60 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, 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.

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.

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.

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.

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.

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.

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.

An enzyme capable of mediating the integration of large DNA fragments into the mammalian genome and its applications are provided. Specifically, novel enzymes capable of integrating large DNA fragments into the genome are provided, including integrases as shown in SEQ ID NO: 1-7. Further, polynucleotides containing nucleotide sequences encoding integrases and host cells containing these polynucleotides are disclosed. A method for recombining target nucleic acids into the human genome using said integrase is also disclosed.

This invention relates to the field of bioinformatics analysis of sequencing data, specifically providing a genotyping method for short tandem repeat sequences based on next-generation sequencing. The detection algorithm considers various positional relationships between sequencing read lengths and STR regions, models each case separately, eliminates the effects of partial sequence mismatches, insertions, and deletions, and integrates all read information to calculate the optimal STR genotyping result that best matches the observation. This method can be used for genotyping detection of short tandem repeat sequences in the human genome.

The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

The application provides a human genome T5 series fragment for multi-cancer identification and use thereof. A set of human genome differential methylation regions for multi-cancer identification, referred to as T5 series fragments (T5-1, T5-2, T5-3, T5-4, T5-5, T5-6, T5-7, T5-8) is disclosed. On this basis, the application provides a multi-cancer methylation technology which can cover more than 20 high-incidence cancer types, has high sensitivity (≥90%) and high specificity (≤5% false positive rate), and can realize rapid and micro-sample detection.

The invention belongs to the technical field of bioinformatics, and discloses a common value evaluation method and device for tumor neoantigens, equipment and a storage medium, missense mutation analysis is performed by acquiring mutation data of a pan cancer sample, a plurality of missense mutation sites are obtained and compared with a human genome to obtain candidate mutation sites, and the candidate mutation sites are used for evaluating the common value of the tumor neoantigens. Extracting the newborn peptide fragment corresponding to each candidate mutation site, inputting the newborn peptide fragment into the prediction model, predicting the binding score of the newborn peptide fragment and the human leukocyte antigen, and calculating the common value score of each newborn peptide fragment according to the number of the newborn peptide fragments generated at the candidate mutation sites and the corresponding binding score of the newborn peptide fragment and the human leukocyte antigen; according to the method, the new peptide fragments are sorted according to the descending order of the scores, and the new antigen sequence is screened out from the sorting result, so that the new antigen value can be effectively evaluated based on the number of the new peptide fragments generated by the site and the binding scores of the corresponding new peptide fragments and the human leukocyte antigen, and the new antigen with higher adaptability is screened out.

This invention discloses a method for constructing sequencing libraries based on blocking primers to remove human nucleic acids, and its application. The blocking primers include blocking primers for binding human repetitive sequences, blocking primers for binding human rRNA sequences, and blocking primers for binding human housekeeping gene sequences. These blocking primers can specifically bind to widely distributed scattered repetitive sequences, rRNA sequences, and housekeeping gene sequences in the human genome. The construction method includes the following steps: constructing a DNA library or an RNA library, or a co-constructed RNA and DNA library; using a library with added sequencing adapters as a template; and performing PCR amplification using adapter primers and blocking primers. The blocking primers can specifically bind to human nucleic acids through annealing and prevent modification by DNA polymerase extension, thus preventing the enrichment of human nucleic acid libraries through PCR amplification, while allowing normal amplification of pathogenic microorganism nucleic acids. This achieves the goal of reducing the proportion of human nucleic acids and provides guidance for pathogen detection.

