291 results about "Whole genome sequencing" patented technology

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 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 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 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 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.

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 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.

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.

The invention discloses a copy number variation detection method, device and equipment based on low-depth whole genome sequencing and a storage medium, and relates to the technical field of medical data processing, the method comprises the following steps: performing sequencing quality control on sample gene data to obtain filtered gene data; performing data preprocessing on the filtered gene data through a dynamic negative reference library and a reference genome to obtain processed gene data and a dynamic Z test result; the dynamic negative reference library is determined according to the GC content of the contrast negative sample set; and performing improved copy number variation detection according to the processed gene data and the dynamic Z test result to obtain a copy number variation detection result. According to the method, sequencing quality control is carried out firstly, and data quality is guaranteed; and then data preprocessing is performed based on a dynamic negative reference library constructed in real time, and finally CNV detection is performed based on optimized processing gene data and a dynamic Z test result, so that systematic deviation is effectively reduced, and the detection reliability is improved.

The invention relates to the use of artificial neural networks, such as autoencoders, in population genomics and individual genome processing to fill-in missing data from genomic assays with significant sparsity, such as low-pass whole genome sequencing or array-based genotyping. An autoencoder-based neural network approach for the simultaneous execution of genetic imputation as well as feature extraction and dimensionality reduction for downstream tasks is provided.

The invention provides a non-lineage animal pairing evaluation method based on genome data, and belongs to the technical field of bioinformatics and protection genetics, the method comprises the following steps: firstly, obtaining whole genome sequencing data of all individuals in a population, and carrying out quality control to obtain a high-quality SNP site set; aiming at all possible male and female pairing combinations in the population, calculating an inter-parent genetic coefficient depKin, an inter-parent heterozygous difference ratio HDR and an inter-parent potential risk load index GRLI, and predicting a fixed proportion Proh of ROH of offspring; performing z-score standardization processing on the four genetic indexes: performing principal component analysis on standardized data, extracting the first two principal components PC1 and PC2, determining a weight according to a variance contribution rate, and calculating a pairing comprehensive score; and generating a pairing candidate recommendation list for each individual according to the comprehensive score, and screening a high-quality pairing scheme. The method disclosed by the invention can be completely independent of pedigree records, and genetic evaluation is directly carried out based on genome data.

The application provides a STR typing method applied to second-generation sequencing data, and relates to the technical field of biology.The method specifically comprises the following steps: customizing an STR locus configuration file; constructing a k-mer index library of a flanking sequence of the STR locus; extracting STR allele sequences from each READ of a sequence alignment file in combination with a CIGAR value and the k-mer index; constructing a PCR ghost peak model of the STR locus, and estimating parameters of the PCR ghost peak model by using a maximum likelihood estimation method; estimating candidate allele frequencies by using a second-generation sequencing sample data set; calculating posterior probabilities of all candidate alleles by using an allele set extracted from a given sequence alignment file, and inferring the most possible allele.The STR typing method has higher detection rate and typing accuracy, and has faster typing speed, and can be used for whole genome sequencing data, high-coverage targeted sequencing data or amplicon sequencing data.

The invention relates to a breeding method of Lingnan pigeons, belongs to the field of poultry genetic breeding, and mainly solves the problems of low growth speed and low meat yield of meat pigeons. The method comprises the following steps: firstly, selecting purebred male Shiqi pigeons and purebred female mimassa pigeons to establish a basic group, and naturally mating according to a male-female ratio of 1: 1 to obtain F1-generation hybrid pigeons; measuring the growth performance index and the reproductive performance index of the F1 generation, calculating the breeding index through an index selection method, and selecting and remaining the first 50% of individuals; mating the selected F1-generation male and female pigeons according to a ratio of 1: 1 to obtain an F2-generation, collecting gene samples of the F1-generation male and female pigeons, carrying out whole genome sequencing, and screening out core genes CTNNB1 and MYO9A for regulating and controlling the growth speed and the meat yield; f2-generation individuals conforming to target traits are selected and reserved based on genotypes for cross-crossing fixation to form two-line hybrid pigeons; and finally, carrying out three-way hybridization on the two-line male pigeons as male parents and American king pigeons as female parents to obtain commercial generation Lingnan pigeons. According to the method, the growth performance, the meat yield and the stress resistance of commercial generation pigeons are remarkably improved through combination of multi-generation hybrid advantage integration and a molecular breeding technology.

The invention discloses an X-chromosome specific molecular marker of micropterus salmoides and application of the X-chromosome specific molecular marker. On the basis of a whole genome sequencing technology, the X chromosome specific molecular marker of micropterus salmoides is obtained. Aiming at the molecular marker, the invention also provides a detection primer pair and a detection method of the molecular marker, and by detecting the molecular marker, rapid and accurate screening of YY supermale fish individuals can be realized to obtain a YY supermale fish population. The obtained YY super-male fish group and a proper female fish group are jointly fed and bred, and then the micropterus salmoides all-male fingerling can be obtained. If the YY super-male fish group and the YY pseudo-female fish group are jointly bred and bred, largemouth bass offspring which is all YY super-male fish can be obtained. Compared with a traditional all-male breeding method of the largemouth black bass, the all-male breeding method of the largemouth black bass is beneficial to simplifying all-male breeding steps of the largemouth black bass, shortening breeding time, and beneficial to cultivation of all-male largemouth black bass fingerlings and popularization of single-male breeding of the largemouth black bass.

