168 results about "Whole genome sequencing" patented technology

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 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.

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 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.

This invention provides a data storage method and system for tuberculosis detection, relating to the field of tuberculosis detection technology. The data storage method for tuberculosis detection includes the following steps: S1. Collecting whole-genome sequencing data of Mycobacterium tuberculosis, host serum IgG titer, and drug sensitivity test results; S2. Calculating genetic distance D based on a reverse evolution model to generate four-dimensional spatiotemporal coordinates (t, x, y); S3. Performing data partitioning and storage based on the drug target barrier value β; S4. Generating dynamic metadata using a host-pathogen dynamics model and compressing and storing it. This invention implements a dynamic storage entropy adjustment algorithm at the hardware and software collaborative level, continuously optimizing the matching efficiency of data compression and physical storage. This results in an intelligent data hub that can perceive the evolutionary pulse of pathogens and autonomously optimize resources, providing support for clinical tuberculosis prevention and control decisions with temporal depth, spatial correlation, and risk evolution.

This invention discloses a method for directed evolution of antibiotic-resistant Escherichia coli strains based on cytidine deaminase, belonging to the field of microbial directed evolution and genetic engineering technology. This method uses E. coli as the host, introducing a recombinant plasmid expressing an optimized double-stranded cytidine deaminase mutant. Utilizing the low toxicity and high mutagenicity of this mutant, continuous passage evolution is carried out under gradient concentrations of aminoglycoside antibiotics (kanamycin and streptomycin). Combined with whole-genome sequencing, molecular docking, and reverse genetics verification, the A145T missense mutation in the wcaE gene is identified as the core functional site. This invention overcomes the shortcomings of traditional spontaneous and chemical mutagenesis, which suffer from low efficiency and significant strain damage. The mutation type is controllable, the evolutionary cycle is short, and the obtained engineered strains can tolerate up to 300 mg / L kanamycin while exhibiting streptomycin cross-resistance, and the genetic stability of the tolerance trait is strong. This method is simple, highly reproducible, and suitable for industrial breeding of stress-resistant E. coli, and can be widely applied in antibiotic fermentation, industrial microbial culture, and other scenarios.

The invention belongs to the technical field of medical software development, and particularly relates to a plateau newborn inherited metabolic disease screening system, a computer readable storage medium and application of the plateau newborn inherited metabolic disease screening system. According to the screening system, an altitude hierarchical multi-level reference value database based on a local healthy newborn queue is established, and the problem that the false positive rate of a plain area screening model in a plateau area is too high is solved by fitting an altitude metabolism marker reference median and a standard deviation curve. By designing a'biochemical primary screening-risk scoring-targeted sequencing automatic triggering 'three-level joint control data processing flow, targeted sequencing guided by a crowd specific pathogenic mutation library is started only when the biochemical risk is high, unnecessary whole genome sequencing is avoided, and the screening cost is remarkably reduced. The system can continuously iterate a reference curve and a risk threshold value according to definite diagnosis data, and closed-loop dynamic optimization from sample collection to report generation is achieved. The method has plateau adaptability, crowd specificity and cost controllability, and has a good clinical application prospect.

This disclosure relates to a technique for identifying tumor-specific mutations through integrated analysis of next-generation sequencing data using machine learning models. In certain embodiments, a computer implementation method is provided, comprising: generating sequence reads from one or more samples collected from the same patient; generating variant calling files by analyzing the sequence reads corresponding to each of the one or more samples; generating a list of candidate somatic variants by comparing the variant calling files; generating a score for each of the candidate somatic variants in the list of candidate somatic variants using a classification machine learning model, wherein the score is generated based on a plurality of classifications generated by the classification machine learning model; determining the ctDNA status for the patient based on the score, wherein the ctDNA status is either positive or negative; and generating a report providing the ctDNA status for the patient.

The application discloses a method, device and storage medium for detecting mitochondrial-derived nuclear genome sequences. The method comprises the following steps: aligning whole genome sequencing data to a mitochondrial reference genome rCRS, retaining the reads aligned to the rCRS, aligning the reads to a reference sequence containing 23 pairs of chromosomes and the rCRS, removing non-unique alignment reads; extracting potential junction reads, clustering the junction reads within a distance of 50 bp according to the alignment positions, locating the coordinates and directions of the integrated mitochondrial DNA fragments, and the nuclear genome integration position; searching for inconsistent alignment read pairs within 100 bp upstream and downstream of a read cluster, and counting the number of the inconsistent alignment read pairs as support information for the existence of non-ref NUMTs. The application utilizes the alignment information of the junction reads, detects the non-ref NUMTs through local assembly and clustering, reduces the false positive rate, can obtain accurate breakpoint and fragment information, is simple to operate, and has low detection cost.

