305 results about "Genetic variation" patented technology

Provided herein are methods of identifying genetic variants in biological samples. In particular, the present disclosure uses spatial transcriptomic templated ligation methods and compositions to identify the presence or absence, and the location of genetic variants in the transcriptome or genome of a biological sample.

Provided herein are methods, compositions, and kits to spatially detect genetic variants in a target nucleic acid via templated-ligation and reversible terminator nucleotides.

This application is directed to multiomic and biomimetic digital twin techniques for identifying disease-specific genetic variants. A computer system obtains information of subject genetic variants that are identified from a plurality of biological samples of a plurality of patients who are diagnosed with a target disease. A subset of subject genetic variants are selected based on a plurality of subject phenotypes of the target disease. The subset of subject genetic variants are ranked based on the plurality of subject phenotypes to generate subject genetic variant information. The computer system further obtains subject medical information of the plurality of patients. The computer system applies a biomimetic information model to process the subject genetic variant information, the subject medical information, and the general genetic variant information of the target disease and identify a set of target genetic variants associated with the phenotype of the disease(s) satisfying a variant selection criterion.

The invention belongs to the field of biological detection, and particularly relates to an ewing sarcoma detection primer group, a kit and application thereof. The Ewing sarcoma detection primer group comprises a primer group A and a primer group B, and totally has 17 primer sequences. The primer group is designed, Ewing sarcoma characteristic variation genes are detected through multiple fluorescent PCR and a high-resolution capillary electrophoresis apparatus, 24 variation types fused by 7 types of genes can be detected at a time, the lowest detection limit is 10 copies, and the shortest detection time is 240 minutes. The detection result of the primer group disclosed by the invention can pass Sanger sequencing verification and is completely consistent with the morphological diagnosis result, the methodological consistency reaches 100%, and a sensitive and efficient Ewing sarcoma genetic variation detection method is provided.

The invention provides a gene detection and phenotype verification health detection method and system, and the method comprises the following steps: collecting multi-source data of a user, locking genetic variation highly related to disease and individual specificity through gene sequencing, and building an individualized genetic risk scoring system; wherein the multi-source data comprises gene sequencing and proteomics data of a user; performing gene phenotype coupling analysis, integrating multi-dimensional data of genes, proteins or phenotypes of the user, and constructing a health assessment system with high confidence; the intervention decision generation is used for generating a decision to intervene the user; through gene-phenotype coupling analysis, the disease risk prediction specificity of healthy people is improved, compared with a conventional health monitoring technology, risks are found in advance, the health behavior compliance rate of a user is increased, seamless connection with mainstream wearable equipment and an electronic medical record system is supported, and the utilization rate of data is increased.

The invention discloses an evidence optimization method and device based on a Bayesian model, computer equipment and a storage medium, and relates to the technical field of medical care informatics. The method comprises the following steps: acquiring a text file containing a variation classification result; calculating posterior probabilities corresponding to 17 evidence combinations given by the ACMG / AMP guide, and when selected evidence combination rules meet posterior probability classification, obtaining theoretical pathogenicity probabilities corresponding to the evidence intensity grades; finely classifying the clinical significance unknown variation VUS into six levels; determining thresholds corresponding to different evidence intensity grades by comparing the positive likelihood ratio or the local positive likelihood ratio with the theoretical pathogenicity probability corresponding to each evidence intensity grade; and the variation is marked with an ACMG / AMP evidence label again, and a pathogenicity classification result of the variation is given. According to the method, the evidence optimization difficulty can be reduced, and the accuracy and consistency of genetic variation interpretation in clinical gene detection can be improved.

Disclosed herein are methods of increasing nitrogen fixation in a non-leguminous plant. The methods can comprise exposing the plant to a plurality of bacteria. Each member of the plurality comprises one or more genetic variations introduced into one or more genes or non-coding polynucleotides of the bacteria's nitrogen fixation or assimilation genetic regulatory network, such that the bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. The bacteria are not intergeneric microorganisms. Additionally, the bacteria, in planta, produce 1% or more of the fixed nitrogen in the plant.

The invention provides a method for constructing a rice epigenetic recombinant inbred line, and belongs to the technical field of molecular biology and genetic breeding. According to the method for constructing the rice epigenetic recombination inbred line, a fertile rice DDM1 gene function weakening mutant is obtained through a CRISPR / Cas9 gene editing technology and hybridized with wild type rice with the same background to obtain F1, then the F1 and the wild type rice are subjected to backcrossing to obtain BC1F1, single-plant offspring selfing with the DDM1 genotype being the wild type is selected, selfing is conducted for multiple generations through a single-grain transmission method, and the rice epigenetic recombination inbred line is obtained. According to the present invention, the strain population with stable inheritance is constructed, such that the rice epigenetic recombinant inbred line is obtained, and has characteristics of rich phenotype, genetic and epigenetic variation so as to provide important population resources for batch identification and the like of important agronomic shape functional sites of rice.

