic acid programmable DNA binding proteins e.g., GeoCas9 or variants thereof, and effector domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing or protein modification are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a GeoCas9 and effector domains, are provided.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing enzymes or enzyme domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing enzymes or domains, are provided.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing proteins or protein domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing proteins or domains, are provided.

A system is disclosed for discreetly assessing the compatibility of two or more human genomes across diverse elements, activities, and engagement platforms relevant to potential mating scenarios. The genomic data is subjected to encryption, with the option of employing homomorphic encryption to safeguard user privacy and security. Processing of the data is facilitated through a personal health database processing system, which may be cloud-based or edge-based. The application of homomorphic encryption ensures that the genomic information of individual users remains encrypted during processing, with the outcome limited to the display of progeny compatibility to the respective end users.

Among other things, provided herein are systems that replace the natural random integration activity of a retrovirus with site-specific integration machinery. This approach allows for a more precise targeting of a gene of interest into a human genome, e.g., for therapeutic purposes. The system may include integration-deficient retrovirus (e.g., lentivirus) (IDLV), in which the natural integration activity has been reduced (e.g., by mutation to the viral integrase polypeptide). Instead, the system may comprise a site-specific recombinase (e.g., a serine recombinase, e.g., a serine integrase) capable of directing insertion of a template DNA, or portion thereof, into a desired site in the human genome.

The invention discloses an annotation method for analyzing a genome centromere region structure, and belongs to the technical field of biological genes. And prerequisites are needed. The method comprises the following steps: firstly, analyzing repetitive monomers of a centromere sequence based on a heuristic strategy, and judging the centromere sequence; when the serial repetition units are identified, an adjacent matrix is obtained based on serial repetition unit information, the analysis problem of the HORs is converted into a graph theory problem of searching a specific structure in the adjacent matrix, and a sliding window strategy is combined to refine the structure analysis result of the HORs. Compared with the prior art, the method has the advantages that the length of the tandem repeat unit can be detected more accurately, and the defect that two continuous tandem repeat units are identified as a single tandem repeat unit by TRASH is effectively overcome. The method has an obvious efficiency advantage. When a human genome centromere area is analyzed, the method is 10 times faster than a current method while the precision is guaranteed.

The invention discloses an early diagnosis marker for B-cell lymphoma, a cross-species screening method based on lamprey and application, and relates to the technical field of molecular diagnosis. In the prior art, tissue biopsy is strong in invasiveness, and a traditional marker is low in early detection rate; in order to solve the problems that a large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large-scale large- When the expression quantity of the gene in a sample is greater than or equal to 1.8 times of that of a normal B cell (HMY2. CIR), the lymphoma is judged to be positive, and the minimally invasive early diagnosis efficiency is remarkably improved.

The present invention discloses an in vitro method for obtaining DNA methylation biomarkers as exquisite DNA methylation positions in the human genome (i.e., CGIDs) that predict cervical cancer especially at as yet inaccessible early stages by examining progression of “categorical” DNA methylation alterations in three stages of premalignant lesions (cervical intraepithelial neoplasia (CIN)), progressing from CIN1 to CIN3. The present invention discloses combinations of CGIDs for detecting with high specificity and sensitivity cervical cancer by measuring their DNA methylation status and deriving a “methylation score”, which is useful as a biomarker for cervical cancer. Also disclosed are kits for predicting cervical cancer using such CGIDs using multiplexed next generation sequencing methylation assays, pyrosequencing assays and methylation specific PCR. The DNA methylation markers (CGIDs) described in the present invention are useful for cervical screening and early detection of cervical cancer by any person skilled in the art to detect cervical cancer.

Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing proteins or protein domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing proteins or domains, are provided.

The invention discloses a compression and decompression method based on generic genome expression, and relates to the technical field of compression and decompression of DNA next-generation sequencing data, in particular to the compression and decompression method based on generic genome expression. The method aims at solving the problems that in the prior art, the capacity of processing population genetic diversity is insufficient, original sequencing quality information cannot be effectively restored during decompression, and memory occupation is too high during large-scale data processing. Obtaining a to-be-compressed sequencing sequence data file, a reference genome sequence and a thousand-person genome variation sample; obtaining a haplotype list, a variation list and a haplotype offset list corresponding to each window block; storing the window number, the haplotype number, the haplotype offset, the head and tail unmatched sequences, the current sequence name and the quality score character string into a single compression block; carrying out binding storage; completing the compression processing of the mass fraction; and obtaining each to-be-compressed sequencing sequence based on the result of the compressed part.

A genetic prime editing screening platform to identify functional variants related to human health and disease, is configured substantially to annotate genome with nucleotide resolution with actionable disease prediction and treatment for personalized medicine.