The invention discloses a primer group and method for human metapneumovirus whole genome sequencing and application. Two groups of specific primer pools are designed for the metapneumovirus, totally comprise 21 primers, can effectively amplify the metapneumovirus type A and the metapneumovirus type B, are high in sensitivity and suitable for multi-platform detection, and provide a new direction for detection, typing, traceability and evolutionary analysis of the metapneumovirus.

The invention relates to the technical field of bioinformatics and crop breeding, and particularly discloses a method, a device and equipment for predicting the close planting yield of brassica napus by using hypocotyl length based on a whole genome selection technology. The method is characterized by comprising the following steps: acquiring whole genome sequencing data of brassica napus germplasm; inputting the whole genome sequencing data into a target model; outputting hypocotyl length data of the brassica napus under a close planting condition through the target model; and according to the hypocotyl length data of the brassica napus under the close planting condition, obtaining a brassica napus germplasm yield potential sorting result. According to the method, whole genome selection and key morphological characters (hypocotyl length) under specific stress (close planting conditions) are combined for the first time, high-yield varieties suitable for close planting cultivation can be efficiently and accurately screened out without on-site close planting tests in the early stage of rape breeding, and the breeding efficiency is remarkably improved.

The invention relates to a primer set for whole genome sequencing of chlamydia psittaci, the primer set comprises a primer subset p1 and a primer subset p2, the primer subset p1 comprises primers with sequences as shown in SEQ ID NO: 1-240, and the primer subset p2 comprises primers with sequences as shown in SEQ ID NO: 241-480. The primer group disclosed by the invention not only can accurately obtain the whole genome sequence of chlamydia psittaci, but also is adaptive to the sequencing modes of all second-generation and third-generation sequencing platforms.

This invention relates to the field of medical technology, specifically to a method for preoperative risk assessment and prediction in liver transplant patients with hepatocellular carcinoma, comprising the following steps: Sample collection: selecting plasma samples and corresponding clinicopathological information from liver transplant recipients of hepatocellular carcinoma, and clarifying the inclusion and exclusion criteria for samples; Plasma cell-free DNA extraction and whole-genome sequencing: extracting and quality-controlling cell-free DNA from the plasma samples collected in step S1, constructing a sequencing library, and performing low-coverage whole-genome sequencing. This invention utilizes plasma-extracted cfDNA for whole-genome sequencing, combined with clinical testing information, to construct a preoperative risk assessment and prediction model for postoperative recurrence in liver transplant recipients of hepatocellular carcinoma based on non-invasive testing. This model can be used to predict the probability of recurrence-free survival before liver transplantation. The model derivation cohort integrates clinical records and circulating tumor DNA data for preoperative recurrence risk prediction.

The invention relates to a method of determining somatic allele-specific copy number alterations (CNAs) in the genomes of cells in a test-sample from a subject, the method comprising: i) providing an indexed-DNA library of DNA fragments resulting from whole-genome amplification of genomic DNA from cells of the test-sample, ii) providing whole genome sequencing data of reference non-cancer cells from a reference-sample from the subject; and iii) determining somatic allele-specific copy number alterations in the genome(s) of the cells of the test-sample; and associated methods and uses in cancer therapy.

The invention discloses a sperm genome methylation detection method for safety evaluation of biological breeding crops by using primates and application, and relates to the technical field of safety evaluation of crops, the sperm genome methylation detection method comprises the following steps: dividing non-human primates into three groups, collecting sperms after long-term feeding, and extracting DNA (Deoxyribose Nucleic Acid); carrying out whole genome sequencing and quality control after bisulfite treatment; the epigenetic safety of crops is comprehensively evaluated by analyzing the methylation level of a whole genome and a functional region and functional enrichment of a differential methylation region and related genes thereof; according to the sperm genome methylation detection method for evaluating the safety of the biologically bred crops by utilizing the primates and the application, by utilizing a high-resolution WGBS technology, subtle epigenetic changes which are difficult to find by traditional toxicology can be detected, and the sperm genome methylation detection method has important significance in cross-generation reproduction effect evaluation, and has a wide application prospect. A food safety evaluation system can be perfected, and a more scientific and reliable safety interpretation basis can be established.

