415 results about "Whole genome sequencing" patented technology

The invention discloses a neurology rehabilitation degree evaluation method and system, and relates to the technical field of medical rehabilitation evaluation.The method comprises the following specific steps that data collection is conducted, specifically, whole genome sequencing is conducted on a neurology patient, and whole genome data of the patient is obtained, the method comprises the following steps: collecting initial disease severity degree data of a patient, and evaluating the symptom expression of the patient when the patient sees a doctor for the first time by a professional neurology doctor according to a set disease evaluation standard. A key gene screening strategy and a synaptic plasticity index establishment method are applied to construct a multi-dimensional and more accurate neurology rehabilitation degree evaluation system, so that the neural function repair level is deeply known from the root level of nerve cell connection reconstruction; and accurate prediction and real-time evaluation of the rehabilitation process are realized through the personalized rehabilitation trajectory prediction model, so that the real rehabilitation state of the patient can be reflected more comprehensively and meticulously.

The invention belongs to the field of corn growth regulation, and discloses a discovery and application method and system of a corn growth regulation molecular marker, and the method comprises the following steps: carrying out whole genome sequencing on a large number of corn varieties (strains), and carrying out large-scale genome association analysis in combination with multi-environment and multi-site phenotypic data; a whole genome selection model is utilized to predict the genetic effect of corn complex characters, and efficient germplasm improvement is carried out; and carrying out functional verification on candidate molecular markers screened by GWAS and GS to ensure the stability and applicability of the candidate molecular markers. The application effect of the corn growth regulation molecular marker can be remarkably improved, the problems that in the prior art, markers are unstable, the analysis capacity is limited, and the number is insufficient are solved, and a more effective technical means is provided for corn growth regulation and breeding.

The invention relates to the technical field of virus whole genome sequencing, and discloses a method for virus whole genome sequencing, which comprises the following steps: S1, extracting a sample genome, operating according to a specification of a commodity kit, extracting RNA (Ribonucleic Acid) of the sample genome, and performing library construction after reverse transcription and targeted amplification. According to the method for sequencing the whole genome of the virus, the whole genome sequence of the virus can be obtained through the sequencing method, and compared with the current detection which only stays at negative and positive detection, the whole genome sequence can be obtained on the basis through the method for sequencing, epidemiological traceability is carried out, and meanwhile the sequencing cost can be effectively reduced.

The invention provides an amplification primer and method for a porcine pseudorabies virus whole genome. The detection primer group for the porcine pseudorabies virus comprises 271 pairs of amplification primers, and the specific sequences of the amplification primers are as shown in SEQ ID NO.1-542. According to the detection primer group provided by the invention, relatively uniform coverage on the porcine pseudorabies virus can be realized, and 100% region coverage of a genome is realized in nanopore sequencing. The preparation method of the sequencing fragment of the porcine pseudorabies virus whole genome is simple, convenient and easy to operate, the amplification effect is good, nanopore sequencing has the advantage of simultaneous sequencing and real-time analysis, the detection time can be greatly shortened, porcine pseudorabies virus infection can be identified and diagnosed at the soonest 15 hours, meanwhile, the whole genome sequence of the porcine pseudorabies virus is obtained, and the method is suitable for large-scale popularization and application. The obtained genome sequence can provide a scientific basis for virus traceability, pathogenic variation tracking, novel strain identification, early warning and the like.

The invention belongs to the technical field of animal genetic breeding, and particularly discloses an SNP (Single Nucleotide Polymorphism) chip for distinguishing five kinds of Hubei native cattle (yi-ling cattle, Dabie mountain cattle, troilin cattle, Enshi cattle and delta mountain cattle). Candidate SNP loci are obtained by combining whole genome sequencing and three selection signals (Tajima's D, FST and pi ratio), then the candidate loci are subjected to random forest scoring, the number of the needed SNP loci is further reduced, finally, an SNP locus combination with variety specificity is obtained, probes are designed according to the SNP loci and 60 bp sequences before and after the SNP loci, and the variety specificity is obtained. The SNP chip for distinguishing five kinds of Hubei native cattle can be developed, technical support is provided for variety breeding of Hubei native cattle, and meanwhile, compared with a traditional pedigree and microsatellite variety identification method, the SNP chip has the advantages of being high in accuracy and easy to operate.

