190 results about "Copy-number variation" patented technology

The invention discloses application of a gene marker in early screening of esophagus, stomach and intestine multiple cancer species, an early screening model construction method and a detection device, and belongs to the technical field of early noninvasive detection of digestive tract tumors. By analyzing the whole genome characteristics of circulating free DNA in peripheral blood, a novel multi-cancer-species screening system is established. On the basis of low-depth whole genome sequencing data, molecular markers in three dimensions, namely a genome copy number variation mode, a DNA fragment distribution characteristic with a specific length and an epigenetics signal of a transcription initiation region, are emphatically detected. An advanced converter neural network architecture is adopted, and the model can efficiently capture complex feature association in a whole genome range through a specific self-attention mechanism. The model design particularly considers the particularity of genome data, introduces an adaptive position coding system, and accurately reflects the spatial distribution relationship of DNA fragments on chromosomes. Therefore, the system can still maintain excellent detection performance under extremely low sequencing depth.

The invention discloses a method for detecting copy number change based on an amplicon capture technology and application of the method. According to the method, the sequencing data difference caused by amplicon sequencing and the deviation caused by PCR reaction can be reduced, so that accurate and stable analysis of the copy number change of the target area is realized, and the method can be applied to analysis of the copy number change of a specific gene or genome area.

The invention provides a primer probe combination and a kit for detecting the copy number of a 22q11 region based on digital PCR and a use method of the primer probe combination. Specific probes of a target gene TBX1, a target gene CRKL, a target gene SMARCB1 and a reference gene GAPDH are integrated in different fluorescence channels, and the copy number of the target gene is detected according to the ratio of the copy number of the reference gene to the copy number of the three target genes. According to the invention, amplification products of different sites in different fluorescence channels are integrated in the same system in digital PCR reaction, so that the detection flux is greatly improved, and low-cost and high-flexibility accurate quantification of 22q11. 2 copy number variation is realized through a single-channel multi-target fluorescence layering strategy; and the dependence on expensive equipment, complex operation and professional analysis in the prior art is overcome.

The invention relates to the technical field of assisted reproduction polygene detection, and discloses an oocyte occurrence and maturation disorder detection panel, a detection kit and application thereof, and the detection panel comprises mutation genes related to the oocyte occurrence and maturation disorder for detection, copy number variation genes and rearrangement event and deletion genes. According to the application, by detecting high-risk genes and mutation sites, the risk of occurrence and maturation disorder of the oocytes is predicted in combination with clinic, the development potential of the oocytes is evaluated, the in-vitro maturation strategy is optimized, and the clinical outcome of assisted reproduction is improved. The detection panel can be used for efficiently detecting gene mutation which has clinical diagnosis and treatment significance on oocyte occurrence and maturation disorders; the method has important guiding significance on genetic counseling, risk prediction, clinical diagnosis, precise treatment and potential personalized intervention measures of patients suffering from recurrent oocyte occurrence disorder, oocyte maturation disorder and low oocyte maturation rate and patients to be subjected to assisted reproduction technology treatment.

The invention provides a gene variation detection method and device, electronic equipment and a storage medium. The gene variation detection method comprises the following steps: acquiring first long read length sequencing data of a to-be-detected sample, and comparing the first long read length sequencing data with a reference genome to obtain first comparison data; determining a region of the target gene in the reference genome, and calculating a first sequencing depth of the target gene according to the determined region and the first comparison data; determining a first base distribution ratio of the first sub-target gene to the second sub-target gene, and calculating a first sub-sequencing depth of the first sub-target gene and a second sub-sequencing depth of the second sub-target gene according to the first base distribution ratio and the first sequencing depth; and calling a pre-trained detection model to perform copy number variation detection based on the first sub-sequencing depth and the second sub-sequencing depth to obtain a target copy number variation type of the to-be-detected sample. According to the embodiment of the invention, the accuracy of gene variation detection can be improved.

The invention discloses a copy number variation detection method, device and equipment based on low-depth whole genome sequencing and a storage medium, and relates to the technical field of medical data processing, the method comprises the following steps: performing sequencing quality control on sample gene data to obtain filtered gene data; performing data preprocessing on the filtered gene data through a dynamic negative reference library and a reference genome to obtain processed gene data and a dynamic Z test result; the dynamic negative reference library is determined according to the GC content of the contrast negative sample set; and performing improved copy number variation detection according to the processed gene data and the dynamic Z test result to obtain a copy number variation detection result. According to the method, sequencing quality control is carried out firstly, and data quality is guaranteed; and then data preprocessing is performed based on a dynamic negative reference library constructed in real time, and finally CNV detection is performed based on optimized processing gene data and a dynamic Z test result, so that systematic deviation is effectively reduced, and the detection reliability is improved.