The invention discloses panda-derived tryptophan-producing streptococcus non-lactolyticus C49 and application thereof, and belongs to the field of microorganisms, the strain is preserved in Guangdong Microbial Culture Collection Center, and the preservation number is GDMCC No: 67209. The strain has good acid-resistant and cholate-resistant characteristics, and can ensure that enough biomass passes through stress of a digestive tract environment; whole genome sequencing finds that C49 is significantly related to the pathway and module of tryptophan biosynthesis. Whole genome sequencing and in-vitro fermentation confirm that C49 has tryptophan biosynthesis capability, and in-vivo animal tests confirm that C49 has synthetic nerve conditioning capability. Therefore, as a probiotic feed additive, the streptococcus non-lactolyticus C49 has a good application prospect in the aspects of improving the feed value, improving the intestinal health of animals, enhancing the immunity of organisms and the like.

The present disclosure provides a method for the preparation and analysis of a biological sample of a xenograft receptor wherein the method comprises extracting fragmented or intact cell-free DNA, RNA (such as mRNA or miRNA) or protein of a sample derived from the xenograft receptor, and measuring the amount of cell-free DNA, RNA (such as mRNA or miRNA) or protein derived from said xenograft enables the assessment of xenograft rejection. The detection of the cell-free DNA or RNA can be carried out by preparing a sequencing library and carrying out whole genome sequencing.

The invention discloses a fiveleaf virus GII.3 whole genome sequencing primer based on an amplicon sequencing technology and application thereof, and belongs to the technical field of virus gene sequencing. According to the whole genome sequencing primer and the sequencing method for the fiveleaf virus GII.3, interference of other microorganisms on sequencing can be avoided, the gene sequencing depth is high, the advantages of being wider in whole genome coverage, high in detection accuracy and high in specificity are achieved, the sequencing result can reflect mutation characteristics of main epidemic strains of the fiveleaf virus, and the sequencing result can be used for detecting the mutation characteristics of the main epidemic strains of the fiveleaf virus GII.3. And a powerful tool is provided for rapid diagnosis and full prevention of the fiveleaf akebia viruses.

Methods for treating and / or assessing a subject having a symptomatic multiple myeloma or a precursor thereof, where the methods involve characterizing a plasma cell dyscrasia (e.g., monoclonal gammopathy of undetermined significance, smoldering multiple myeloma, multiple myeloma, plasma cell leukemia) in a biological sample from a subject as being high, medium, or low risk by assigning to the plasma cell dyscrasia a multiple myeloma (MM)-like score. The methods may involve sequencing DNA from the biological sample using whole-genome sequencing (WGS).

The invention discloses an assembly method of extended chromosome telomeres. The assembly method comprises the following steps: obtaining a chromosome sequence through an assembly technology; the method comprises the following steps: detecting a chromosome sequence to obtain a target genome chromosome sequence without telomere information, and obtaining an ONT reads sequence containing telomere information from whole genome sequencing data; comparing the ONT reads sequence containing the telomere information with a target genome chromosome sequence, and extracting an ONT reads target sequence containing the telomere information according to a comparison result; the obtained ONT Ultra-long reads target sequence containing the telomere information is subjected to consistent sequence assembly, and a chromosome extension candidate sequence is obtained; comparing the obtained residual ONT reads target sequence containing telomere information to the chromosome extension candidate sequence, and carrying out error correction to obtain a high-quality chromosome extension candidate sequence; and connecting the high-quality chromosome extension candidate sequence to a target genome chromosome sequence to prepare a chromosome sequence containing telomere information. According to the method, the sequencing length advantage of Nanopore and the sequencing precision advantage of HiFi are successfully fused, accurate extension of the chromosome sequence deletion telomere is realized, and a high-quality telomere-to-telomere assembly result is obtained.

The invention relates to a disease-specific quantitative trait locus identification method based on multi-omics integration. The method comprises the following steps: acquiring variation sites of whole genome sequencing data of a target object, and molecular phenotypes and molecular abundance of molecular phenotype data; determining an association significance probability value of an association pair formed by the variation point and the molecular phenotype based on the variation point and the molecular abundance, and screening a first association pair from the association pair based on the association significance probability value and condition analysis; determining a consistent second association pair in the normal association pair and the disease association pair, and determining a third association pair with a disease interaction effect in the second association pair; calculating a first effect estimation value and a second effect estimation value of each third association pair; and based on the first effect estimation value and the second effect estimation value of the third correlation pair, determining a target correlation pair related to the Parkinson's disease, and taking the target correlation pair as the identified quantitative trait site. By adopting the method, the Parkinson's specific pathogenic heritable variation can be accurately identified.