45 results about "Sequence variation" patented technology

The invention discloses a DNA sequence reconstruction method and system based on multi-scale attention and contrast learning, and relates to the technical field of DNA storage data reconstruction. Comprising the following steps: collecting a plurality of DNA sequence copies, screening out abnormal length sequences, and constructing a standardized clustering data set; performing one-hot coding and filling processing on the DNA sequence; extracting context dependent features and cross-sequence variation features; an Inter-Sequence multi-head attention mechanism is constructed to calculate the similarity between the sequences, and a weighted sequence tensor is generated; a global dependency relationship in the sequence is extracted through an Intra-Sequence multi-head attention mechanism; local offset features caused by insertion and deletion errors are extracted through a multi-size convolutional network; inputting a double-layer long-short-term memory network for sequence-level modeling, and outputting base reconstruction probability distribution; and constructing positive and negative sample pairs, calculating comparison loss, combining cross entropy loss to form a joint loss function, and outputting a high-precision DNA sequence reconstruction result. The method has high accuracy and robustness under the conditions of complex noise and multiple types of errors.

An information processing apparatus selects a target sequence variation possessed by a subject and having a risk of being harmful. The information processing apparatus includes a filtering unit that classifies one or more sequence variations specified by sequencing a nucleic acid included in the subject into different categories according to a degree of risk of being harmful on the basis of one or more classification criteria, and a control unit that classifies a base sequence including a sequence variation of which a category to which the sequence variation is to belong is known into each of the categories according to the degree of risk of being harmful on the basis of at least one of the classification criteria, and compares a classification result with the category to which the sequence variation is to belong, an information processing method, and an information processing program.

The present invention relates to an information processing apparatus, an information processing method, and an information processing program relating to genetic information. Provided are an information processing apparatus that selects a target sequence variation possessed by a subject and having a risk of being harmful, the information processing apparatus including a filtering unit 2 that classifies one or more sequence variations specified by sequencing a nucleic acid included in the subject into different categories according to a degree of risk of being harmful on the basis of one or more classification criteria, and a control unit 3 that classifies a base sequence including a sequence variation of which a category to which the sequence variation is to belong is known into each of the categories according to the degree of risk of being harmful on the basis of at least one of the classification criteria, and compares a classification result with the category to which the sequence variation is to belong, an information processing method, and an information processing program.

The invention relates to a full-length sequence amplification primer, an amplification method and a three-generation sequencing method of an HLA-I antigen gene, and belongs to the field of gene detection. The HLA-I antigen gene is subjected to PCR (Polymerase Chain Reaction) amplification by using 8 pairs of characteristic amplification primers. And each gene can be subjected to high-yield specific amplification on a full-length sequence containing complete intron and exon regions only through one round of amplification and enrichment, and 7.8 Kb long-fragment genes can be captured once at most. The experimental deviation caused by simultaneous amplification of a single gene by using a plurality of pairs of segmented primers and the indirect error caused by gene splicing are effectively avoided. The method comprises the following steps: carrying out quality inspection and purification on amplicon PCR (Polymerase Chain Reaction) products, mixing samples, constructing an HLA-I type antigen gene library, carrying out accurate and complete sequencing on the full-length sequence of the HLA-I type antigen gene by adopting a three-generation PacBio Sequel II platform, and ensuring that the Hifi reads base accuracy can reach 99% or above. The reading of HLA-I type antigen gene full-length sequence variation information and the haplotype analysis at a high resolution level can be realized.

Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and / or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.

A method of enhancing grain yield of a Gramineae plant is provided. The method comprises:(a) crossing a recipient plant with a donor plant comprising a sequence variation in a TPR allele, said sequence variation imparting enhanced grain yield; and(b) selecting a progeny plant of said crossing comprising said sequence variation by identifying said variation, said progeny plant being characterized by an improved grain yield relative to said recipient plant. Also provided are plants and processed products resultant of the method.