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 provides a method for detecting genes related to early growth traits of Inner Mongolia down producing goats based on copy number variation (CNV). The method comprises the following steps: acquiring whole genome re-sequencing data of 461 Inner Mongolia down producing goats; the method comprises the following steps: detecting autosomal CNV by using CNV native software, and screening out 26,003 non-redundant CNV which covers 1, 015.4 Mb (38.97%) of an autosomal genome; gWAS analysis is carried out on the basis of CNV, 11 CNVs obviously related to early growth traits (birth weight CSZ, weaning weight DRZ, daily gain ADG before weaning and 12-month-old weight ZWT) are identified, and two CNVs influence ADG and DRZ at the same time; seven key candidate genes (ZN845, SOX15, FGF11, GPS2, DVL2, SPRY4 and STAT2) are analyzed and identified through bioinformatics, and GO and KEGG function enrichment analysis is utilized to find that the genes participate in biological pathways such as cell proliferation, differentiation and protein phosphorylation. The invention provides a theoretical basis for molecular marker-assisted breeding of Inner Mongolia down producing goats, and has important scientific value and application prospect.

The invention discloses application of NOR1 copy number variation in prediction of the mature period of pears, and belongs to the technical field of plant molecular markers, by analyzing genomes of pear varieties in different mature periods, it is found that copy number variation exists in DNA fragments where NOR1 is located, the copy number of the NOR1 is positively correlated with the mature period on the basis of analysis of genome assembly and three-generation sequencing data, and the mature period of the pear varieties is predicted. And determining the mature period of the pear according to the copy number of the NOR1. The molecular marker developed by the invention can predict the mature period of the filial generation in the seedling stage, and the breeding efficiency of early-maturing varieties is greatly improved.

The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

The invention discloses a method for accurately identifying benign and malignant cells based on multi-dimensional characteristics of a single cell transcriptome, and belongs to the technical fields of bioinformatics, tumor molecular biology and cell identification. On the basis of single cell transcriptome sequencing data of tumor tissues and para-carcinoma tissues, three types of information including copy number variation, allele specific copy number variation and tumor-related transcriptional characteristics are synthesized, and final benign and malignant identification is performed on each EpCAM positive epithelial cell through a multi-evidence voting strategy. The method disclosed by the invention has relatively high stability and accuracy in a multi-patient, multi-sample and early tumor scene, particularly improves the recognition capability of early lesion and malignant cells in benign and malignant boundary transition state cells, and provides a reliable technical means for precise diagnosis and individualized treatment of tumors.

According to the application of the HTATSF1 gene in regulation and control of cattle muscle growth and development and breeding, the influence of the HTATSF1 gene on muscle growth and development and the correlation between HTATSF1-CNV and cattle growth traits are verified, a reliable molecular marker is provided for cattle seed selection and breeding, and help is provided for cattle variety improvement. A foundation is laid for association between copy number variation and growth traits of the cattle HTATSF1 gene, cattle molecular marker-assisted selection breeding work can be accelerated, the method is simple, rapid and convenient to popularize and apply, and a complete solution from fundamental research to industrial application is provided for improvement of cattle germplasm resources.

The application discloses a kind of marker for predicting oocyte copy number variation and application thereof, the marker includes the combination of CLEC11A, P4HB, EFEMP2, IL32, FTL, FLNA, COL6A3, ACPP and APOO protein.By the marker of the application, the expression level of granulosa cell secretory protein can be determined by granulosa cell transcriptome sequencing, and the genomic CNV condition of corresponding oocyte can be inferred.The detection object of the technical solution is discarded granulosa cell in assisted reproductive technology, so it will not have any impact on oocyte, and it is non-invasive;The present study is a transcriptome and methylation group detection from single cell level, with high-throughput characteristics, and all granulosa cells and oocytes are one-to-one matched, which can reflect the difference between single cell level COCs.

The present invention provides a method, device, and application for detecting tumor molecular typing based on low-depth whole-genome sequencing. The method comprises: independently dividing low-depth whole-genome sequencing data into non-fixed bin groups and fixed bin groups; using the copy numbers of the non-fixed bin groups and the fixed bin groups to calculate the average copy number and mutation region ratio of each group; establishing a scoring model based on the average copy number and mutation region ratio to determine the copy number variation type at each structural level of the chromosome, and then deriving the corresponding molecular typing; wherein the non-fixed bin group includes a first target region belonging to the exon and an anti-target region outside the exon; the fixed bin group includes a second target region of 1M in length and a third target region of 10K in length obtained by continuous division. In this way, the copy number variation type of the chromosome at different hierarchical structural positions is obtained, thereby achieving more accurate molecular typing detection of the size of tumor chromosomes at each level.

