514 results about "Genomic sequencing" patented technology

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.

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 discloses bacillus velezensis Scm3 and application thereof.The bacillus velezensis Scm3 is obtained by screening a strain Scm with an inhibition effect on aeromonas hydrophila from turbot intestinal contents and then conducting ultraviolet mutagenesis on the strain to obtain a strain Scm3 with an enhanced antagonism effect on aeromonas hydrophila, and the strain Scm3 is applied to the preparation of the bacillus velezensis Scm3 and the application of the bacillus velezensis Scm3 to prepare the bacillus velezensis Scm3. 16SrDNA (deoxyribonucleic acid) sequence identification and genome sequencing prove that the strain is bacillus velezensis, and the inhibition mechanism of the bacillus velezensis Scm3 on aeromonas hydrophila is researched by a non-contact co-culture method.

The invention relates to a method for predicting river nitrogen metabolism gene abundance and key influence factors thereof based on automatic machine learning. Comprising the following steps: collecting a river water sample, detecting water quality physicochemical indexes, and performing metagenome sequencing to obtain nitrogen metabolism gene abundance; taking conventional water quality physicochemical indexes as explanatory variables, taking nitrogen metabolism gene abundance as a target variable, adopting automatic machine learning to construct a model, evaluating the performance of the model through a mean square error (MSE) and a fitting coefficient (R), and selecting an optimal algorithm for prediction; the model analyzes the relative contribution of each water quality index through an SHAP value graph, and reveals the relationship between each water quality index and gene abundance by using a partial dependency graph (PDP). The method shows high precision and good generalization performance in the aspect of predicting the abundance of the nitrogen metabolism gene, and is suitable for describing the nitrogen dynamic process of a river water body. The model can explain, analyze and quantify the influence of different water quality indexes on the nitrogen metabolism gene afterwards, and a scientific basis is provided for river water quality management and nitrogen metabolism optimization regulation and control.

The invention relates to the field of medical detection, in particular to a group of biomarkers for diagnosing hypertension in children, a kit and application of the biomarkers. According to the method, tongue coating / intestinal tract samples of obese children hypertensive patients, obese children and healthy people are collected, metagenome sequencing is carried out, sequencing data statistics is carried out by using bioinformatics, tongue coating / intestinal tract florae related to diseases are found, the tongue coating / intestinal tract florae and disease information are integrated, a flora biomarker combination is obtained, and the method is applied to diagnosis and treatment of the hypertensive patients, the obese children and the healthy people. The hypertensive patients of obese children can be detected to the maximum extent through the binary classification prediction model constructed through the combination.

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 discloses an environmental microbial community state evaluation method based on unsupervised clustering, and the specific implementation mode is as follows: obtaining metagenome sequencing data in an environmental sample, and carrying out microbial species annotation and abundance calculation; based on abundance data, sample microbial species richness and Shannon diversity indexes are calculated, microbial functional gene annotation and abundance calculation are carried out, standardization processing, principal component analysis, Euclidean distance calculation, Ward clustering and contour coefficient evaluation are carried out on the data, and dimensionality reduction and clustering are carried out on the multi-dimensional features. Therefore, comprehensive indexes with obvious differences are provided. According to the comprehensive indexes obtained through the method, original data can be reserved, the complexity of the data can be greatly reduced, the analysis process is simplified, and an intuitive and operable means is provided for overall state evaluation of the environmental microbial community, so that the analysis efficiency and accuracy are improved, and the method is suitable for popularization and application. And determining the overall influence of the environmental change on the microbial community state.

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 provides a sample preparation method for microbiological detection, a sample, a detection method, a kit and application. The method comprises the following steps: a treatment step: taking an in-vitro host cell sample, and treating the in-vitro host cell sample with a host cell lysis reagent and nuclease to degrade host nucleic acid, the treatment being carried out in a liquid with a salt concentration of 10-600mM; a nuclease inactivation step: providing conditions to inactivate the nuclease; and obtaining microbial nucleic acid: extracting total nucleic acid to obtain the sample for detecting the microorganisms. According to the method disclosed by the invention, the interference of the host cell genome on the sample detection sensitivity can be effectively reduced in metagenome sequencing, and effective sequencing data of microorganisms in a detection result is improved, so that the positive detection rate of the microorganisms and the sensitivity of detecting the microorganisms are improved.