A gene-leader editing screening platform for identifying functional variations associated with human health and disease, substantially configured to annotate genomes with nucleotide resolutions, accompanied by operable disease prediction and treatment for personalized medical treatment.

Disclosed are methods of preparing a composition of non-naturally occurring DNA, comprising: (a) extracting DNA from a sample of a subject; (b) contacting the extracted DNA or its derivative with a panel of oligonucleotide probes designed to hybridize to a plurality of preselected genomic regions, thereby generating selected DNA, wherein at least 50% of the preselected genomic regions are CpG regions that each comprises at least 3 CpG sites and a CpG density of at least 0.02 CpG / bp, wherein the preselected genomic regions cover 10-500 Mb of sequence space in human genome, wherein the extracted DNA or its derivative or the selected DNA or its derivative is further treated with an agent or a combination of agents that discriminates between methylated and unmethylated cytosines; and (c) performing high-throughput sequencing on the selected DNA or its derivative and generating sequencing reads.

Provided herein are vectors, and compositions thereof, comprising at least two guide RNAs (gRNAs) that targets and hybridizes to a target sequence on a DNA molecule, wherein each of the at least two gRNAs hybridizes at least two genomic DNA locations selected from human chromosome 2 at location 60725424 to 60725688 according to GRCh37 / hg19 human genome reference build (+55 functional region); human chromosome 2 at location 60722238 to 60722466 GRCh37 / hg19 human genome reference build (+58 functional region); or human chromosome 2 at location 60718042 to 60718186 according to GRCh37 / hg19 human genome reference build (+62 functional region). Methods for the use of such vectors are further provided.

The present invention discloses a method for screening non-small cell lung cancer markers based on enhancer methylation differences, as well as the markers and applications thereof. Abnormal DNA methylation in the enhancer regions of the human genome can lead to abnormal gene expression regulation in non-small cell lung cancer. The method for screening non-small cell lung cancer markers described in the present invention is based on this principle and further combines paired-end tag sequencing analysis of chromatin interaction technology (ChIA-PET) to screen out DNA methylation markers in the genomic enhancer regions that cause abnormal gene expression regulation in non-small cell lung cancer. This screening method has the advantages of accuracy, rapidity, and high throughput. The DNA methylation markers described in the present invention are cg00787780, cg16434331, cg21862081, and cg24327132. The markers have good diagnostic efficacy for non-small cell lung cancer, showing high accuracy, high sensitivity, and strong specificity, and can better help improve the detection rate of non-small cell lung cancer.

The invention belongs to the technical field of biological medicines, and particularly discloses a primer probe combination and a kit for detecting genotypes of SMA carriers based on a chromosome level and application of the primer probe combination and the kit. Wherein the primer probe combination comprises a primer probe group for detecting an exon 7 of an SMN1 gene, a probe for detecting an exon 7 of an SMN2 gene, a primer probe group for detecting a short-arm reference gene of a chromosome 5, a primer probe group for detecting a long-arm reference gene of the chromosome 5 and a primer probe group for detecting a reference gene of a human genome. The primer probe combination can eliminate chromosome copy number variation interference, greatly improves the specificity of SMA carrier genotype detection, can simultaneously detect the type I and type II of the SMA carrier genotype, has the detection sensitivity of 99%, and is suitable for large-scale population screening.

A method for detecting fetal CNVs through non-invasive prenatal testing, comprising steps: (a) collecting blood samples from pregnant women; (b) extracting cfDNA fragments from the blood samples, performing whole genome sequencing on extracted cfDNA fragments to obtain cfDNA sequencing data, and preprocessing cfDNA sequencing data by removing adapters, aligning and mapping reads to a referenced human genome; (c) performing quality control on obtained cfDNA sequencing data for being accepted for the prediction; (d) dividing referenced genome into a plurality of non-overlapping bins and filtering the bins based on a predetermined GC-content threshold for bins; (e) defining a CNV detection window, a bin size, a set of features for machine learning / deep learning models and fine-tune model for detecting fetal CNV for selecting a final model; and (f) applying the final model to predict fetal CNVs, including microdeletion syndromes, or microduplications, or aneuploidies, or the number of sex chromosomes.

The present invention relates to a method for constructing an optic nerve injury model of a tropical clawed frog, a model and an application method thereof, wherein the modeling is implemented as follows: under microscopic observation, laser is used to damage the retrobulbar optic nerve of an anesthetized juvenile tropical clawed frog, thereby obtaining a tropical clawed frog optic nerve injury model; the method of using laser to damage the retrobulbar optic nerve of an anesthetized juvenile tropical clawed frog to obtain the tropical clawed frog optic nerve injury model, which is first of its kind in China and abroad, has the following advantages: the tropical clawed frog's body is transparent when young, and the laser can be directly observed, accurately focused, and quantitatively damaged; this optic nerve injury modeling method is accurate, controllable, has a high success rate, and has a low mortality rate; the tropical clawed frog's genome is highly homologous to the human genome, and its eyeball, retina, optic nerve, visual pathway tissue structure, and visual information conduction pathway are highly similar to those of humans; the tropical clawed frog's optic nerve is regenerative, which is conducive to the study of regeneration and repair mechanisms after injury, and opens up new approaches and methods for optic nerve protection research.

