61 results about "Genetic variants" patented technology

A system and method for processing genomic data using dynamic latent manifolds that transforms multi-modal genomic datasets into geometric representations within a curved manifold space. The system receives genomic datasets including DNA sequences, genetic variants, and expression data, then extracts biological features and assesses importance using trained neural networks. Manifold curvature values are computed based on biological significance, and genomic data is embedded as geometric structures where semantic relationships are represented through distance and curvature properties. The system generates compression pressure fields that influence processing decisions and computes optimal geodesic paths through the manifold to minimize cognitive action functionals. Adaptive compression rates are determined for different genomic regions based on geometric properties and biological importance. The manifold structure evolves through use, strengthening frequently accessed pathways while applying thermodynamic decay to unused concepts. The system supports hierarchical organization across biological scales, reversible navigation, and federated learning capabilities that enable privacy-preserving collaboration.

The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subject's genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.

Examples may use pathogenicity evidence data associated with genetic variants and health conditions to create input data for a causal machine learning model. Examples may apply a causal machine learning model to input data to produce a trained causal model. A graphical representation of the trained causal model may include nodes connected via acyclic directed edges. A first node of the nodes may represent a pathogenic evidence variable associated with the health condition. The at least one second node may represent a cause of the pathogenic evidence variable. The at least one third node may represent the impact of the pathogenic evidence variable. The non-cyclic directed edge may represent a relationship between two nodes. Examples may output prediction data sampled from the trained causal model.

Described herein are methods for making genetically modified cells by introducing combinations of genetic variants (designed or random) or constructs (genes or otherwise arbitrary DNA) into a population of cells, and for tracking each variant combination by sequentially building an array of barcodes at a common locus (chromosomal or plasmid), termed the barcode locus. Also described are the cells made by such methods.

The invention relates to a computer-implemented method for determining pharmacogenetic star alleles from high-throughput sequencing data, the method comprising the following steps: providing a plurality of result files which have been output by a plurality of different computer programs for genotyping and which each have a plurality of result elements, wherein each result element has at least one gene designation; shortening the allele designation as far as possible on the right for each result element of the plurality of result elements from each result file of the plurality of result files; and outputting the gene designation and a specific result diplotype. The invention also relates to a computer-implemented method for determining rare genetic variants. Finally, the invention also relates to a device having a processor and a memory in order to carry out such methods.

Systems and methods herein provide for rapid patient information to healthcare providers such that the healthcare providers can make more informed diagnoses. One method includes storing gene sequencing data and called genetic variants of a patient in a data structure. The method also includes receiving a request from a healthcare provider for results of a test that reports at least a portion of the called genetic variants in relation to a diagnosis of the patient by the healthcare provider, and delivering the results of the test to the healthcare provider if a quality control value of said at least a portion of the called genetic variants meets or exceeds a predetermined threshold of quality for assisting the healthcare provider.

Methods and apparatus for selecting genetic variants for a tumour-informed assay are provided. The method includes receiving a sample collected from a patient, the sample being associated with a cancer type, generating a mutational catalogue for the sample, the mutational catalogue indicating a proportion of genetic mutation types observed in the sample, selecting a set of signatures associated with the cancer type, the set including one or more signatures, each signature comprising a mutational profile, determining, based on the set of signatures associated with the cancer type and the mutational catalogue, a set of genetic variants most likely to be genuine somatic variants associated with the sample, and outputting the set of genetic variants for use in creating a tumour-informed assay for the patient.

Disclosed are methods, systems and computer-program products for the determination of complex genetic variants. The disclosed methods, systems and computer-program products may include obtaining a mutant scaffold nucleotide sequence that comprises a sequence that includes mutations characteristic of the complex genetic variant; obtaining a wild-type scaffold nucleotide sequence having a wild-type sequence; generating an alignment of at least one sequence from the sample to the mutant scaffold and to the wild-type scaffold; and determining that the sample contains a mutation characteristic of the complex genetic variant based on alignment to the mutant scaffold and not the wild-type scaffold.

An apparatus for generating personalized risk assessments for neurodegenerative diseases includes a computing device that receives user data containing genetic and medical information. It processes the data to create genotype identification and gene detection modules, identifying user genotypes and relevant genetic markers. The user's mitochondrial haplogroup is examined to refine the assessment. A risk calculation module employs machine learning to weigh genetic variants against population-based data, calculating a polygenic risk score (PRS). The PRS forms a personalized risk profile, displayed through a visual interface. The disclosed systems offer a comprehensive approach to accurate risk assessment, enabling targeted interventions and informed decision-making in neurodegenerative disease management.

The present invention refers to an in vitro method for predicting whether cattle are susceptible or resistant to paratuberculosis (PTB), or for classifying and / or selecting cattle according to whether they are susceptible or resistant to PTB; and / or for preventing susceptibility to PTB or to increase resistance to PTB.