The invention discloses a multi-modal large model fusion training method and system based on a biological evolutionary algorithm, and relates to a method and system for performing fusion and model selection on a multi-modal large model by using a framework of the biological evolutionary algorithm, selecting characteristic parameters and capabilities to form different models, performing fusion training in a manner similar to biological evolution, and obtaining high-performance AI (artificial intelligence). According to the concept, natural selection, genetic variation and other mechanisms in biological evolution are mainly used for reference and applied to the optimization process of an artificial intelligence model, a self-adaptive training system is formed, and the AI performance is continuously improved in continuous iterative training.

To provide an evaluation method for purebred Hu sheep marked with SNP molecules.SOLUTION: Provided is an evaluation method for identifying purebred Hu sheep, which performs genetic variation detection within the whole genome for Hu sheep, Small-tailed Han sheep, Dorper sheep, and hybrid populations of Dorper sheep and Hu sheep by using population-level high-throughput data, and identifies genetic features exclusive to Hu sheep by bioinformatics methods. The method provides a scientific foundation for the conservation, development, and utilization of Hu sheep breed resources.SELECTED DRAWING: Figure 1

The invention discloses a method for obtaining leymus chinensis mutants by using heavy ion beams to irradiate seed calluses, relates to the technical field of leymus chinensis breeding biology, and solves the three-low problems of low heading rate, low maturing rate and low germination rate of leymus chinensis seeds. After the leymus chinensis callus is subjected to induction culture, selecting faint yellow granular callus obtained by induction culture, and transferring the faint yellow granular callus into a culture dish filled with an induction culture medium for subculture; carrying out irradiation treatment by using a 5Gy carbon ion beam, transferring the callus subjected to irradiation treatment into a sterile culture bottle filled with a differential culture medium, and culturing to obtain adventitious buds; cutting off callus adhered to the base under a sterile condition, and inserting into a rooting culture medium for rooting culture after a rooting point is exposed; and after obvious root systems grow out, carrying out potting culture to obtain the leymus chinensis mutant. According to the invention, new genetic variation can be created, early in-vitro selection is realized, more effective mutants are obtained as new germplasm resources of leymus chinensis, and the breeding process of leymus chinensis is accelerated.

The invention belongs to the technical field of molecular biology, and particularly discloses a cotton 10K functional site breeding chip and application thereof. The breeding chip is named as' Cotton Core No.1 ', and comprises a 10K functional site targeting capture probe group designed based on a reference genome of disease-resistant, high-quality and high-yield modern upland cotton No.8, the probe group comprises 11159 SNP (Single Nucleotide Polymorphism) loci, 3981 of the SNP loci are functional loci associated with 13 important agronomic characters, and 7178 of the SNP loci are background loci reflecting genetic diversity; the SNP site information is shown in the specification table 1. The invention discloses a cotton 10K functional site breeding chip and application thereof, the breeding chip contains functional sites with more index function genetic variation, has higher detection accuracy among different cotton varieties, is applied to cotton molecular marker-assisted selection breeding, whole genome selection breeding and whole genome correlation analysis, and has higher detection accuracy. The breeding efficiency can be obviously improved, and the practical application is wider.

The invention discloses a phytolacca americana seed EMS mutation library establishment method, and belongs to the technical field of mutation library construction.The phytolacca americana seed EMS mutation library establishment method comprises the steps that concentrated sulfuric acid is used for pretreating phytolacca americana seeds, then germination accelerating is conducted on the seeds, and the seeds are treated with an EMS solution when the seeds are white, so that the problems that phytolacca americana seed coats are thick, and the sensitivity to EMS is low are solved; according to the mutagenesis method disclosed by the invention, high-density series allele point mutation can be induced and generated, the mutagenesis frequency is relatively high, and meanwhile, chromosome distortion is less caused. In the mutagenesis process, abundant genetic variation can be more efficiently created, and more possibilities are provided for screening mutants with excellent characters. Besides, the method has a remarkable advantage in the aspect of cost, the required chemical reagent is cheap, the experimental operation process is simple, and complicated equipment and technology are not required like common irradiation. The breeding cost is reduced, the working efficiency is improved, and wide popularization and application are facilitated.

The invention provides a morchella sextelata strain pleurospermum hookeri No.5 and application thereof, and relates to the technical field of strain breeding, the morchella sextelata strain pleurospermum hookeri No.5 is subjected to aerospace carrying to induce genetic variation, then characters capable of being stably inherited are screened out through subculture, and the morchella sextelata strain pleurospermum hookeri No.5 is obtained through fruiting screening test screening. The pleurospermum hookeri

The present disclosure provides a systems and methods for processing genetic variations and phenotypic data. The systems and methods may be used to generate one or more databases comprising genetic variations and associations with phenotypes. The system and methods may be used to determine a pathogenicity of a genetic variation. The systems and methods may comprise human interpretation using pre-determined criteria.