The present invention pertains to a method for determining DNA sequence variation in a fetus from samples of the fetus and parents using a Bayesian framework. The method comprising the following steps: receiving the samples comprise genomic sequence data covering one or more genomic regions of interest in relation to the fetus and the parents; processing the received samples at least in part based on a reference genome; computing a probability of fetal genotypes based on the samples using the Bayesian framework, where the Bayesian framework computes a posterior probability of whether a DNA sequence variant is present in the samples based on a prior probability and a likelihood function; and determining, based on the posterior probability of fetal genotypes, whether the DNA sequence variant is present in the fetus.

The present invention provides a method for detecting single-cell gene sequence variation in rice and its application, which belongs to the field of agricultural technology. The method of the present invention mainly includes three aspects: sampling, sequencing and bioinformatics analysis, wherein the sampling is to obtain a single rice microspore sex cell. The present invention successfully isolates a single rice microspore sex cell, and improves the defects of the existing rice single-cell variation detection technology process, such as weak integrity and detection consistency that need to be improved. In addition, the authenticity of the mutation site is identified and confirmed by heavy ion mutagenesis technology. The method of the present invention broadens the source range of rice single-cell mutagenic materials, and provides new ideas and methods for creating more diverse breeding materials and conducting more efficient mutagenic breeding. At the same time, microspore sex cells serve as male gametes, and the mutations carried in the genome can be passed into the offspring through hybridization, which can realize the inheritance and fixation of mutations, and also provide a way to quickly utilize excellent mutant genes.

The invention relates to the field of molecular biology diagnosis, in particular to a detection kit for SMN1 and SMN2 gene sequence variation, and gene variation types mainly comprise SMN1 and SMN2 gene point variation, insertion and deletion variation in a gene range and the like. The kit provided by the invention can realize detection and diagnosis of SMN1 and SMN2 point variation, small insertion and deletion, sequence variation of SMN1-SMN2 partial transformation types, structural recombination in genes and the like.

The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

The invention discloses a hybrid production flexible assembly job shop scheduling method considering multi-assembly sequence change and transportation tasks based on a Q-Learning model algorithm. The method comprises the following steps: S1, establishing a scheduling model taking total production completion time, total inventory time and total manpower cost as optimization targets; s2, providing a Q-Learning memetic algorithm to solve the scheduling model, designing a five-layer segmented mixed chromosome coding structure and a two-subgeneration chromosome updating method, and introducing a variable neighborhood search strategy and an elite retention strategy; s3, adaptively adjusting the cross range of the chromosomes through Q-Learning to improve the algorithm efficiency; and S4, through comparison with other three algorithms, validity and robustness of the proposed algorithm are verified. Based on the scheduling method provided by the invention, the processing and assembling sequences of product parts can be optimized simultaneously in the scheduling process of multi-product mixed production and consideration of transportation tasks, and meanwhile, machines, workers and AGV resources are reasonably allocated, so that the production cycle of products is effectively shortened.

A method for sequence variant detection using deep learning is disclosed. This disclosure provides methods, systems, and computer program products for accurately and effectively detecting variants in biopolymer sequencing data, particularly suboptimal sequencing data, using embeddings of candidate variant information and deep learning models.

Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3′ ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.

Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and / or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.

Methods and systems are provided for validating variant calls. Sequencing data is received for a sample read along the genomic sequence of interest. An indication is received of a potential variant call at a designated position within the sequence of nucleotides along the genomic sequence of interest. The methods and systems obtain baseline variant frequencies at the designated position within one or more baseline genomic sequences, determine a sample variant frequency at the designated position for the genomic sequence of interest, analyze the baseline and sample variant frequencies at the designated position to obtain a quality score, and validate the potential variant call for the genomic sequence of interest based on the quality score.

The present disclosure relates to methods and compositions for the approximately simultaneous amplification of RNA / cDNA and genomic DNA. The present disclosure further provides methods of producing an RNA library for transcriptome analysis and a DNA library for DNA sequence variation analysis. The present disclosure further provides methods of identifying a DNA sequence variation or a transcriptome variation in a sample. Aspects of the present disclosure further relate to a DNA library or RNA library produced by the methods of the present disclosure.