The invention relates to a pollution monitoring kit suitable for multiple targeted sequencing, a monitoring method and application thereof. The pollution monitoring kit comprises a plurality of different molecular tags, each molecular tag has unique identifiability, and the plurality of different molecular tags are artificially synthesized base sequences and have more than 90% difference from human genomes and pathogen genomes. Different molecular tags have the same 5 '-terminal base sequence and 3'-terminal base sequence, and the intermediate base sequences of different molecular tags have more than 90% difference. The monitoring method comprises the following steps: S1, introducing a molecular tag into each to-be-detected sample, wherein different molecular tags are introduced into different to-be-detected samples; s2, adopting a commercially available pathogenic microorganism nucleic acid extraction kit to obtain nucleic acid of the to-be-detected sample mixed with the molecular tag; s3, taking the nucleic acid mixed with the molecular tag as a template, performing multi-targeted amplification through a targeted amplification primer pool, and enriching a target sequence; s4, establishing a database for the enriched target sequence, and sequencing on a machine; and S5, carrying out quality control on the molecular tag in the off-machine data, and judging whether pollution exists in the sample to be detected or not.

A computer implementable system manages genetic information associated with a human genome of a target subject and displayed via a graphical user interface (GUI). The target subject genetic information is encrypted. The system compares the clinical data of the target subject with clinical data in its database to provide a first ranking of possible genetic diseases. Then the genetic information of the target subject is compared to the genetic information in the database to re-rank via a weight score evaluation based on predetermined criteria thereby providing a second ranking of possible genetic diseases. Allowing a user to decrypt a portion or portions of the encrypted target subject genome that are related to the possible genetic diseases and blocking decryption of the rest of the genome. Providing access to the decrypted portions of the target subject genome via the GUI.

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.

The invention relates to a method for constructing a CDKL5 deficiency humanized mutation animal model and application of the CDKL5 deficiency humanized mutation animal model. The method comprises the step of knocking human CDKL5 gene R550X mutation and upstream and downstream genome sequences thereof into experimental animal genome CDKL5 gene loci. The human CDKL5 gene R550X mutation and upstream and downstream genome sequences thereof are knocked into experimental animal genome CDKL5 gene loci, CDKL5 protein C-terminal structural domain disease mutation is simulated, and the model has humanized mutation loci and nearby genome sequences, namely, has a to-be-repaired gene sequence same as that of a clinical patient, and can be applied to the field of clinical diagnosis and treatment of CDKL5 protein C-terminal structural domain disease mutation. The constructed model shows behavioral abnormality of a CDKL5 deficiency symptom, can be used for disease simulation and pathogenesis analysis of the CDKL5 deficiency symptom, can be used for directly testing gene editing and repairing strategies and therapeutic drugs of human genome specificity in the model body, and has important significance in the field of CDKL5 deficiency symptom treatment.

The invention relates to the technical field of molecular auxiliary diagnosis, and discloses a specific methylation marker for auxiliary diagnosis of renal papillary cell carcinoma, the marker is cytosine which takes a human genome GRCh38.p14 Primary Assessment as a reference genome and is located in at least one CpG site in a Chr7: 99392794-99392876 region, and the marker is one or more of cytosine at the positions of Chr7: 99392813, Chr7: 99392820, Chr7: 99392831, Chr7: 99392855 and chr7: 99392871. According to the invention, CpG site cytosine in the Chr7: 99392794-99392876 region is limited as a methylation marker, so that the problems of difficult cancer species identification and high missed diagnosis rate caused by the situation that traditional renal cell carcinoma diagnosis mostly depends on imaging subjective interpretation or generalization of tumor markers are improved.

The present application relates to a method, device, equipment and readable storage medium for screening metagenomic sequencing data. The method includes: obtaining similar sequence alignment information corresponding to multiple non-human genome similar sequences, wherein the non-human genome similar sequence is a non-human genome sequence in all non-human genome fragments that has a similar relationship with the reference human genome sequence; based on the similar sequence alignment information and the reference human genome sequence, detecting the original non-human genome similar sequence and the original non-human genome sequence in the original metagenomic sequencing data, and taking the detected original non-human genome similar sequence and the original non-human genome sequence as potential non-human genome sequences; based on the alignment relationship between the potential non-human genome sequence and the reference non-human genome sequence, screening the original metagenomic sequencing data to obtain a data screening result. The use of this method improves the accuracy of metagenomic sequencing data screening.