A molecular marker related to body weight traits of Hu sheep and an application are provided. The whole genome sequencing of Hu sheep is carried out in the invention, the combination of QTL and GWAS is adopted, the candidate genes related to the weight traits are analyzed and the three molecular markers of MAP3K1, ABCB1, and MEF2C are selected as candidate genes for the weight traits of Hu sheep, and the two molecular markers of ANKRD55 and TRNAW-CCA-87 can be used as potential candidate genes for the weight traits of Hu sheep, these candidate genes can be used as molecular markers for application, the guidance of Hu sheep breeding will help to understand the genetic mechanism of weight traits of Hu sheep and further guide Hu sheep breeding.

The invention relates to the field of molecular biology, and discloses a fish DNA bar code database and a construction method and application thereof based on a mitochondrial genome complete sequence. The method comprises the steps of fish directory determination, fish collection, classification and identification, DNA extraction, mitochondrial whole genome sequencing and analysis, DNA bar code database building and database application. Based on the research basis of the target water area and fish historical data, the fish directory in the target water area is determined, the fish DNA bar code database is constructed by utilizing the mitochondrial whole genome sequencing technology, and accurate database support is provided for fish investigation and monitoring by applying the environment DNA technology. The problems that an existing fish public database is insufficient in integrity, miscellaneous in data source, uneven in quality and insufficient in region pertinence, possibly causes small population species comparison loss, comparison results are wrong, false positive results such as non-target region species cannot be effectively eliminated, and related species with high gene similarity are difficult to accurately identify are solved.

The invention provides an amplification primer and method for an avian leukosis virus whole genome. The detection primer group for the avian leukosis virus comprises 18 pairs of amplification primers, and the specific sequences of the amplification primers are as shown in SEQ ID NO.1-36. The detection primer group provided by the invention can realize relatively uniform coverage on the avian leukosis virus, and 100% region coverage of a genome is realized in nanopore sequencing. The preparation method of the sequencing fragment of the avian leukosis virus whole genome is simple, convenient and easy to operate, the amplification effect is good, nanopore sequencing has the advantage of simultaneous sequencing and real-time analysis, the detection time can be greatly shortened, infection of the avian leukosis virus can be rapidly identified and diagnosed, meanwhile, the whole genome sequence of the avian leukosis virus is obtained, and the application prospect is wide. The obtained genome sequence can provide a scientific basis for virus traceability, pathogenic variation tracking, novel strain identification, early warning and the like.

The invention discloses application of a gene marker in early screening of esophagus, stomach and intestine multiple cancer species, an early screening model construction method and a detection device, and belongs to the technical field of early noninvasive detection of digestive tract tumors. By analyzing the whole genome characteristics of circulating free DNA in peripheral blood, a novel multi-cancer-species screening system is established. On the basis of low-depth whole genome sequencing data, molecular markers in three dimensions, namely a genome copy number variation mode, a DNA fragment distribution characteristic with a specific length and an epigenetics signal of a transcription initiation region, are emphatically detected. An advanced converter neural network architecture is adopted, and the model can efficiently capture complex feature association in a whole genome range through a specific self-attention mechanism. The model design particularly considers the particularity of genome data, introduces an adaptive position coding system, and accurately reflects the spatial distribution relationship of DNA fragments on chromosomes. Therefore, the system can still maintain excellent detection performance under extremely low sequencing depth.

The invention discloses a primer composition and application of the primer composition in detection of animal bifidobacterium subsp. Lactis HN019. According to the present invention, bifidobacterium animalis subsp. Lactis HN019 is adopted as an object, bacterial strain specific genetic markers are screened through whole genome sequencing and single nucleotide polymorphism analysis, and a fluorescent quantitative PCR technology is combined so as to obtain the efficient, specific and stable HN019 quantitative detection primer composition and the method thereof; through system verification, the method is suitable for an HN019 strain level detection technical framework in scientific research and industrial application scenes, and also provides key technical support for market supervision and industrial healthy development of probiotic foods.