The invention relates to a method of determining somatic allele-specific copy number alterations (CNAs) in the genomes of cells in a test-sample from a subject, the method comprising: i) providing an indexed-DNA library of DNA fragments resulting from whole-genome amplification of genomic DNA from cells of the test-sample, ii) providing whole genome sequencing data of reference non-cancer cells from a reference-sample from the subject; and iii) determining somatic allele-specific copy number alterations in the genome(s) of the cells of the test-sample; and associated methods and uses in cancer therapy.

The application discloses a single cell whole genome amplification sequencing method. The application comprises the following steps: 1) separating a single cell, adding a single cell lysis solution to sufficiently lyse the single cell and digest proteins combined on the genomic DNA; 2) using a Tn5 transposome with a specific adapter sequence to fragment the DNA, while adding adapters to both ends of the fragments; 3) after end repair, using a ribonuclease to cut modified ribonucleotide residues on the adapter sequence; 4) using the adapter sequence as a primer to linearly amplify the fragmented DNA by using a single primer PCR method; and 5) adding sequencing adapters to both ends of the DNA fragments by using a chain extension and PCR method to obtain a final sequencing library. The method disclosed by the application can amplify single cell whole genome DNA with high coverage, uniformity and fidelity, and simultaneously and accurately detect chromosomal copy number variation CNV and single nucleotide mutation SNV on a single cell genome.

The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.

The invention belongs to the technical field of biological medicines, and particularly discloses a primer probe combination and a kit for detecting genotypes of SMA carriers based on a chromosome level and application of the primer probe combination and the kit. Wherein the primer probe combination comprises a primer probe group for detecting an exon 7 of an SMN1 gene, a probe for detecting an exon 7 of an SMN2 gene, a primer probe group for detecting a short-arm reference gene of a chromosome 5, a primer probe group for detecting a long-arm reference gene of the chromosome 5 and a primer probe group for detecting a reference gene of a human genome. The primer probe combination can eliminate chromosome copy number variation interference, greatly improves the specificity of SMA carrier genotype detection, can simultaneously detect the type I and type II of the SMA carrier genotype, has the detection sensitivity of 99%, and is suitable for large-scale population screening.

A method for detecting fetal CNVs through non-invasive prenatal testing, comprising steps: (a) collecting blood samples from pregnant women; (b) extracting cfDNA fragments from the blood samples, performing whole genome sequencing on extracted cfDNA fragments to obtain cfDNA sequencing data, and preprocessing cfDNA sequencing data by removing adapters, aligning and mapping reads to a referenced human genome; (c) performing quality control on obtained cfDNA sequencing data for being accepted for the prediction; (d) dividing referenced genome into a plurality of non-overlapping bins and filtering the bins based on a predetermined GC-content threshold for bins; (e) defining a CNV detection window, a bin size, a set of features for machine learning / deep learning models and fine-tune model for detecting fetal CNV for selecting a final model; and (f) applying the final model to predict fetal CNVs, including microdeletion syndromes, or microduplications, or aneuploidies, or the number of sex chromosomes.

The invention provides an exon copy number variation detection method, device and equipment, and relates to the technical field of high-throughput sequencing, the method comprises the following steps: inputting feature information of a to-be-detected sample in each target interval into a target hybrid expert model, and outputting a reliability score of copy number variation of the to-be-detected sample in each target interval; obtaining the reliability grade of the copy number variation of the exon interval according to the reliability grade of the copy number variation of each target interval; updating the reliability grade of the copy number variation of the exon interval of the to-be-detected sample to obtain the reliability grade of the copy number variation of the updated exon interval; and filtering the copy number variation of the exon interval, and determining an exon copy number variation detection result of the sample to be detected. According to the method provided by the embodiment of the invention, exon copy number variation can be accurately detected.

The disclosure provides methods, systems, and algorithms to identify and report genome or chromosome level structural information, such as the presence of structural variations. In some cases, structural variations include copy number variations, inversions, deletions, tandem duplications, or inverted duplications. Further provided herein are methods, systems and algorithms for assembling read-paired genomic data, including creating and optimizing scaffo

The invention discloses application of a GYPB gene in cattle molecular breeding, and belongs to the technical field of molecular genetics research. The method comprises the following steps: amplifying a copy number variation region of a GYPB gene through a qPCR (Quantitative Polymerase Chain Reaction) technology by taking bovine genome DNAs of different varieties as templates and a BTF3 gene as a contrast; and analyzing the copy number and judging the copy number variation type of the individual by adopting a 2 * 2-delta delta Ct statistical method. The method provided by the invention is beneficial to correlation analysis between the cattle GYPB gene CNV and growth traits, and the application of molecular marker-assisted selection in cattle genetic breeding is expanded.