The invention discloses a CAPS molecular marker developed based on a ZmMYB24 gene and related to salt resistance and low temperature resistance of corn and application of the CAPS molecular marker. Sequence variation of a ZmMYBR24 gene coding region induced and expressed by salt stress and low-temperature stress in different corn homozygous inbred lines is analyzed, correlation analysis is carried out on salt tolerance and low-temperature resistance of the corn homozygous inbred lines, correlation sites are mined, and then the CAPS molecular marker related to salt tolerance and low-temperature resistance of corn is developed and named as CAPs814. The molecular marker CAPs814 is used for marker-assisted selection, the average detection efficiency in identification of maize inbred lines with medium salt resistance and medium low temperature resistance or above is 80.56% and 86.11% respectively, and the molecular marker CAPs814 provides a new technical means for screening maize materials with medium salt resistance and low temperature resistance.

The present invention provides a nucleic acid carrier, a nucleic acid drug, and a preparation method and application thereof. The nucleic acid carrier contains sequences a, b, and c, and the nucleic acid carrier is selected from DNA, RNA, or a DNA-RNA hybrid carrier; sequences a, b, and c self-assemble to form the nucleic acid carrier, and sequences a, b, and c include a backbone sequence including the following core sequences: the a1 sequence shown in SEQ ID NO: 1 or 4, the b1 sequence shown in SEQ ID NO: 2 or 5, and the c1 sequence shown in SEQ ID NO: 3 or 6, or any variant sequences of at least one of the a1 sequence, b1 sequence, and c1 sequence, and the variant sequences include insertions, deletions, or substitutions of at least one base; the DNA-RNA hybrid carrier is a carrier self-assembled from a combination of the sequence of the DNA carrier and the sequence of the RNA carrier. This carrier has high delivery efficiency, a more stable delivery system, and is also simpler and more efficient in the preparation process.

The invention relates to the technical field of biological information, and discloses a virus host prediction model and a training method and device.The virus host prediction model comprises a basic model and a classification model, and the basic model comprises an autoregression pre-training model and a low-rank adaptation unit inserted into the autoregression pre-training model; on the basis of the human genome sequence, the sequence characteristic relation of the genome is learned in an autoregression mode, and the sequence characteristic relation is represented as the general representation of the gene sequence; furthermore, a low-rank adaptation unit is added when transfer learning is carried out on the autoregression pre-training model, and the low-rank adaptation unit continuously learns subtle features which are difficult to perceive in a virus sequence by utilizing a causal relationship before and after a gene sequence, so that the sensitivity and the adaptability to virus sequence variation are improved. The virus host prediction model has good generalization ability after being fully trained, and can perform effective potential host prediction on unknown or new virus sequences.

The present invention discloses a specific primer ZMEH_1 for identifying or assisting in identifying the heading date of rice materials and use thereof, and a breeding method of rice cultivars with early-heading without yield drag. The ZMEH_1 is a pair of PCR primers corresponding to the upstream and downstream of the fragment with sequence variation 1 of the rice Os03g0122600 gene between the late- heading parent MH63 and the early-heading parent DEH229. ZMEH_1 can explain about 86.0% of the phenotypic variation of the progeny from the MH63 / DEH229 population, which meets the needs of industrial applications. DEH229 has the characteristic of early-heading without yield drag, and its progenies derived from various rice cultivars all continue to have the characteristic of early-heading without yield drag. The specific primer ZMEH_1 can be used to quickly screen out the materials with early-heading characteristic among the progeny rice materials derived from DEH229, and carry out rapid breeding and utilization to promote the breeding process of early-maturing rice without affecting the yield.

The invention relates to the field of biological medicine, and discloses an integrated genome analysis method based on low-depth sequencing, and the method comprises the following steps: obtaining whole genome low-depth sequencing data; after quality control and comparison, SNV, Indel and CNV are calculated; performing multi-dimensional function annotation by combining genome position, coding influence, splicing disturbance, conservative property, regulatory element and three-dimensional chromatin interaction; database information such as ClinVar and HGMD is integrated, and according to a phenotype-driven rule engine, a clinical interpretable report is generated according to the ACMG / AMP standard. According to the method, a complete analysis chain covering sequence variation detection, multi-dimensional function annotation, three-dimensional genome association, public database integration and phenotype driven interpretation is constructed, so that the fundamental defect that only an original variation list is output and a clinical action basis cannot be provided in traditional low-depth sequencing is overcome.