The invention discloses bacillus subtilis capable of producing beta-amylase and application of the bacillus subtilis, and belongs to the technical field of bioengineering, the bacillus subtilis is named as bacillus subtilis JXJY-0811, the bacillus subtilis is preserved in China General Microbiological Culture Collection Center (CGMCC) on June 7, 2024, and the preservation number is CGMCC NO.30886. The invention further discloses a preparation method of the bacillus subtilis capable of producing beta-amylase and application of the bacillus subtilis capable of producing beta-amylase. A strain which can secrete beta-amylase in an extracellular mode and is high in amylase activity is screened from soil through a transparent ring method, and the strain is identified as bacillus subtilis through whole genome sequencing. The appropriate temperature condition of the extracellular beta-amylase of the strain is 50-75 DEG C, the appropriate pH value is 3.5-6.5, the extracellular enzyme activity is 9640.10 U / mL, and the highest enzyme activity of the beta-amylase in a 5L fermentation tank after fermentation for 60 hours can reach 51980.36 U / mL. The beta-amylase obtained through fermentation is used for treating a soluble starch solution, the main product is maltose, and the beta-amylase can be used for producing maltose and high maltose syrup.

The invention discloses a colorectal cancer early-stage accurate diagnosis model based on plasma cfDNA multi-dimensional fragment omics and a construction method and application thereof. The method comprises the following steps: a) collecting and processing a sample; b) performing whole genome sequencing (WGS) and bioinformatics processing; c) fragment omics feature extraction; and d) constructing and optimizing a machine learning model. According to the method, cfDNA is extracted from a plasma sample of a colorectal cancer patient, the fragment size distribution and terminal sequence characteristics of the cfDNA are analyzed by utilizing a high-throughput sequencing technology, and then a specific cfDNA fragment mode related to CRC is identified through bioinformatics analysis. Based on the identified cfDNA fragment features, an economically feasible and highly sensitive diagnosis model is constructed, and early diagnosis of CRC is realized.

The invention relates to the technical field of breeding methods, in particular to a precise breeding method based on single nucleotide polymorphism, which comprises the following steps: carrying out whole genome sequencing and screening SNP (Single Nucleotide Polymorphism) markers related to target traits; designing a genotype detection chip based on the SNP marker, and performing genotyping; constructing a genetic evaluation model and predicting a breeding value; designing a matching scheme based on the breeding value; performing performance verification on the offspring and continuously improving the breeding strategy. By integrating whole genome sequencing, transcriptome and metabolome data and combining bioinformatics and an artificial intelligence algorithm, efficient screening of functional SNPs related to complex characters is achieved, and the problems of multi-character collaborative improvement and insufficient environmental adaptability in a traditional method are effectively solved.

The invention relates to a primer composition and a method for whole genome sequencing of American type porcine reproductive and respiratory syndrome virus and application of the primer composition and the method. The sequences of the primer composition are as shown in SEQ ID No. 1 to SEQ ID No. 35. According to the sequencing method, RNA (Ribonucleic Acid) of a sample to be detected is taken as a template to perform reverse transcription reaction, the primer combination is adopted to perform PCR (Polymerase Chain Reaction) amplification on the whole genome of the American type porcine reproductive and respiratory syndrome virus, and an amplification product is subjected to three-generation sequencing library building and sequencing to perform species identification and genetic typing. The full-length PCR detection method is high in specificity and sensitivity, the efficiency of detecting the whole genome of the virus is greatly improved, rapid and accurate detection of the American type porcine reproductive and respiratory syndrome virus is achieved, accurate typing and evolutionary analysis can be achieved by utilizing the assembled whole genome, and the method is suitable for large-scale popularization and application. Traceability of the reproductive and respiratory syndrome virus is realized, and the method is of great significance to early screening, prevention and control of the American porcine reproductive and respiratory syndrome virus.