The invention discloses a crested ibis habitat ecological quality trend analysis method and system, and relates to ecological quality monitoring. The method comprises the following steps: S1, constructing an intelligent sensing network, synchronously obtaining multi-source data of a habitat, identifying activity events of crested ibis, and generating a multi-dimensional habitat parameter table; s2, collecting environmental samples, and generating a microbial functional gene abundance matrix through metagenome sequencing and bioinformatics analysis; s3, taking the activity events of the crested ibis as behavior tags, and generating habitat function health indexes by coupling the parameter table and the matrix training machine learning prediction model; s4, performing spatial interpolation and trend analysis based on the habitat function health index to generate an ecological quality space-time evolution graph; and S5, based on the ecological quality space-time evolution graph, performing quantitative analysis by using a spatial differentiation statistical model, and generating a trend analysis report. By fusing multi-source data, real-time dynamic evaluation of habitat ecological quality and quantitative analysis of driving factors are realized, and a direct decision basis is provided for accurate protection.

A copy number variation detection method based on high-throughput transcriptome sequencing data of a single sample. The detection method comprises: first, aligning genome sequencing data to a human reference genome, and calculating the amount of data aligned to reads on each gene, so as to obtain an expression matrix; and then inputting the expression matrix into a detection model, so as to obtain a copy number variation detection result, wherein the detection model is obtained by means of performing training on the basis of a deep neural network model and by using pre-processed known database samples as a data set. By means of the detection method, the genome structure and variation of a single individual are better understood; with lower costs and in less time, gene expression level information is provided, and copy number information of genes can also be acquired, such that functions and regulatory mechanisms of genomes and the impact of copy number variations on gene expression can be better understood; and the method is of great significance for research on genetic diseases, rare diseases and complex diseases.

The invention discloses a low-abundance pathogen detection method and system based on metagenome sequencing data, and belongs to the technical field of bioinformatics. The system comprises a species specificity sequence screening module (BactAlert2SSRs), a reference genome database construction module (BactAlert2Lib), a sequence alignment reference genome module (BactAlert2Map), a sequence alignment result analysis module (BactAlert2ID), and an SSRs posterior probability correction module (BactAlert2Rec). The detection system realizes efficient, accurate and reliable detection of low-abundance pathogens, and is suitable for analyzing third-generation metagenome sequencing data.

The invention relates to the technical field of bioinformatics data processing, in particular to a genome sequence compression method and system. The method comprises the following steps: acquiring genome sequencing data; comparing the sequencing data with a reference genome to determine a difference site; differentiating the difference sites as sequencing errors or real variations through a time sequence difference neural network model; performing differential compression coding according to an identification result; a friendly variation detection format is constructed, and rapid variation query is supported through a multi-level index structure and a variation metadata table. According to the method provided by the invention, the sequencing error and the real variation can be accurately distinguished through the time sequence differential neural network model, and important biological variation information is protected while the compression efficiency is improved by adopting the differential compression coding strategy.

The invention belongs to the technical field of genetic breeding, and particularly relates to a molecular marker for identifying sheep backfat thickness and application of the molecular marker, the nucleotide sequence of the molecular marker is shown as SEQ ID NO.1, and single nucleotide C-A mutation occurs at the 101bp site of the molecular marker. The molecular marker influencing the sheep backfat thickness is screened out through methods such as genome sequencing, variation site recognition, screening and annotation, whole genome association analysis and the like. By selecting sheep individuals with the genotype of CC as male parents or female parents, the backfat thickness of offspring can be reduced.