Various embodiments relate generally to the field of nucleic acid amplification and detection, in particular loop-mediated isothermal nucleic acid amplification and the detection of amplicons using designed detection probes. Moreover, various embodiments also relate to methods and kits for determining the presence or quantity of point mutations in a target nucleic acid molecule in a sample using loop-mediated isothermal amplification, which may be used for identifying genetic variants. In one aspect, the detection probe is a single-stranded probe comprising a nucleotide sequence fully complementary to a nucleotide sequence of the probe binding site comprising the point mutation. In another aspect, the detection probe comprising a nucleotide complementary to the point mutation at the penultimate base relative to the 3′ end of the detection probe.

The invention relates to a genetic variation interpretation method and device, computer equipment, a readable storage medium and a program product, and the method comprises the steps: obtaining to-be-interpreted genetic data, determining the multi-modal data of a reference corresponding to at least one variation site in the to-be-interpreted genetic data based on a pre-constructed search database, and obtaining the multi-modal data of the reference corresponding to at least one variation site in the to-be-interpreted genetic data; and according to the at least one variation site and the multi-modal data of the corresponding reference, determining a corresponding variation rating evidence and a support basis of the variation rating evidence, and based on an upgrading and degrading strategy corresponding to the variation rating evidence, carrying out upgrading and degrading processing on the variation rating evidence according to the support basis of the variation rating evidence. And obtaining a variation rating result. According to the method, full automation of ACMG literature evidence rating is achieved by automatically reading literature content, and the working efficiency of genetic variation interpretation can be remarkably improved; and the accuracy and the reliability of the final variation rating result can be remarkably improved by performing upgrading and downgrading processing on the variation rating evidence.

The invention discloses a genetic typing chip for synergistically breeding fast-growing and high-temperature-resistant characters of procambarus clarkii and an application method of the genetic typing chip. Aiming at the technical bottlenecks that the traditional procambarus clarkia breeding period is long, the character selection efficiency is low and multi-character collaborative breeding is difficult to realize, a 50K cGPS liquid-phase breeding chip, namely 'Hailongcore No.1', is constructed by taking procambarus clarkia populations of different geographical populations as genetic variation sources; single nucleotide polymorphism molecular markers obviously associated with fast-growing and high-temperature-resistant characters of the procambarus clarkii are screened through whole genome association analysis, and a breeding model is constructed according to the single nucleotide polymorphism molecular markers and is applied to improvement of economic characters of the procambarus clarkii. According to the method, rapid typing of procambarus clarkii individuals can be achieved, the problems that traditional selective breeding is long in period, poor in accuracy, low in efficiency and free of theoretical basis are solved, an efficient molecular tool is provided for improved variety breeding of procambarus clarkii, the breeding efficiency of stress-resistant high-yield new varieties is remarkably improved, and the method has important industrial application value.

The present invention discloses the application of TMPRSS9 gene in the diagnosis and treatment of venous thromboembolism, and belongs to the field of medical diagnosis and treatment technology. The present invention verifies the association between missense mutations of TMPRSS9 gene and thrombophilia in human population, in vivo and in vitro, and draws the following conclusions: nonsense mutations and missense mutations at the sites of c.334C>T, c.692C>T, c.917G>A, and c.1709C>T of TMPRSS9 gene are representative in the effect of TMPRSS9 gene mutation on the occurrence of venous thrombosis. The discovery of the above-mentioned pathogenic gene mutations can prevent and treat thrombophilia at an early stage, which is of great significance for the diagnosis, treatment and management of thrombophilia. At the same time, the inclusion of the new TMPRSS9 gene enriches the genetic variation spectrum of venous thromboembolic diseases, which is of guiding significance for the screening of diseases.

The invention discloses a bidirectional correlation analysis method for gene interaction of plants and pathogenic bacteria and application, and belongs to the technical field of biology. Comprising the following steps: (1) obtaining genetic variation information of a plant, genetic variation information of pathogenic bacteria and an anti-infection phenotype of the plant to the pathogenic bacteria; (2) carrying out forward whole genome correlation analysis, and locating pathogenic bacteria effect factors from plant disease-resistant genes; (3) carrying out reverse whole genome correlation analysis, and locating a plant disease-resistant gene from a pathogenic bacterium effect factor; and (4) disease-resistant genes obtained by forward whole genome correlation analysis and reverse whole genome correlation analysis are the same as the effect factors, and the disease-resistant genes and the effect factors are gene pairs interacting in plants and pathogenic bacteria. The method provided by the invention can efficiently, accurately and simultaneously screen out the interaction gene pair of the plant disease-resistant gene and the pathogenic bacterium effect factor, provides powerful support for analyzing a resistance mechanism exerted by the plant disease-resistant gene, and lays a foundation for cultivating a new variety of durable and broad-spectrum disease-resistant plants.