The invention provides a method for screening disease-related gene targets based on whole genome association analysis, and belongs to the technical field of disease genetic risk assessment, the method comprises the following steps: collecting and recording a sample information data set; performing whole genome sequencing on the samples to obtain SNP data, and combining the SNP data of all the samples to obtain a training data set; performing principal component analysis on the SNP matrix, and screening the top 10-30 SNPs as covariables of the model; and carrying out whole genome association analysis on the training data set and constructing a logistic regression model, and screening out the SNP related to the disease according to the P value. According to the method, confounding factors can be effectively controlled by adopting the logistic regression model and introducing covariables (such as age, gender and the number of weekly exercises), high-dimensional data are processed through a regularization method, and the risk of over-fitting is reduced. The method can also capture interaction between SNPs, and provides more accurate disease-related SNP recognition.

The present disclosure relates to somatic mutation determinations. An example method includes performing whole genome sequencing using a high-throughput sequencing system on nucleic acids from a sample obtained from a subject to generate raw data, transmitting the raw data from the high-throughput sequencing system to a computing system, processing the raw data by the computing system to generate candidate variants and a set of feature values for each candidate variant of the candidate variants, processing the feature values by the computing system using a trained machine learning model to identify somatic mutations from the candidate variants, transmitting results based on the somatic mutations from the computing system to an end device, and displaying a report on the end device based on the results.

The invention relates to a key gene for duck meat and egg character differentiation and a method for excavating the key gene based on whole genome sequencing, the key gene is a duck SIK1 gene, and the nucleotide sequence of the key gene is shown as SEQ ID NO: 1. The key gene SIK1 influencing the differentiation and domestication process of laying ducks and meat ducks is found by using a method for analyzing the key gene in the domestication process of duck meat traits and egg traits through whole genome re-sequencing. The gene SIK1 plays a role in regulating glycometabolism and cell proliferation. The genome of the Jinding duck is assembled by using a whole genome re-sequencing technology for the first time and is compared with the genome of other duck species such as Beijing duck, another key gene SIK1 for meat and egg trait differentiation of ducks is excavated, molecular breeding of ducks is facilitated, and a new thought is provided for searching key genes for meat / egg duck trait differentiation in future.

In various embodiments, the disclosure provides compositions, such as polypeptides, polynucleotides, gene editing systems, small molecules, vectors, or host cells, comprising and / or modulating the expression or activity of an immunomodulatory-related protein, such as a cytokine. In various embodiments, the disclosure also provides for the treatment of a disease or condition (e.g., a disease or disorder) using an agent comprising and / or modulating the expression or activity of an immunomodulatory-related protein. The present invention relates to methods for identifying such agents (e.g., diseases or conditions associated with whole genome association studies (GWAS), cancer genome maps (TCGA), whole genome sequencing, whole phenotype group association studies (PheWAS), expression quantitative trait locus (eQTL) studies, or combinations thereof), and methods for identifying such agents.

The invention discloses a schizophrenia risk structure variation identification and function evaluation method based on three-generation sequencing, and relates to the field of molecular biology, whole genome sequencing is performed on peripheral blood DNA of a patient through three-generation sequencing, multi-tool joint detection is adopted, multi-sample results are integrated, and a high-confidence SV data set is generated; through cross-queue comparison, the patient specific SV is screened, and the high-risk potential pathogenic SV is identified in combination with an SV priority ordering tool SVJudge. By combining transcription factor binding analysis, SCZ drug target data and histocyte specific expression data, the influence of SV on gene regulation is evaluated, and the potential action mechanism of SV in SCZ is analyzed. The SCZ risk gene is screened based on SVJudge scoring and patient carrying conditions, the genetic risk and pathogenic mechanism of the SCZ are analyzed and verified through pathway enrichment, a protein interaction network and a functional module, and a new technical means and theoretical basis are provided for genetic research of the SCZ.

The invention belongs to the technical field of microbiome clinical diagnosis, and particularly relates to a marker combination, a model and a method for predicting the prognosis risk of a colorectal cancer patient. The method comprises the steps of whole genome sequencing data analysis, human source sequence filtering, microorganism sequence extraction and annotation and machine learning diagnosis model construction. The method has the advantages of being high in accuracy and free of culture, tissue-specific microbiota still exist in low-biomass tumors, and promising diagnostic value is shown. A large amount of clinical patient sequencing data can be subjected to secondary development and utilization, the accuracy of tumor diagnosis is improved, and the method can be widely applied to prognosis survival evaluation of patients.