The invention discloses a primer group and a kit for high-flux targeted detection of pathogens and drug-resistant genes of camel mastitis and application of the primer group and the kit. The primer group consists of 185 pairs of primers with nucleotide sequences as shown in SEQ ID NO: 1-370. According to the primer group, the kit and the detection method disclosed by the invention, specific amplification is carried out on key areas of 20 pathogen target genes and 77 drug-resistant genes of camel mastitis; the kit has the following remarkable advantages: 1) high precision and specificity: sequencing is performed for a specific region, so that the detection accuracy is remarkably improved, low-abundance pathogenic bacterium nucleic acid can be effectively detected, and early diagnosis is assisted; 2) high efficiency and economy: parallel detection of various pathogenic bacteria and drug-resistant genes can be realized through a single experiment, and the detection flux is greatly improved; compared with whole genome sequencing, the cost of targeted sequencing is lower; 3) the method is simple, convenient and universal, the data analysis complexity is remarkably reduced, the method is suitable for various clinical samples such as blood, tissues and secretions, and a unified and efficient detection scheme is provided for different sample types.

The invention relates to the technical field of biomedical detection, in particular to a multi-dimensional tumor marker joint detection device and a using method thereof.The device comprises a sample processing module, a sequencing module, a marker extraction module, a feature fusion and detection module and a result output module, and 6 types of markers such as chromosome copy variation, microsatellite instability and the like are extracted respectively. The method comprises the following steps: collecting a body fluid sample to extract cfDNA, directly constructing a library without special treatment, obtaining effective data through whole genome sequencing, synchronously extracting six types of markers through each module of the device, optimizing an algorithm to adapt to low-depth data, inputting an integrated learning model to output a risk score, and finally outputting related information by a result output module. The method does not need special experimental treatment, realizes low-cost and high-accuracy joint detection, and meets the clinical large-scale screening requirements.

The bacterial strain Arasana bacillus (CECT 30655) belongs to Gram-positive bacterial flora and bacillus subtilis, and is a stimulant capable of stimulating adaptive metabolism of plants to resist water stress, an improving agent for plant yield and nutrition and an improving agent for polyphenol content. The strain is separated from rhizosphere soil of pinus coast, is cultured on a nutrient agar culture medium (PCA), and is identified as a new strain from the aspects of morphology, biochemistry and genetics for identification through whole genome sequencing. Under a water stress condition, the strain can enhance CO2 fixation and transpiration, optimize photosynthesis energy capture and reduce oxidative stress, so that the strain can be used for increasing yield; as a biological fertilizer, nutrient absorption can be promoted no matter whether water stress exists or not; and the content of antioxidant polyphenols in plant species with medicinal or edible values can also be improved, so that the fruit quality is improved.

The invention discloses a primer group and a kit for whole genome sequencing of influenza A virus, and the primer group comprises an external targeting primer with a sequence as shown in SEQ ID NO.1-35 and an internal nested targeting primer of a primer with a sequence as shown in SEQ ID NO.36-89. Based on the primer group, the influenza A virus whole genome detection method is established, sequencing and typing of the influenza A virus whole genome can be completed within 10 hours, a complete genome sequence can be obtained without assembling sequencing data, and compared with a conventional NGS detection technology, the detection method has the advantages that the detection efficiency is greatly improved, and the detection cost is reduced. The accuracy and the stability of influenza A virus detection can be greatly improved.

The application discloses a D type influenza virus isolate D / HY11 and application thereof in a mink infection model, and belongs to the field of biological medicines. The application takes the D type influenza virus isolate D / HY11 of an IDV northeast isolate as a research object, establishes a mink transmission model, evaluates the transmission dynamics characteristics of the strain among minks, identifies amino acid mutations possibly related to host adaptability through whole genome sequencing, analyzes the amino acid substitution on receptor affinity based on computer simulation of protein conformation and receptor molecule docking, explores the host adaptation evolution law of the virus in the transmission process, and provides an important scientific basis for early warning and prevention and control of a public health crisis possibly caused by the IDV.

