264 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.

A method for performing local alignment based on a query sequence of DNA and a reference sequence of DNA includes: obtaining a bit matrix H; determining at least one diagonal based on the bit matrix H; for each of the at least one diagonal, calculating an initial score for the diagonal, determining at least one trace region, determining a sub-alignment for each of the at least one trace region, consolidating the diagonal and the sub-alignment respectively of the at least one trace region to obtain an alignment, and obtaining an alignment score based on the initial score and the partial score respectively of the sub-alignment respectively of the at least one trace region; and among each of the at least one alignment thus determined respectively for each of the at least one diagonal, reserving one of the at least one alignment that has the highest alignment score therefrom.

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.

The present disclosure provides compositions and methods for prime editing with improved editing efficiency and / or reduced indel formation by inhibiting the DNA mismatch repair path way while conducting prime editing of a target site. Accordingly, the present disclosure provides a method for editing a nucleic acid molecule by prime editing that involves contacting a nucleic acid molecule with a prime editor, a pegRNA, and an inhibitor of the DNA mismatch repair pathway, thereby installing one or more modifications to the nucleic acid molecule at a target site with increased editing efficiency and / or lower indel formation. The present disclosure further provides polynucleotides for editing a DNA target site by prime editing comprising a nucleic acid sequence encoding a napDNAbp, a polymerase, and an inhibitor of the DNA mismatch repair pathway, wherein the napDNAbp and polymerase is capable in the presence of a pegRNA of installing one or more modifications in the DNA target site with increased editing efficiency and / or lower indel formation. The disclosure further provides, vectors, cells, and kits comprising the compositions and polynucleotides of the disclosure. The present disclosure also provides compositions and methods for prime editing with improved editing efficiency and / or reduced indel formation with modified prime editor fusion proteins. The disclosure further provides, vectors, cells, and kits comprising the compositions and polynucleotides of the disclosure.

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.

Provided herein are methods for determining allele-specific telomere length (ATL) and telomere variant repeat (TVR) sequences from long read sequencing data. In some embodiments, the methods include clustering telomere reads together into individual alleles using their adjacent TVR regions from which allele-specific TL can then be determined.

Methods for detecting a tumor using a sample in which tumor DNA fragments are present only in a very low concentration, beyond the statistical limit of detection, where methods include: obtaining sequence data for tumor nucleic acid from a tumor from a subject and analyzing the sequence data to identify a plurality of tumor-specific variants that are in the tumor nucleic acid and that are not in non-tumor nucleic acid of the subject; selecting a marker variant that appears duplicated in tumor nucleic acid (compared to non-tumor nucleic acid) a greater number of times than other ones of the tumor variants; performing an assay to detect the marker variant in a sample from the subject; and reporting the presence of the tumor in the subject when the assay is positive for the marker variant in the sample.

The invention discloses a double-CRISPR (clustered regularly interspaced short palindromic repeats) coupled isothermal amplification efficient detection technology, and a double-CRISPR coupled isothermal amplification reagent provided by the invention comprises a pair of efficient Cas12a variant-guide RNA (Ribonucleic Acid) complexes, an isothermal amplification system, bovine serum albumin, a fluorescence resonance energy transfer single-stranded DNA (Deoxyribose Nucleic Acid) probe, a reaction buffer solution and target nucleic acid to be detected, the double CRISPR coupling isothermal amplification detection technology disclosed by the invention has the remarkable advantages of high reaction speed, high signal-to-noise ratio, high sensitivity and strong specificity, can efficiently detect low-copy or low-quality target nucleic acid, and can be combined with a 3D printing chip to realize reagent freeze-drying and simultaneous detection of multiple types of target nucleic acid; the method shows a great application prospect, and particularly has a great potential in detection of bacteria deployed on site.

The present application is directed to a method for identifying at least one candidate (Loc), namely a gene location and / or a sequence variant, indicative for at least one selected (phenotypic) trait of an organism, in particular of a plant, comprising the steps of:a. receiving a plurality of candidate lists (Can1, Can2, Can3) of candidates (Loc), the candidate lists being ordered;b. receiving a reference set (RefDB) with gene locations and / or sequence variants;c. matching at least a subset of candidates (Loc) from the candidate lists (Can1, Can2, Can3) with the reference list (RefDB) to determine an evaluation value (EV) for at least the subset;d. assigning each evaluation value (EV) to the respective candidate (Loc) in the respective candidate lists (Can1, Can2, Can3);e. calculating for each candidate list a performance value based on the evaluation value (EV), in particular by using the evaluation values (EV);f. selecting at least one candidate (Loc) as (preferred) candidate (Loc) from one of the candidate lists (Can1, Can2, Can3) using the performance values.

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 disclosed embodiments concern methods for determining sequences of interest using targeted unique molecular index (TUMI) sequences that are uniquely associated with individual polynucleotide fragments in plants, such as those present in a transgenic event, a site-specific mutation or a wild type variant. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

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.

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.

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 are disclosed for adding adapters to fragmented nucleic acids for next generation sequencing, including providing numerical codes based on variable adapter molecular barcode lengths on both sides of the fragmented nucleic acids and identifying reads from the same fragment based on both barcodes. The methods and products allow for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids and also for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject.

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 invention relates to a computer-implemented method for predicting a genome-related feature (458) from genomic data of multiple individuals (402), the method comprising: —receiving (102) genomic marker data (434, 442) of each of the individuals, the genomic marker data being indicative of a plurality of first marker positions assigned to identified marker variants (1140-1142) and multiple second (1144) marker positions have a missing or ambiguous marker variant assignment; —computing (104) a haplotype-block library (448) comprising a plurality of haplotype-blocks (1126-1136), each haplotype-block comprising start and stop coordinates and a series of marker positions referred to as ‘comparison marker positions’ lying within the start and stop coordinates; —performing (106) a haplotype-block-guided marker imputation; —supplementing (108) the genomic marker data with the imputed marker variants; and—using the supplemented genomic marker data (454) for computationally predicting the feature (458) of the individuals.

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.

The present invention provides a, preferably fully automated and / or multiplex, method for the simultaneous detection of a plurality of molecular genetic analytes in a collective and continuous reaction set up and at least one analyte specific oligonucleotide TX probes with a cleavable hydrolysis product for use in said method. Through the method the plurality of cleavable hydrolysis products is specifically released by a nuclease from the respective TX probes. Following a separation step, preferably in a capillary electrophoresis, for each hydrolysis product a clear and distinguishable from others signal is achieved. Each separated hydrolysis product respectively results in a signal enabling the qualitative and / or quantitative detection of each analyte comprising a molecular variant, e.g. single nucleotide polymorphism (SNP), deletion-insertion polymorphism (DIP) or other, respectively, that was targeted specifically by the plurality of TX probes. Preferably, the method is suitable to detect qualitatively and / or quantitatively small molecular variants as such SNP.

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.

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.

The present invention relates to a peptide of 12 to 30 amino acids, said peptide comprising the sequence SEQ ID NO: 1 represented by:(SEQ ID NO: 1)V-X1-X2-R-X3-E-W-X4-X5-X6-Y-W,wherein each of X1, X2, X3, X4, X5, and X6 independently corresponds to any amino acid, andwherein said peptide binds to the EGF receptor variant III (EGFRvIII), as well as products incorporating such peptide and uses thereof.

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.