The invention discloses a fiveleaf virus GI.2 whole genome sequencing primer based on an amplicon sequencing technology and application thereof, and belongs to the technical field of virus gene sequencing. The primer group composed of 18 pairs of primers is preferably obtained according to an amplicon sequencing technology, the primer group can effectively improve the primer amplicon coverage degree, it is guaranteed that the primer amplicon coverage degree is 1.5-1.8 times that of a virus sequence, the amplification time is shortened, the amplification difficulty is reduced, the primer amplicon coverage degree and the whole genome capture efficiency are improved, and the primer amplification efficiency is improved. And the method has important significance on epidemic situation traceability and propagation trend of the fiveleaf virus GI.2.

The invention discloses a forest tree genotype-environment interaction modeling method based on multi-modal deep learning, and relates to the technical field of forest tree breeding, the method comprises the following specific steps: multi-modal data acquisition: adopting a high-throughput phenotype platform, a whole genome sequencing technology and soil nutrient detection equipment to acquire multi-modal data; sNP locus genotype data, soil key physicochemical index environmental data and growth-related morphology and biomass parameter phenotype data of forest trees are collected respectively; forest genotype, environment and phenotype multi-modal data are collected through the system, the genotype-environment interaction algorithm and the phenotype prediction model are constructed after preprocessing and fusion, the model can accurately predict forest phenotypes, the breeding screening period is remarkably shortened, the breeding selection precision and efficiency are greatly improved, and the method is suitable for large-scale popularization and application. The method effectively solves the problem that a traditional breeding mode is short in time and efficiency, enables breeding work to respond to market demands and environmental changes more quickly and accurately, and provides powerful support for sustainable development of the forestry industry.

The invention discloses a genetic characteristic index quantitative evaluation method based on embryo genetic information processing and a computer program product, and particularly relates to the technical field of genetic information processing.The method comprises the steps that firstly, whole genome sequencing is conducted on an embryo sample, and pathogenic related mutations are screened through a variation recognition algorithm; then extracting variation points and structural features, and constructing vector description data; further generating two fixed value indexes of pathogenic load and structural stability as model input to calculate an embryo genetic health score; and finally, sorting is performed according to a scoring result, so that the embryo transplantation priority is determined, and scientific and accurate embryo optimization is realized. According to the method, comprehensive identification of embryo genetic states is realized through whole genome sequencing, a pathogenic load and structural stability double-index system is constructed, three-dimensional quality evaluation is realized, and the scientificity, accuracy and individualized clinical application capability of embryo screening are improved by combining a grading result and a family medical history calibration mechanism output by a grading model.

The invention discloses a colorectal cancer plasma circulating microbial marker, a reagent, a kit and application thereof, and belongs to the technical field of biomedical detection. The plasma circulating microbial marker for colorectal cancer comprises alternaria alternata, alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous alophilous The colorectal cancer plasma circulating microbial marker can be used for early screening of colorectal cancer, has relatively high sensitivity and specificity, and remarkably improves the accuracy and reliability of detection; the limitation of traditional ctDNA detection is broken through, and the detection rate of early colorectal cancer is improved. The colorectal cancer plasma circulating microbial marker in a colorectal cancer plasma sample is detected through low-depth whole genome sequencing, the requirement for depth in an experiment is reduced, the cost can be greatly reduced while high sensitivity and specificity are guaranteed, and the method is more suitable for large-scale screening.