Human-derived virus-like particles (heVLPs), comprising a membrane comprising a phospholipid bilayer with one or more HERV-derived envelope proteins on the external side; one or more HERV-derived GAG proteins in the heVLP core, and a cargo molecule, e.g., a biomolecule and / or chemical cargo molecule, disposed in the core of the heVLP on the inside of the membrane, wherein the heVLP does not comprise a gag protein, except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome, and methods of use thereof for delivery of the cargo molecule to cells.

To provide nucleic acid molecules targeting a BCL11A enhancer functional region, compositions comprising the nucleic acid molecules, and methods for increasing a fetal hemoglobin level in cells by disrupting BCL11A expression at the genomic level.SOLUTION: Disclosed is a nucleic acid molecule comprising a nucleic acid sequence being: a. complementary to the plus or minus strand of the human chromosome 2 at location 60725424 to 60725688 (+55 functional region); b. complementary to the plus or minus strand of the human second chromosome at location 60722238 to 60722466 (+58 functional region); or c. complementary to the plus or minus strand of the human chromosome 2 at location 60718042 to 60718186 (+62 functional region), where the human chromosome 2 is that according to UCSC Genome Browser hg 19 human genome assembly.SELECTED DRAWING: Figure 3G

A method of altering a eukaryotic cell is provided including transfecting the eukaryotic cell with a nucleic acid encoding RNA complementary to genomic DNA of the eukaryotic cell, transfecting the eukaryotic cell with a nucleic acid encoding an enzyme that interacts with the RNA and cleaves the genomic DNA in a site specific manner, wherein the cell expresses the RNA and the enzyme, the RNA binds to complementary genomic DNA and the enzyme cleaves the genomic DNA in a site specific manner.

A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variants from next generation sequencing reads out of a pool of enriched genomic patient samples without suffering from next generation sequencing workflow biases such as those introduced by sequencing errors in particular in repeat patterns regions of the human genome such as homopolymers or heteropolymers. The variant calling module may estimate the probability distribution of the length of the repeat pattern for each patient sample and cross-analyze it against other samples in a single experimental pool to identify best-fit variant models for each pair of samples. The variant calling module may further group samples according to their matching best-fit variant models and identify which group of patient samples carries the wild type reference without the need for control data in the pool. The variant calling module may subsequently characterize the homozygous or heterozygous repeat patterns variants for each patient sample with improved specificity and accuracy even in the presence of next generation sequencing biases.

The invention discloses a colorectal cancer diagnosis system and application thereof, and the colorectal cancer diagnosis system comprises human SDC2, SFRP2 and TFPI2 gene methylation PCR detection reagents, 20 ng / L of unmethylated human genome standard substances, 50 excrement sample nucleic acids with the concentration of 5-40 ng / L and clinically and clearly diagnosed as normal people, and a kit for detecting the colorectal cancer. The kit is characterized in that the kit comprises 20 ng / L of 100% methylated human genome standard substance and 30 cases of excrement sample nucleic acid of patients with colorectal cancer stage I clinically and clearly diagnosed, wherein the concentration of the excrement sample nucleic acid is 5-40 ng / L. A multi-layer composite interpretation system formed by a multi-component system or a calculation method is used for effectively interpreting whether methylation of the gene in the sample to be detected is positive or negative, the positive rate of colorectal cancer diagnosis can be effectively increased, and therefore the value of early screening of the colorectal cancer is greatly increased.

The invention relates to the technical field of biological medicine, in particular to a molecular marker of alveolar rhabdomyosarcoma and application of the molecular marker, the molecular marker is a circPAX3R-loop site, and a DNA-RNA hybridization region of the molecular marker is located on chr2: 2230 94913-2230 95853 of a human genome. According to the application disclosed by the invention, a large number of R-loop structures exist in an alveolar rhabdomyosarcoma cell through DRIP-seq, a plurality of circRNAs exist in a cell nucleus of the alveolar rhabdomyosarcoma through circRNA sequencing, the existence of circPAX3R-loop is proved through qPCR after a DRIP product is subjected to RNase R and RNase H treatment, and the result shows that circPAX3R-loop exists in the cell nucleus of the alveolar rhabdomyosarcoma in the cell nucleus of the alveolar rhabdomyosarcoma in the cell nucleus of the alveolar rhabdomyosarcoma. The important clinical application value is realized on developing a reagent or a kit for diagnosing the alveolar rhabdomyosarcoma, a medicine for preventing and / or treating the alveolar rhabdomyosarcoma or a gene treatment strategy aiming at the target spot.