The disclosure relates to analysing genetic data. In one arrangement, a method operates on input data comprising strengths of association between one or more phenotypes including a target phenotype and a plurality of genetic variants. A fine-mapping algorithm is applied to all or a subset of the input data to identify one or more independent phenotype-variant associations. A set of one or more fine-mapped variants is identified for each association. A fine-mapping predictive model is calculated on the basis of the input data and the set of fine-mapped variants. The effect on the target phenotype of the set of fine-mapped variants is subtracted from the input data to obtain residual association data. A machine learning algorithm is applied to the residual association data to identify further predictive correlations between the target phenotype and the plurality of genetic variants.

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

The present disclosure provides, in part, a method of identifying genetic variants in an embryo. The method comprises: (a) obtaining two or more analyte sources from the embryo; (b) analyzing the two or more analyte sources to obtain genetic information for each source; (c) comparing the genetic information for each source to one or more reference genomes using at least one variant call program, wherein the variant call program identifies variants between each source and the reference genomes; and (d) combining the variants to identify the difference presented only by the source, wherein the difference is a genetic variant in the embryo.

The invention relates to a method for detecting changes of nucleotide sequences by using an isothermal nucleic acid amplification technology, a primer set for detecting selected genetic variants and components of a reaction mixture.

The present invention relates to a vascular endothelial growth factor (VEGF) inhibitor for use in the treatment of wet macular degeneration, wherein the VEGF inhibitor is adapted to be administered intravitreally to a patient, wherein the patient has previously been treated intravitreally with the VEGF inhibitor for approximately one year, and has one or more genetic variants that are single nucleotide polymorphisms selected from rs2106124, rs1879796, rs12148845, rs12148100, rs17482885, and rs17629019.

Bag3 is a multifunctional protein expressed predominantly in the heart, the skeletal muscle, the central nervous system and in many cancers. Although BAG3 was cloned only a decade ago, studies have shown that genetic variants, particularly those that result in haplo-insufficiency, can lead to severe left ventricular dysfunction; however, the full mechanisms responsible have remained obscure. To obviate the influence of heart failure itself on the biology of Bag3, transgenic mice harboring a single allele knock-out were studied between 8 and 10 weeks of age before any obvious signs of heart failure were evident. The results were surprising and informative. First, it was found that despite a normal phenotype, young Bag3+ / − had marked changes in the proteome that were characterized by changes in proteins associated with metabolism and apoptosis. Consistent with this finding, a decrease in the levels of critical proteins charged with maintaining the mitochondrial membrane potential was observed. It was also found that young mice shifted from a balance between the extrinsic and intrinsic pathways of apoptosis. However, in the presence of stress and the absence of Bag3 there was a shift from a balanced to an extrinsic dominant system (cleaved caspase 8). The diverse array of critical pathways regulated by Bag3 suggests a more important role especially during stress and that this role might include serving as an intracellular glue that holds proteins where they can be most effective rather than having them meet accidentally.

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.

This invention discloses a method and system for selecting functional gene variant sites, relating to the field of gene site selection. The method includes: acquiring chromatin accessibility distribution information across the entire genome; performing convolutional block transformation based on the accessibility distribution information to obtain accessibility feature values; determining genomic information across the entire genome based on regulatory maps; determining an initial weight value set based on the accessibility feature values ​​and genomic information; the initial weight value set is a set of initial weight values ​​corresponding to each of the accessibility feature values ​​and genomic information; inputting the accessibility feature values, genomic information, and the initial weight value set into a site selection model, and outputting selected functional gene variant site information and regulated susceptibility gene information; the selected functional gene variant site information includes: site variant bases that meet set threshold conditions and their corresponding site coordinates; this invention can improve the selection efficiency of functional gene variant sites.

The present invention provides to an improved high-throughput system and method for generated and screening of genetic variants by combinatorial modifications. Also provided are optimized SpCas9 enzyme variants produced by this system.

The present application relates to a gene mutation and phenotype information association analysis method and system, belonging to the technical field of automatic medical analysis. The method comprises the following steps: S1: obtaining a high-frequency pathogenic gene mutation white list; S2: obtaining genotype data of the object to be analyzed, comparing with the gene mutation in the white list, taking the intersection, and obtaining the high-frequency pathogenic gene mutation; S3: obtaining the high-frequency pathogenic gene mutation and the phenotype information of the object to be analyzed, performing high-frequency pathogenic gene mutation association analysis, and obtaining the associated high-frequency pathogenic gene mutation set; S4: obtaining the genotype data and the phenotype information of the object to be analyzed, performing conventional association analysis, and obtaining the associated gene mutation set; S5: obtaining the associated high-frequency pathogenic gene mutation set and the associated gene mutation set, taking the union, and outputting the gene mutation list in the union, which is the candidate pathogenic gene mutation list. The method can solve the problem of false negatives in conventional analysis methods (software).

Described herein is an improved method of treating a patient in need of such treatment with iloperidone or an active metabolite thereof wherein the patient has a gout history or carries a genetic variant associated with an increase in serum uric acid concentration induced by iloperidone. The improved method comprises monitoring a serum uric acid level of a patient; when the serum uric acid level of the patient exceeds a reference level, a uric acid lowering treatment is initiated or a dose thereof is increased.

