154 results about "Variome" 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 invention provides a vaccine target screening system based on calculation model simulation. The vaccine target screening system comprises a multi-source heterogeneous database, wherein the multi-source heterogeneous database integrates and standardizes pathogenic genes, protein structures, literatures and experimental data; the feature calculation module calls a calculation biological model to carry out structural analysis, immunogenicity simulation and stability prediction; the intelligent screening and sorting module applies a multi-objective optimization algorithm to perform parallel evaluation and outputs optimal target spots; a structure iteration optimizer automatically iteratively corrects the optimized target spots to generate a high-potential variant library; and the process suitability simulation module couples the variants with the preparation formula and the process parameters to simulate production storage behaviors and feeds back an optimization target. According to the invention, efficient screening and optimization of vaccine targets can be realized, the accuracy and efficiency of target screening are improved, the research and development cost is reduced, and the research and development process of vaccines is accelerated.

To improve allele discrimination, the inventors adapted the system combining Cas13a detection sensitivity with allele-specific PCR amplification to propose CASPER (Cas13a Allele-Specific PCR Enzyme Recognition) as a new versatile, easy-to-implement, and highly sensitive method to detect low-frequency of sequence variant. CASPER enabled specific and sensitive detection of KRASG12D with low DNA input such as DNA extracted from patient's pancreatic ultrasound-guided fine-needle aspiration fluids. CASPER is easy to implement and a versatile reliable method virtually adaptable to any point mutation.

A genetic prime editing screening platform to identify functional variants related to human health and disease, is configured substantially to annotate genome with nucleotide resolution with actionable disease prediction and treatment for personalized medicine.

The application discloses a method for quantitatively regulating gene translation and application thereof. The method comprises the following steps: sequencing translation efficiency of Kozak sequences and variants thereof before a start codon of a target gene or before an upstream open reading frame of a non-coding region of the target gene, and performing gene editing on the Kozak sequences according to a sequencing result, so as to realize in-situ manipulation of the Kozak sequences and quantitatively regulate gene translation, and the Kozak sequences and the variants thereof are 3-6 bp in length respectively. The application establishes a highly efficient, flexible and widely applicable gene expression regulation method. By using a precise gene editing tool to customize the Kozak sequences of the target gene in-situ, the expression level of the target gene can be quantitatively controlled at the gene translation stage.

This invention provides the nucleotide and amino acid sequences of the Dip gene, as well as its (functional) homologs, fragments, and variants, which provide ploid sporophyte formation as part of apomixis. It also provides ploid sporophyte-forming plants, methods for their preparation, methods for using them, and methods for preparing apomixis seeds.

The present disclosure relates to an in vitro or ex vivo use of ALDH3A2 downstream noncoding variant, wherein said ALDH3A2 downstream noncoding variant is a sequence identical to a sequence selected from the list consisting of SEQ. ID 2, SEQ. ID 3, SEQ. ID 4, as a biomarker for determining the color phenotype of a Psittaciforme species.

Disclosed herein is one or more subtilisin variant, nucleic acid encoding same, and compositions and methods related to the production and use thereof, including one or more subtilisin variant that has improved stability compared to one or more reference subtilisin.

The invention provides a SpuFz1 variant derived from eukaryotes and application of the SpuFz1 variant in gene editing, particularly provides the SpuFz1 variant and modified omega RNA, and finds that the modified omega RNA and SpuFz1 mutant combination can remarkably improve the editing efficiency and greatly reduce the off-target rate for the first time.

The present disclosure relates generally to (CRISPR) RNA (crRNA) for the precision silencing of transcripts. In some embodiments, the crRNA are enriched for guanosine (G) nucleotides at key spacer positions, which is useful in enhancing the silencing efficacy of otherwise inefficient crRNA, thereby expanding the targeting spectrum of Cas13 endonucleases, e.g., Cas13b and Cas13d. In other embodiments, the crRNA comprise a spacer sequence having at least one nucleotide mismatch relative to the target RNA sequence, wherein the target RNA sequence is a wild-type transcript and / or a variant transcript (e.g., a transcript comprising a single nucleotide variant (SNV)). The present disclosure also provides RNA editing systems comprising the crRNA described herein in complex a Cas13 effector protein and a target RNA sequence, methods for the selective targeting of transcripts encoding proteins that are difficult to target, or are not amenable to pharmacological targeting, e.g., oncogenic fusion transcripts or oncogenic transcripts comprising single nucleotide variant(s), and methods for the design and selection of potent crRNA.