Disclosed in the present invention is a use of an MP1 gene copy number variation detection reagent in preparation of an NK / T cell lymphoma prognosis kit. The present invention further provides a detection kit comprising the LMP1 gene copy number variation detection reagent, a use thereof, and an NK / T cell lymphoma prognosis method. In the present invention, a copy number variation event of LMP1 gene in an EB virus genome is used as a novel prognosis marker, which has a good prediction value for the overall survival and progression-free survival prognosis of an NK / T cell lymphoma patient, and can realize more accurate and effective prognostic assessment for the NK / T cell lymphoma patient.

The invention relates to the technical field of biomedicine, and discloses a chromosome copy number variation detection method, device and equipment, a medium and a product, and the method comprises the following steps: obtaining sequencing depth data of a to-be-detected chromosome in a to-be-detected nucleic acid sample; determining a copy number type set according to the sequencing depth data and a normal distribution function set corresponding to the to-be-detected chromosome; wherein the normal distribution function set comprises normal distribution functions corresponding to a copy number deletion type, a copy number repetition type and a copy number normal type respectively, and the copy number type set comprises labeled copy number types of a plurality of second nucleic acid windows; according to the copy number type set, splicing the plurality of second nucleic acid windows to obtain at least one copy number variation region; wherein the second nucleic acid window is a first nucleic acid window of the to-be-detected chromosome or a recombinant nucleic acid window obtained by combining a plurality of first nucleic acid windows based on a preset window number and a preset window step length, and the detection precision of chromosome copy number variation is improved.

The invention discloses a probe group for detecting copy number variation of pathogenic genes of limb development defect diseases as well as a design method, a kit and application of the probe group, and belongs to the technical field of biomedicine. The probe group comprises probes of which the nucleotide sequences are as shown in SEQ ID NO. 1 to SEQ ID NO. 516. The invention also discloses a design method of the probe group, a kit comprising the probe group, and a method for detecting copy number variation of the pathogenic gene of the limb development defect disease by using the probe group or the kit. The probe group and the kit provided by the invention can realize high-throughput, high-resolution, high-accuracy and low-cost copy number variation detection.

Provided herein are, inter alia, are methods and systems for amplifying a chromosomal fragment DNA sequence. The methods and systems provided herein are, inter alia, useful for detecting copy number variation, structural variation, and / or extrachromosomal DNA within the chromosomal DNA of a plurality of cells. In addition, the methods provided herein are, inter alia, useful for jointly analyzing chromatin architecture and gene expression at a single cell level. The methods provided herein can be, inter alia, used to analyze chromosomal heterogeneity, clonal shifts, and / or evolutionary shifts between different cells.

The application provides an exon copy number variation detection method, device and equipment, and relates to the technical field of high-throughput sequencing, which comprises the following steps: inputting characteristic information of a sample to be detected in each target interval into a target hybrid expert model, and outputting reliability scores of copy number variations of the sample to be detected in each target interval; obtaining reliability classification of copy number variations of an exon interval according to the reliability scores of copy number variations of each target interval; updating the reliability classification of copy number variations of the exon interval of the sample to be detected, and obtaining updated reliability classification of copy number variations of the exon interval; and filtering the copy number variations of the exon interval, and determining an exon copy number variation detection result of the sample to be detected. The method of the application embodiment realizes accurate detection of exon copy number variations.

The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5′- and 3′-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on 5′-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on 3′-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing”).

This invention discloses a method and system for assessing tumor content in liquid biopsies. The method performs quality control on high-throughput sequencing data from body fluid samples, filtering germline variations, clonal hematopoietic-related variations, and sequencing errors to obtain copy number variation (CNV) information and somatic mutation characteristic information. A weighted mean squared error loss function is constructed based on the CNV information, and the tumor content is solved using a constrained gradient descent method. When the CNV signal does not meet preset judgment conditions, the system switches to the mutation characteristic module, constructing a negative log-likelihood function based on a binomial distribution based on the principal clonal cluster, and solving for the tumor content through iterative optimization. In extreme cases, a backoff mechanism is triggered. This invention combines the stability of CNV at high tumor content with the sensitivity of mutational VAF at low content, achieving adaptive assessment from low to high tumor content.

The invention discloses a resequencing-based space mutagenesis peanut population genotype variation map and a construction method thereof, and belongs to the technical field of plant biotechnology and plant molecular breeding, and the technical key points are as follows: a space mutagenesis peanut mutant plant is utilized, based on a whole genome resequencing technology, genetic variation sites in a genome are systematically detected, and the genotype variation map of the space mutagenesis peanut population is obtained. A variation map of a space mutagenesis peanut population genome is constructed, the map comprises no less than 500,000 mononucleotide variations (SNP), 100,000-200,000 insertion and deletion (InDel), about 3000 copy number variations (CNV) and about more than 3000 structural variations (SV), and 66 genes related to peanut grease anabolism are screened out. The construction method comprises the following steps: obtaining a mutant plant, extracting DNA, sequencing, detecting and identifying SNP, InDel, CNV and SV variation sites, and the like.