The invention discloses a method for inducing litchi girdling callus and peripheral bud differentiation in a field, and relates to the technical field of plant propagation, the method comprises the following steps: cutting off the top of a trunk branch of a litchi growing vertically, and carrying out spiral girdling below the section of the top until the girdling depth reaches a wood layer; soaking absorbent cotton in a bud differentiation inducer to obtain an induction matrix; after the top section and the girdling opening of the litchi branch are covered with the induction matrix, bud differentiation treatment is conducted on the litchi branch; after bud differentiation treatment is completed, the litchi branches are subjected to moisture preservation and light shielding treatment, and adventitious buds are obtained. According to the method, wound induction is directly carried out on the litchi plants in the field, the browning problem in the in-vitro culture process is avoided by utilizing a plant self-repairing mechanism and combining with local medicament treatment, adventitious bud differentiation around girdling openings is promoted, a stable material source is provided for field screening of the polyploidy plants, the equipment and labor cost is reduced, and the method is suitable for large-scale popularization and application. Meanwhile, the survival rate of genetic variants is improved.

A system and method for determining a respective carrier status of an individual is provided. In one implementation, a method includes training a neural network model based on predetermined information related to at least one genetic variant and determining the respective carrier status based on a normalized read depth for the gene in a genome of the individual and allele dosage data for the gene using a machine learning algorithm. The method is configured to receive, as inputs, the normalized read depth and allele dosage data, and output the respective carrier status of the individual for the at least one genetic variant. In another implementation a system includes a recurrent neural network. The recurrent neural network includes a plurality of long short-term memory (LSTM) network cells linked sequentially in the recurrent neural network, a plurality of layers of long short-term memory (LSTM) network cells; and a fully connected sigmoid module.

Methods for correlating a genetic variant with intraretinal fluid as a marker of response to anti-VEGF therapy in age-related macular degeneration (AMD). Further methods for correlating a genetic variant with visual acuity, anatomical outcomes, or treatment frequency are disclosed herein. The genetic variants identified were found in a non-gene region on the X chromosome p.22.3 in the MICOM gene in the NTRK3 gene and in the ANK2 gene.

The present disclosure provides methods and systems that can ascertain how genetic variants impact molecular phenotypes. Such methods and systems may use additional conservation information. In an aspect, the present disclosure provides a method for training a molecular phenotype neural network (MPNN), comprising: (a) providing a molecular phenotype neural network (MPNN) comprising one or more parameters; (b) providing a training data set comprising (i) a set of one or more inputs comprising biological sequences and (ii) for each input in the set of one or more inputs, a set of one or more molecular phenotypes corresponding to the input; (c) configuring the one or more parameters of the MPNN based on the training data set to minimize a total loss of the training data set, thereby training the MPNN; and (d) outputting the one or more parameters of the MPNN.

The invention provides a method for the automated calculation of the reproductive risk of genetic disorders from Next Generation Sequencing (NGS) data of male and female subjects. The method includes (i) online data collection from male and female subjects; (ii) processing raw sequencing data to detect genetic variants; (iii) assessing variant pathogenicity using a scoring metric that comprises multiple types of supporting evidence; (iv) text mining of male and female family history and phenotype description; (v) association of genetic disorders to the identified pathogenic variants based on a comprehensive database with automated updating functionalities; (vi) calculation of the reproductive risks using data from male and female subjects; (vii) digital report generation. The method enables efficient and accurate identification of pathogenic variants in a wide range of gene-disease associations, which can be scaled in a computer system.

The present application relates to a kind of ankylosing spondylitis polygenic risk score processing method, its main features are, the method includes the following steps: (1) the whole genome data of patient is collected, and it is carried out corresponding data preprocessing;(2) according to the preset proportion, the patient data and healthy control data obtained are divided into training set and test set, determine the association effect value between each genetic variant and ankylosing spondylitis AS, and obtain the corresponding association site;(3) extract the single nucleotide polymorphism SNP associated with ankylosing spondylitis AS, and the polygenic risk score PRS of individual is calculated using the weighted summation method;(4) the ankylosing spondylitis AS risk assessment of corresponding patient is carried out according to the polygenic risk score PRS obtained by calculation.This ankylosing spondylitis polygenic risk score processing method of the present application provides an ankylosing spondylitis related genetic variation and onset risk assessment system suitable for east Asian population.

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

Disclosed herein are methods and compositions for associating a genetic variant with intraretinal fluid. Also disclosed herein are methods and compositions for associating a genetic variant with visual acuity, anatomic outcomes or treatment frequency.

Provided are methods for determining a disease risk associated with an embryo that comprise constructing the genome of the embryo based on (i) one or more genetic variants in the embryo, (ii) a paternal haplotype, (iii) a maternal haplotype (iv) a transmission probability of the paternal haplotype, and (v) a transmission probability of the maternal haplotype; assigning a polygenic risk score to the embryo based on the constructed genome of the embryo; determining the disease risk associated with the embryo based on the polygenic risk score; and determining transmission of disease causing genetic variants and / or haplotypes from the paternal genome and / or maternal genome to the embryo. Also provided are methods of determining a range of disease risk for potential children for a mother and a potential sperm donor. Also provided are methods of determining disease risk in an individual.