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 discloses a flora regulation and control method and system for soil micro-ecology, and belongs to the technical field of microbial flora regulation and control, and the method comprises the steps: continuously collecting real-time environment data based on a target soil region, combining future climate prediction data, and generating a predicted scene sequence through Monte Carlo simulation; constructing a microbial community composition table, screening core strains, and performing metagenome sequencing; taking the core strain as a game participant, constructing a participant strategy set, calculating an income matrix library, setting an environment correction coefficient for each scene, carrying out scene-based game solving, and generating a balanced summary table; a regulation response prediction model is constructed, multiple optimization objectives are set, robustness constraints and expert rules are introduced, candidate regulation schemes are generated, optimal scheme solving is carried out, it is ensured that regulation measures can achieve an expected effect by guiding inter-species competition, and original flora balance is prevented from being damaged.

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 discloses a primer combination developed based on idesia polycarpa whole genome sequencing and application of the primer combination, and belongs to the technical field of molecular biology. The idesia polycarpa primer combination comprises 18 pairs of SSR primer pairs and / or 30 IRAP primers. Through multiple rounds of screening and verification, the idesia primer combination has the characteristics of codominance, high repeatability, high polymorphism, good stability and the like, can be applied to idesia genetic diversity analysis and genetic relationship analysis, and can also be used for idesia and related genus germplasm genetic identification, breeding and the like. The SSR primer pair and the IRAP primer in the primer combination can be used independently or combined for comprehensive analysis, a more reliable molecular marker is provided for idesia genetic diversity analysis and variety genetic relationship analysis, and the primer combination has important theoretical and practical values.

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 discloses a method for screening molecular markers based on apparent annotation information to carry out whole genome selective breeding, which comprises the following steps: step A, carrying out phenotype determination and genome sequencing on growth traits of a litopenaeus vannamei breeding population to obtain phenotype data and SNP (Single Nucleotide Polymorphism) typing data; step B, performing GS analysis by using phenotype data and SNP typing data, predicting a genome breeding value of a breeding population through a mainstream breeding model, and screening out an optimal breeding model; and step C, classifying chromatin states through ChromHMM analysis by combining the optimal breeding model with the key histone modified region, and screening out the functional SNPs with the key histone modified region. The SNPs have relatively strong functional relevance, are used for different regional groups, and can provide more accurate molecular markers for growth character genetic analysis of bred animals by using less SNPs under the same prediction accuracy, so that the accuracy of genetic breeding value estimation and the cross-group effect are remarkably improved, and the breeding process is accelerated.

The invention relates to the field of forensic medicine, and discloses a method and system for identifying smoking behaviors and application of the method and system. The construction method comprises the following steps: respectively obtaining saliva and excrement of a smoking object and a non-smoking object; performing metagenome sequencing to obtain original microbiome data; after processing the original microbiome data, extracting multi-omics feature information, including species information and gene function annotation information; based on a statistical analysis method, carrying out diversity analysis and screening microbial markers and functional genes significantly related to smoking behaviors; constructing a training set and a test set, and training a machine learning model and model evaluation by taking the microbial markers and / or the functional genes as input features; and performing smoking behavior identification on a target sample by using the model, and outputting a prediction result. The accuracy rate of model identification reaches 0.7966, the sensitivity is 0.8750, the specificity is 0.7037, and the method can be applied to health assessment and judicial expertise.

The invention relates to the technical field of medical care informatics, in particular to a respiratory infectious disease risk early warning method and system. The method comprises the following steps: acquiring a respiratory tract sample of a mutant virus infected person; the method comprises the following steps: extracting a mutant virus from a respiratory tract sample, carrying out genome sequencing on the mutant virus, positioning starting and ending positions of a spike protein coding gene in a genome by virtue of a biological information comparison method, extracting a spike protein coding sequence, and translating the spike protein coding sequence into an amino acid sequence; inputting the amino acid sequence into an immune escape prediction model to predict the immune escape score of the mutant virus; and performing risk assessment based on the immune escape score in combination with clinical monitoring information, and outputting a respiratory infectious disease risk early warning value. According to the invention, the risk of respiratory infectious diseases can be early warned better.