The invention provides a screening method and application of a human low-recombination-rate region micro-haplotype genetic marker. The screening method comprises the following steps: dividing a human genome into a low-recombination-rate region and a high-recombination-rate region; identifying a haplotype which is less than 200bp in length and contains 2-5 SNPs from a low recombination rate region, and taking the haplotype as a micro haplotype; calculating forensic medicine parameters of each micro haplotype; the forensic parameters comprise individual identification capability, non-father exclusion rate and effective allele number; screening out micro haplotypes with forensic parameters within a preset range; and evaluating the paternity identification efficiency of the screened micro-haplotypes by using the contribution degree of the product, and sequencing. According to the invention, the genetic marker is screened from a low recombination region, so that the interference of exchange recombination between homologous chromosomes in a cell meiosis (passage) process on a paternity identification result can be effectively avoided; meanwhile, the paternity identification efficiency of the genetic marker is evaluated through the product contribution degree, the individual identification ability and the paternity exclusion rate can be comprehensively considered, and a favorable basis is provided for selection of the genetic marker.

There is provided a method of altering a eukaryotic cell comprising transfecting the eukaryotic cell with a nucleic acid encoding an RNA complementary to genomic DNA of the eukaryotic cell, transfecting the eukaryotic cell with a nucleic acid encoding an enzyme that interacts with the RNA and cleaves the genomic DNA in a site-specific manner wherein the cell expresses the RNA and the enzyme, and modifying the eukaryotic cell with the nucleic acid encoding an enzyme that interacts with the RNA and cleaves the genomic DNA in a site-specific manner. The RNA binds to complementary genomic DNA and the enzyme cleaves the genomic DNA in a site-specific manner.

The invention discloses a site for detecting leprosy risk and application thereof, which comprises the following steps: detecting genotypes of 25 leprosy susceptible SNP sites in a human genome of a to-be-detected individual, converting the genotypes into leprosy risk values, and predicting leprosy risk level of the to-be-detected individual according to the risk values, the risk of 28.06 is high, and the risk is 18.17 lt; the risk is medium when the GRS is less than or equal to 28.06, and the risk is low when the GRS is less than or equal to 18.17. Prediction and efficiency of the leprosy disease risk prediction model established by the invention are well verified in leprosy convalescents and close contact people, and the method can be applied to screening of the close contact people of the leprosy patients.

The invention belongs to the technical field of molecular biology, and particularly relates to a metagenome sequencing data analysis method of a sample, electronic equipment and a system. The metagenome sequencing data analysis method comprises the following steps: acquiring sequencing data of a sample; comparing the sequencing data with a host reference genome, and splitting to obtain host genome data and microbiome data; and respectively analyzing the host genome data and the microbiome data. The invention aims to realize that data information of double omics, including microbiome data information and human genome data information, can be simultaneously obtained through one-time sampling from an analysis technology level. In addition, according to the analysis method, a reference gene set iHSMGC for human skin microbiome is integrated in a functional gene annotation analysis module suitable for microorganisms, and accurate annotation of skin microorganism habitat specific functional genes can be achieved.

This invention relates to the field of biomedical technology and discloses a broad-spectrum antimicrobial peptide and its applications. The invention obtains a broad-spectrum antimicrobial peptide H by mining non-classical open reading frames (ncORFs) in the human genome. Experimental verification shows that the broad-spectrum antimicrobial peptide H has significant inhibitory effects on both Gram-positive bacteria (Staphylococcus aureus ATCC 29213) and Gram-negative bacteria (Escherichia coli K88). Furthermore, the broad-spectrum antimicrobial peptide H can form an α-helix. The α-helix structure projection diagram shows that one side is rich in positively charged hydrophilic amino acid residues, and the other side is rich in hydrophobic amino acid residues, exhibiting good amphiphilicity. In addition, the broad-spectrum antimicrobial peptide H provided by this invention has low hemolytic activity and no cytotoxicity, ensuring in vivo safety while achieving highly efficient bactericidal activity. It also features a short synthetic sequence, small molecular weight, and is easy to chemically synthesize.

The present application relates to the technical field of biological medicine, and in particular to a molecular marker of alveolar rhabdomyosarcoma and application thereof, wherein the molecular marker is circFOXO1R-loop site, and a DNA-RNA hybridization region thereof is located at chr13:41133915-41134263 of a human genome. In the present application, the circFOXO1R-loop site is verified by CUT&Tag-qPCR and DRIP-qPCR, and it is found that the circFOXO1R-loop can promote the combination of FOXO1 gene and RNAPol II and DNA damage, and it has important clinical application value for developing a reagent or kit for diagnosing alveolar rhabdomyosarcoma, a drug or a gene therapy strategy for preventing and / or treating alveolar rhabdomyosarcoma aiming at the target.