The invention discloses an individual identification method and system based on whole genome single nucleotide polymorphism data, and relates to the technical field of forensic genetics, and the method specifically comprises the following steps: obtaining intersection SNP sites of a to-be-identified sample pair, and constructing an SNP site set with linkage balance; performing individual recognition capability evaluation on the linkage-balanced SNP site set based on the efficiency evaluation index to generate an optimal SNP site set; under the set mutual exclusion hypothesis, the probability value of each optimal SNP site is calculated based on the population genotype frequency and the prior typing error rate, and the total likelihood ratio is calculated based on the probability value of each optimal SNP site; a support hypothesis or hypothesis is selected based on a relationship between the total likelihood ratio and a preset threshold. The unavoidable typing errors in the whole genome sequencing data can be scientifically processed and explained by introducing the semi-continuous likelihood ratio calculation model integrating the typing error rate.

The present disclosure provides method of whole genome sequencing of microorganisms such as Gram-positive bacteria, Gram-negative bacteria, viruses, and fungi. The various methods comprising steps of isolating nucleic acid from the microorganism and preparing a library of the isolated nucleic acid. Preferably, the methods of whole genome sequencing described herein are automated to provide a robust and efficient sequencing product for various utilities.

Methods are provided for diagnosing and treating idiopathic pulmonary fibrosis (IPF) in humans and canine idiopathic pulmonary fibrosis (CIPF) in canines. The methods include detecting expression of genes found to indicate a predisposition, a risk, or a presence of IPF: SDHAF2, CPSF7, and MUC5B. One variant, rs22669389, corresponding to position 54992254 on canine (CanFam3.1) chromosome 18, was identified at a suggestive level of significance to be associated with CIPF. The methods further comprise performing whole genome sequencing (WGS) of DNA in the sample to confirm detection of a variant indicating a predisposition, a risk, or a diagnosis of IPF or CIPF. The method further includes treating a subject for IPF or CIPF, based on the diagnosis of IPF or CIPF.

The invention discloses a carbapenem drug resistance marker screening method and system based on a cross-species compressed Debrueine diagram and a medium. The method comprises the following steps: starting from whole genome sequencing data of gram-negative bacteria belonging to different species and carbapenem drug phenotypes of the gram-negative bacteria, constructing a compressed Debrueine graph based on cross-species joint data, and taking existence / deletion of nodes in the graph as unified genetic variation characteristics. Performing correlation analysis on the nodes and the drug resistance phenotypes by using a linear hybrid model to obtain a candidate node set related to the phenotypes; k-mer is extracted based on the candidate node sequence, and secondary statistical screening is completed in combination with chi-square test and mutual information; and finally determining a group of carbapenem drug-resistant genetic markers which can be applicable across species through a hierarchical feature selection strategy of random forest and XGBoost. Efficient dimension reduction of large-scale cross-species genome data, cross-species consistent variation representation and high-interpretability marker screening are achieved.

The invention belongs to the field of microbial engineering, and provides a gentamicin C1a high-yield biological manufacturing method based on metabolic network modeling and reverse metabolic engineering renovation, which comprises the following steps: S1, constructing a genome scale metabolic model of a target production strain, predicting and screening a first target gene in positive correlation with gentamicin biosynthesis by using the model; s2, performing whole genome sequencing on the gentamicin high-yield mutant strain, and identifying a second target gene related to the high-yield character through comparative genomics analysis; s3, combining the first target gene predicted in the step S1 and the second target gene identified in the step S2, and constructing to obtain a recombinant engineering strain; s4, carrying out fermentation culture on the recombinant engineering strain, and supplementing materials in the fermentation process; by remarkably improving the production efficiency and strain performance of gentamicin C1a, important technical support and theoretical basis are provided for green biological manufacturing of antibiotics.

This application relates to the technical field of biological gene detection, specifically disclosing a miniature pig SNP molecular marker combinatorial system and its application. The miniature pig SNP molecular marker combinatorial system disclosed in this application includes at least one of 221 SNP molecular markers. The physical locations of these 221 SNP molecular markers are determined based on sequence alignment during 10× coverage whole-genome sequencing of miniature pigs. The site information of the 221 SNP molecular markers is shown in Table 1. The miniature pig SNP molecular marker combinatorial system provided in this application is used for detecting SNP genotyping in miniature pigs and possesses novel, stable, cost-effective, and efficient properties.