The invention relates to the field of plant breeding, and particularly provides a method for fixing rice heterosis by using an OsZFPP gene. The method comprises the following steps: firstly, constructing an OsZFPP1 gene or OsZFPP2 gene expression cassette driven by an OsECA1 promoter; then, an expression box of rice with three target points of OsPAIR1, OsREC8 and OsOSD1 being knocked out of CRISPR / Cas9 is constructed; integrating the expression cassette into the same vector to transform hybrid rice; screening three-gene homozygous mutation and OsZFPP positive plants, and identifying diploid cloned offspring through flow cytometry and genome sequencing. According to the method, the rice OsZFPP gene is combined with MiMe to provide a novel method for fixing the heterosis of the rice through apomixis, the heterosis of the rice can be successfully fixed through the method, an apomixis system with the high maturing rate can be obtained, and a novel solution is provided for fixing the heterosis of the rice through the apomixis.

The invention discloses methanogen lyase with the same protein family annotation as PeiR lyase and application of the methanogen lyase, and the methanogen lyase is obtained through homologous screening of Pfam protein family database annotation based on known PeiR lyase characteristics aiming at methanogen cell wall peptide bonds. The PeiR lyase protein can participate in the biological process of hydrolyzing archaea cell walls, methanogens are effectively killed, methane production is reduced, and the protein homologous with the protein has potential methane reduction potential. According to the invention, by integrating metagenome sequencing data of rumen microorganisms, screening methanogenic bacterium virus protein by using series bioinformatics software, and combining Pfam functional domain annotation to carry out homologous relationship analysis, a series of lyase is finally identified and is successfully expressed in a prokaryotic expression system, and meanwhile, an in-vitro gas production experiment result also shows that the methanogenic bacterium virus protein can be successfully expressed in a prokaryotic expression system. The crude enzyme liquid can significantly reduce the methane generation amount.

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.

This invention relates to the field of medical testing, specifically to a set of biomarkers, reagent kits, and their applications for diagnosing hypertension in children. This invention involves collecting tongue / intestinal samples from obese children with hypertension, obese children, and healthy individuals, performing metagenomic sequencing, and statistically analyzing the sequencing data using bioinformatics to identify disease-related tongue / intestinal flora. By integrating tongue / intestinal flora with disease information, a combination of flora biomarkers is obtained. A binary classification prediction model constructed using this combination can maximally detect hypertension in obese children.

The invention belongs to the technical field of soil heavy metal pollution remediation, and discloses a heavy metal pollution soil bioremediation method and system based on soil metagenome sequencing, and the method comprises the following steps: carrying out gene sequencing on experimental microorganism class groups in heavy metal pollution soil to determine functional microorganisms containing heavy metal resistance genes; heavy metal resistant microorganism species in the soil can be accurately identified by judging whether functional genes are contained or not, and ecological unbalance possibly caused by blind introduction of alien species is avoided; a remediation strategy taking a microbial resistance mechanism as a core can effectively reduce the bioavailability of heavy metals in the soil, and also can improve the physicochemical properties of the soil through metabolic activity to form a sustainable remediation effect; the method has the advantages of being environmentally friendly, controllable in cost, lasting in effect and the like, and an innovative path is provided for soil ecological function restoration.

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.

Genome sequencing identified a new gene associated with a cardiac arrhythmic disease, TAXI -binding protein 3. From cell line models and a conditional knock-out mouse models of the gene deletion, it was found that a specific molecule, transient receptor potential vanilloid 4 (TRPV4), is up-regulated and is associated with calcium mediated arrhythmic depolarizations.

The invention relates to the technical field of bioinformatics, in particular to an analysis method of pathogen metagenome sequencing data, the host background is greatly reduced through two-stage host filtering (especially ML fine filtering), and the detection capacity of low-abundance pathogens is greatly improved and the false negative rate is reduced by combining a low-abundance enhancement module (UMI / denoising); the dynamic database integration ensures that the coverage is wide and newest; a priority ranking algorithm is combined with clinical metadata, so that the ranking of real pathogenic bacteria is effectively improved, and the interference of non-pathogenic bacteria / contaminating bacteria is inhibited; the confidence evaluation of the low-abundance module reduces false positive; dynamically updated databases and intelligent sequencing effectively cope with the problems of new pathogens and incomplete databases, and missing detection is reduced; false detection is reduced through strict denoising, confidence evaluation and interpretation based on clinical rules.