The present disclosure relates to genetic copy number variation (CNV) detection. Particularly, aspects are directed to sequencing nucleic acid obtained from a biological sample obtained from a subject to generate sequencing data. The sequence reads are ordered by mapping the sequence reads to a reference genome and stored in an ordered format, A global segmentation of the target region is performed based on the stored sequence reads and a set of segments of the target region is identified and used to determine a copy number variation (CNV) metric. A first status of a genetic condition for the subject is determined based on the CNV metric, and a report of the corresponding genetic condition screening test is determined based on the CNV metric and the status.

The invention discloses a monogenic disease genetic variation intelligent interpretation method and device and a medium, and relates to the technical field of bioinformatics, and the method comprises the steps: generating an enhanced similarity matrix through a disease-specific phenotype template and a cosine similarity algorithm based on a standardized phenotype feature vector, and obtaining a dynamic weight vector through a dynamic adjustment function; integrating the dynamic weight vector into a normalized multi-omics data matrix, calculating a preliminary disturbance score through a path integral formalization algorithm, and obtaining a path disturbance score; and fusing the pathway disturbance score and the dynamic weight vector, calculating a pathogenicity score through a multi-level evidence fusion algorithm inspired by a quantum field theory, and generating a comprehensive report of variation pathogenicity grading and clinical suggestions according to a thermodynamic partition function model. According to the method, nonlinear and high-dimensional collaborative modeling and thermodynamic stability optimization of heterogeneous biological evidence are realized, and the interpretability of pathogenicity judgment under a complex genetic background is also improved.

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

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.

Organs-on-chips are microfluidic devices for culturing living cells in micrometer sized chambers in order to model physiological functions of tissues and organs. Engineered patterning and continuous fluid flow in these devices has allowed culturing of intestinal cells bearing physiologically relevant features and sustained exposure to bacteria while maintaining cellular viability, thereby allowing study of inflammatory bowl diseases. However, existing intestinal cells do not possess all physiologically relevant subtypes, do not possess the repertoire of genetic variations, or allow for study of other important cellular actors such as immune cells. Use of iPSC-derived epithelium, including IBD patient-specific cells, allows for superior disease modeling by capturing the multi-faceted nature of the disease.

The invention relates to the field of gene detection, and particularly discloses a gene detection device and method applying Beidou satellite positioning, and the device comprises a sample collection and preprocessing module which is used for obtaining a body fluid or tissue biological sample of a user, and carrying out cell lysis, DNA / RNA extraction and purification operation on the sample; the gene sequencing analysis module is connected with the sample collecting and preprocessing module and is used for performing gene sequencing on the purified nucleic acid sample and identifying gene variation information related to tumors; the high-precision positioning capability of the Beidou system is utilized to obtain the environmental parameters of the geographic position of the user in real time, then the genetic variation data and the regional environmental carcinogenic factors are subjected to weighted fusion analysis through the risk assessment algorithm, and finally a highly personalized detection report is generated. In this way, the detection result can truly reflect the specific influence of the external environment on the individual health, and the accuracy and practicability of the report are remarkably improved.

The invention discloses antisense oligonucleotide for adjuvant therapy of oral squamous cell carcinoma and application of the antisense oligonucleotide. According to the invention, the rs737540 site and the mutant allele rs737540-T thereof are identified, so that the problem of lack of specific biomarkers and targeted therapy means in the prior art is solved. By designing the antisense oligonucleotide aiming at the rs737540 mutation site, selective splicing of TARDBP and EGFR exon 4 can be specifically blocked, and OSCC cell proliferation is inhibited. Besides, the EGFR targeted drug cetuximab is used in a combined manner, so that a stronger anti-cancer effect is realized, and the blank in the existing treatment means is filled. The core breakthrough of the technology is that genetic variation and targeted therapy are combined, and a new research thought and a clinical application prospect are provided for precise medicine of oral squamous cell carcinoma.

Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and / or extended flow cycle orders having five or more nucleotide flows per flow cycle.

Provided herein are computer-implemented methods for assigning maternal or fetal origin to one or more genetic variations in cell-free DNA (cfDNA) of a sample from a pregnant mammal, preferably a pregnant human, it uses a probabilistic model for assigning maternal or fetal origin to genetic variations in DNA from a sample obtained from a pregnant mammal, where the model assigns maternal or fetal origin based on a combination of fetal fraction and DNA fragment size.