Methods and systems for producing a filtered read sequence information data set by identifying one or more split sequence reads in a set of test sequence reads obtained from cell-free nucleic acid (cfNA) in a biological sample obtained from a subject, wherein each split sequence read comprises at least one breakpoint; and, suppressing, in the set of test sequence reads, (i) at least a portion of one or more of the split sequence reads and / or at least a portion of one or more of the test sequence reads that comprise at least one sequence variant within a selected number of nucleotides from a given breakpoint, thereby producing the filtered sequence information data set, or, (ii) one or more base calls of the split sequence reads and / or one or more base calls of the test sequence reads that comprise at least one sequence variant within a selected number of nucleotides from a given breakpoint, thereby producing the filtered sequence information data set.

The invention relates to an intron variant capable of accurately splicing and enhancing gene transcription and application of the intron variant, and belongs to the technical field of biological breeding, the intron variant is a variant of a Cat1mu intron, the Cat1mu intron has a nucleotide sequence as shown in SEQ ID NO.2, and the nucleotide sequence of the intron variant is formed by mutating base AG at the 182th to 183th sites of the sequence as shown in SEQ ID NO.2 into tG, Ac, At, cG, Aa, ta, tt, tc, cc, ct or ca. According to the present invention, the sequence analysis and the saturation mutation are performed on the Cat1mu, the screening is performed to obtain the Cat1mu series variant Cat1mu2-12, the accurate splicing effect of the Cat1mu2-12 during the fusion gene expression process is verified, and the Cat1mu6, the Cat1mu7, the Cat1mu8 and the Cat1mu10 can further enhance the fusion gene expression effect.

The present invention relates to methods and devices for identification and quantification, including low abundance nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicing, exon insertions, exon deletions, intron insertions, or other rearrangements and / or methylated nucleotide bases at the genomic level.

The invention discloses a promoter mutant and an application of the promoter mutant in production of isoleucine. The invention provides a DNA molecule which is any one of the following: A1) a DNA molecule with a nucleotide sequence as shown in SEQ ID No.2; a2) is a variant which is obtained by substitution, deletion or addition of one or more nucleotides at other positions except the 66th nucleotide in the nucleotide sequence as shown in SEQ ID No.2, and the obtained DNA molecule has the same or enhanced promoter activity. Experiments prove that a series of promoter mutants with different strength and regulation characteristics are constructed to replace natural promoters, so that the transcriptional level of a target gene in a key period of fermentation is accurately improved, and the yield of the target gene is increased. The promoter engineering strategy provides a new direction for improving the production performance of industrial microorganisms by optimizing endogenous stress-resistant elements.

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.

Disclosed herein are methods, systems, and kits for detecting copy number variants in a nucleic acid segment from a genomic DNA sample. In some embodiments, the methods include generating sequence reads from fragments of the genomic DNA sample bound to a flow cell; determining linkage information between the sequence reads based on the geographic location of each fragment on the flow cell and aligning the sequence reads to a reference genome using the linkage information; estimating one or more copy numbers for the nucleic acid segment based on a sequencing depth by applying a correction factor to the sequencing depth, wherein the correction factor is determined based on linkage information; and detecting a copy number variant in the genomic DNA based on the estimated copy numbers.

Disclosed herein are one or more subtilisin variants, nucleic acids encoding the same, and compositions and methods relating to the production and use thereof, including one or more subtilisin variants having improved stability and / or soil removal compared to one or more reference subtilisin.