Transgene-free genome editing of plants in T0 generation is highly desirable but challenging, especially in perennials and vegetatively propagated plants. Here is provided a co-editing strategy for generating transgene-free, gene-edited plants via Agrobacterium-mediated transient expression of cytosine base editor (CBE) / gRNA-Cas 12a / crRNA-GFP in plants. Specifically, CBE / gRNA was used to base edit the AES gene to confer resistance to herbicide chlorsulfuron as a selection marker, which has no negative effects on plant phenotypes; Casl2a / crRNA was used for editing genes(s) of interest; GFP was used for selecting transgene-free transformants. Using this approach, transgene- free genome-edited plants were efficiently generated for various genes (either individual or multiplex) in tomato, tobacco, potato, and citrus in the T0 generation. The biallelic / homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 8% to 50%. Whole genome sequencing further confirmed transgene-free and absence of off- target mutations in the edited plants. The co-editing strategy is efficient for generating transgene- free, genome-edited plants in the T0 generation, thus being a potent tool for plant genetic improvement.

The present disclosure relates to a method for determining a copy number variation profile, which is executed by one or more processors, and includes acquiring results of whole-genome analysis associated with a target sample collected from a subject, calculating a read depth associated with the target sample for each of a plurality of predetermined bins on genome based on the acquired results of whole-genome analysis, correcting the read depth associated with the target sample, and determining a copy number variation profile associated with the target sample using the corrected read depth.

The invention discloses a fingerprint spectrum of an oyster mushroom P2101 strain as well as a construction method and application of the fingerprint spectrum, and belongs to the field of oyster mushroom strain detection. The fingerprint spectrum is composed of 10 pairs of InDel markers developed on the basis of oyster mushroom whole genome sequencing. The InDel marker fingerprint spectrum of the oyster mushroom P2101 strain can be used for identifying the specificity of the oyster mushroom P2101 strain, has the advantages of short detection time, high accuracy and good repeatability, and has the specificity of the oyster mushroom P2101 strain in 48 collected oyster mushroom strains.

The invention discloses a method for screening a cancer specific cfDNA fragment feature combination in peripheral blood based on whole genome sequencing and application of the method. According to the method, multi-dimensional cfDNA fragment information is combined to screen characteristic indexes closely related to cancers, a brand-new index F-Index for evaluating fragment length distribution characteristics is provided, and obvious difference exists between a cancer sample and a healthy sample; in addition, motif characteristics of six basic groups at the tail end of a cfDNA fragment and distribution characteristics of the cfDNA fragment in a 10kb window on a genome are applied, a plurality of machine learning algorithms are applied, a series of cancer-specific molecular characteristic combinations are obtained through identification, and the cancer-specific molecular characteristic combinations are suitable for risk assessment and prediction of early cancers. The feature combination screened based on the method has excellent prediction performance in different classification models, and the judgment accuracy is high.

The invention relates to the technical field of plant breeding, in particular to a construction method and application of a genetic map of a fruit tree F1 population. The construction method comprises the following steps: mining and screening whole genome sequencing data of a fruit tree F1 group and parents thereof to obtain SNP loci; the sites in accordance with the lmxll or nnxnp separation type in the SNP sites are taken to construct an MNP molecular marker; dividing bins for each chromosome according to a predetermined length, and endowing each bin with a corresponding separation type according to the separation type of the MNP molecular marker in the bins; and constructing a genetic map according to the separation type data of each bin. The construction method provided by the invention can correct errors and deletion of SNP, has high marker detection and positioning precision, consistent linkage relationship and recombination rate, can significantly improve the breeding efficiency when applied to plant breeding, and has significantly high practical application value.

The present invention provides primers and methods for amplifying the entire genome of avian leukosis virus. The detection primer set for avian leukosis virus includes 18 pairs of amplification primers, the specific sequences of which are shown in SEQ ID NOs. 1 to 36. The detection primer set provided by the present invention can achieve relatively uniform coverage of avian leukosis virus, and in nanopore sequencing, 100% regional coverage of the genome is achieved. The method for preparing sequencing fragments of the entire genome of avian leukosis virus provided by the present invention is simple and easy to operate, with good amplification effect. Nanopore sequencing has the advantage of real-time analysis while sequencing, which can greatly shorten the detection time and can quickly identify and diagnose avian leukosis virus infection. At the same time, its entire genome sequence can be obtained. The obtained genome sequence can provide a scientific basis for virus tracing, pathogen mutation tracking, new strain identification and early warning, etc.