Provided herein is method for, among other things, estimating the number of sequence variations in a sample of DNA. In some embodiments, the method can be used to estimate the mutational load of a sample. In some embodiments, the method makes use of a set of primers that have 3′ ends that specifically hybridizes to a sequence that is repeated multiple times in the genome. Thermocycling a reaction mix containing the primers may produce a reaction product comprising at least 50 amplicons having a total length of at least 100 kb. This product can be sequenced to provide an estimate of the number of sequence variations in the sample, and thus the mutational load of the sample.

The present disclosure relates to methods and compositions for producing a DNA sequencing library for one or more DNA sequences of interest using a k-mer analysis strategy. The present disclosure further provides methods of producing a DNA library for analysis of one or more DNA sequences of interest and methods of identifying a DNA sequence variation or a modification in a DNA sequence of interest. Aspects of the present disclosure further relate to a DNA library produced by the methods of the present disclosure.

The invention provides novel methods for evaluating levels of microsatellite instability in a sample and evaluating the biological significance of sequence variations identified in a sample during sequencing. The invention further relates to the use of novel microsatellite instability markers for evaluating levels of microsatellite instability in a sample and evaluating the biological significance of sequence variations identified in a sample during sequencing. Corresponding kits are also provided.

Provided herein is a method for the analysis of minimal residual disease, the method comprising obtaining multiple pairs of primers, performing a targeted multiplex amplification using the multiple pairs of primers to produce amplicons, sequencing the amplicons or an amplification product thereof, thereby generating sequence reads, calculating a score based on the minority of sequences containing identified sequence variations, and using the calculated score to determine the presence or absence of minimal residual disease in the patient.

In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.

Disclosed are methods for detecting a single nucleotide variant in a tissue sample. The methods comprising; a) obtaining or having obtained the tissue sample, wherein the tissue sample comprises DNA, non-RNA molecules, and RNA, wherein the RNA comprises a single nucleotide variant; b) permeabilizing the tissue sample; c) substantially degrading the DNA in the tissue sample; and d) introducing to the tissue sample a primer or a probe specific to the single nucleotide variant, wherein the primer or probe binds to the single nucleotide variant; and e) detecting the primer or probe bound to the single nucleotide variant, thereby detecting the single nucleotide variant in the tissue sample.

The invention belongs to the technical field of molecular biology, and particularly relates to a transcriptional activation domain AD, an artificial transcription factor and application thereof. The invention provides a transcriptional activation domain AD. A skeleton sequence of the transcriptional activation domain AD comprises: (1) at least one core sequence 1-5 as shown in SEQ ID NO.11-15; and (2) a variation sequence of at least one of the core sequences 1-5, wherein the variation sequence and at least one of the core sequences 1-5 have at least 98% sequence consistency. The transcriptional activation domain AD provided by the invention can be subjected to fusion expression with original transcription factors of an organism, activates expression of biosynthesis related genes of anthocyanin and glycoside derivatives of the anthocyanin, has stronger transcriptional activation capability compared with original protein, and promotes accumulation of the anthocyanin and the glycoside derivatives of the anthocyanin of plants.

A nucleic acid vector, a nucleic acid drug, a preparation method therefor, and the use thereof. The nucleic acid vector comprises sequences a, b, and c; and the nucleic acid vector is selected from DNA, RNA or a DNA-RNA hybrid vector; sequences a, b, and c self-assemble to form the nucleic acid vector, and sequences a, b, and c comprise backbone sequences with the following core sequences: sequence a1 as represented by SEQ ID NOs 1 or 4, sequence b1 as represented by SEQ ID NOs 2 or 5 and sequence c1 as represented by SEQ ID NOs 3 or 6, or any variant sequence of at least one among sequence a1, sequence b1, and sequence c1, a variant sequence comprising the insertion, deletion, or substitution of at least one nucleobase; and the DNA-RNA hybrid vector is a vector formed by self-assembly of a combination of a DNA vector sequence and an RNA vector sequence. The vector has high delivery efficiency, and the delivery system is more stable. In addition, the preparation process is simpler and more efficient.