A machine learning (ML) model may be trained and / or implemented to assist in quality control of variant calls in cohort level sequencing data. A computing device may receive a variant call file comprising cohort level sequencing data during training. Training data may be identified based on a predefined set of features related to genotyping rate or quality distribution. The training data may include positive labeled training data from at least one high-confidence region of the genome for variant calling and / or negative labeled training data from the variants identified from at least one low-confidence region of the genome for variant calling. The training data may be used to train the ML model to predict a machine learning site quality (MLSQ) score. The trained ML model may predict the MLSQ score for each variant. The MLSQ score may be used to filter the variants identified in the cohort level sequencing data.

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.

Provided is use of an endogenous micropeptide in cancer diagnosis or treatment. Particularly, the present invention relates to use of a micropeptide encoded on a long non-coding RNA as a tumor marker, a tumor treatment drug, and / or a tumor treatment target. Specifically, two micropeptides and variants thereof have been discovered for the first time. Moreover, provided are nucleotide sequences encoding the described micropeptides and recombinant vectors containing these nucleotide sequences, and also provided are use thereof in the preparation of a reagent or a drug for diagnosing, preventing, alleviating, or treating a tumor, and use of a drug or a reagent for an interfering micropeptide or a coding nucleic acid thereof in the preparation of a medicament or a pharmaceutical composition for preventing, alleviating, or treating a disease. The micropeptides not only provide biomarkers for the diagnosis of tumors, but also provide therapeutic drugs or therapeutic targets for the treatment of tumors.

Disclosed herein includes a method of determining the RhD genotype of a fetus, comprising: (a) extracting cell-free DNA from a sample of a pregnant person, wherein the extracted DNA comprises a mixture of maternal cell-free DNA and fetal cell-free DNA; (b) performing targeted multiplex amplification on the extracted DNA to amplify a plurality of target loci together in the same reaction mixture using a plurality of primer pairs, wherein at least three of the primer pairs each targets a different exon or intron of the RhD gene and the RhCE homologue gene and is each designed to amplify a target locus that comprises a variant between the RhD gene and the RhCE homologue gene; and (c) sequencing the amplicons by high-throughput sequencing and determine the RhD genotype of the fetus using the sequencing reads of the amplicons targeting the RhD gene and the RhCE homologue gene.

A computer-implemented method for identifying a genomic variant is provided. The method includes obtaining one or more reference molecular sequences and sequencing data pertaining to a biological sample. One or more candidate variant positions are determined from the sequence reads for the biological sample. A classifier model is applied to each candidate variant position for selecting between a haplotype-aware or haplotype-agnostic variant analysis respectively. The classifier model is trained from haplotype structure and / or sequence reads identified with germline variants in a plurality of regions. Based on the application of the classifier model, respectively applying a haplotype-aware or haplotype-agnostic variant analysis to generate a variant identification for each candidate variant position.

The present invention relates to: a composition for validating next generation sequencing (NGS) panels, comprising homozygote DNA and control genomic DNA; a kit for validation of NGS panels, comprising the composition; a validation method for NGS panels through the analysis of false negative variants, limit of detection, and false positive variants; and a method for providing information to enhance the specificity of NGS panels. In particular, the validation method of the present invention enables the objective analysis of the frequency of false negative variants, the frequency of false positive variants, and the limit of detection for NGS panels, making it effectively usable in the validation of NGS panels.

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 disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

Disclosed is a method of providing genetic information analysis results performed by at least one hardware processor. The method may include displaying a user interface configured to provide genetic information analysis results for a specimen. The user interface includes: a list of genes associated with a specific disease in a first region within the user interface; a first browser configured to visualize and search for information regarding a variant obtained from analysis of the specimen in a second region within the user interface; and a second browser configured to search for sequence information obtained from analysis of the specimen in a third region within the user interface. The method may further include displaying, in response to user input received through the user interface, interactive response information comprising details of the genetic information analysis results to at least one region within the user interface.

The present invention relates to base editing using dead uracil DNA glycosylase (dUDG). The present invention is useful for C-to-T base editing in nuclear DNA or organelle DNA, and in particular, is useful for C-to-T base editing in organelle DNA such as chloroplasts or mitochondria. The present invention also relates to a UDG variant and a novel DNA base editing use thereof.

The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.