92 results about "Deep sequencing" patented technology

The invention relates to the field of noninvasive prenatal diagnosis, and particularly discloses a preeclampsia noninvasive screening method based on deep sequencing 8bp oligonucleotide double-fragment characteristics, which comprises the following steps: collecting preeclampsia and healthy pregnant woman peripheral blood samples, and extracting free DNA for high-throughput sequencing; the method comprises the following steps: extracting core 8-mer sequences' GTGCGCCC 'and' GATGGGGT 'in a long fragment of 150-200bp through bioinformatics analysis; an integrated support vector machine, K-nearest neighbor, extreme gradient lifting, a random forest and a multi-layer perceptron are combined with a logistic regression element classifier to construct a stacking model, the frequency of a core sequence is normalized, machine learning analysis is carried out, and the preeclampsia risk is predicted. According to the invention, two 8bp oligonucleotide characteristic fragments are specifically screened, and a deep learning architecture of multi-model fusion is combined, so that the limitations of low specificity and invasive detection of a traditional screening method are effectively broken through.

The invention discloses a tiny residual focus detection method and system based on ultra-high depth sequencing, and relates to the technical field of tiny residual focus intelligent detection.The tiny residual focus detection method comprises the following steps that on the basis of a sequencing library, splitting is conducted according to a sample index to obtain a to-be-detected sample, and a consensus sequence is obtained according to a molecular identifier of the to-be-detected sample; based on a consensus sequence, filtering out the consensus sequence of which the mass value is less than 25 or the family size is less than 3, and combining a variation type and a distance from a fragment edge as noise introduced into an original nucleic acid molecular chain; a context sequence (context) and a chain direction are used as noise for introducing the capture level of PCR amplification; on the basis of the noise level, the circulating tumor DNA level is estimated in combination with tumor priori knowledge, and the MRD state is determined by detecting the significance of molecular signal sources. According to the invention, the sensitivity and specificity of MRD detection are improved.

The invention relates to a method for carrying out rapid paternity test through a polymorphic site linkage region block, application of the method and the like. The method comprises the following steps: establishing a linkage relationship database of polymorphic sites, obtaining low-depth WGS sequencing data of a sample, obtaining a mapping relationship between point locations and linkage polymorphic relationships, and determining the low-depth WGS sequencing data of the sample according to the low-depth WGS sequencing data and the mapping relationship between the point locations and the linkage polymorphic relationships. And carrying out paternity test by taking a plurality of sites forming the linkage polymorphic relationship as units. The method is short in period, paternity test results can be obtained within 24 hours without capturing polymorphic sites in a specific area, and the method has wide application prospects.

The invention discloses a targeted sequencing method for various pathogenic microorganisms. The targeted sequencing method specifically comprises the following steps: collecting a biological detection material containing the pathogenic microorganisms; extracting nucleic acid in the pathogenic microorganisms to be detected; designing specific primers and probes according to the target pathogenic microorganisms; amplifying a nucleic acid sequence through a PCR (Polymerase Chain Reaction) technology; carrying out deep sequencing based on a high-throughput sequencer; according to the present invention, the specific primers and the probe are designed, such that the nucleic acid sequence of the target pathogenic microorganism can be efficiently enriched, and the high-throughput sequencing technology is adopted to perform the deep sequencing so as to significantly improve the sensitivity and the accuracy of the detection of the plurality of pathogenic microorganisms; the method can be used for simultaneously detecting various different types of pathogenic microorganisms such as bacteria, viruses, fungi and the like, is simple and convenient to operate, short in time consumption and low in cost, and can provide powerful support for quickly and accurately identifying the pathogenic microorganisms and timely taking effective prevention and control measures.

The invention relates to the technical field of genetic relationship identification, in particular to a construction method, an identification method and application of a primary genetic relationship identification model based on ultralow deep sequencing. According to the identification model obtained by using the construction method of the genetic relationship identification model provided by the invention, the genetic relationship can be identified by adopting ultra-low depth sequencing (0.01 *), the genetic relationship can be determined according to the heterozygosity index between samples to be identified, the prediction accuracy is up to 99.9%, and the construction method is a first-grade genetic relationship detection technology with low cost and high accuracy; the method has the advantages of simple and convenient scheme, high accuracy, high credibility, high repeatability and high economic benefit, has multiple application scenes, and can advance an embryo paternity test window from antenatal / postpartum to before embryo implantation, thereby avoiding physical, mental and economic losses of a patient; ovum / sperm fertilization errors can be found in advance, non-parent embryo transplantation is avoided, and loss caused by embryo wrong transplantation is prevented.

The invention discloses a high-specificity minimal residual disease (MRD) monitoring method and system based on circulating tumor DNA (ctDNA). The method comprises the following steps: receiving tumor tissue sequencing data of an UTUC patient, and generating a double-Panel target list containing personalized and fixed Panel; respectively extracting plasma cfDNA and leukocyte gDNA; performing vacuum concentration, hybrid capture and sequencing on the cfDNA library by using the double Panel lists, and performing deep sequencing on the leukocyte gDNA; constructing an individualized clonal hematopoietic mutation filtering database; actively filtering and rejecting clonal hematopoietic background mutation by utilizing a filtering database; and calculating an MRD load score based on the filtered tumor-derived mutation and outputting a report. The system comprises corresponding modules which are used for automatically executing the process. According to the invention, through cooperation of four major technologies of double-Panel design, process optimization, UMI error correction and active clonal hematopoietic filtration, MRD monitoring with extremely high sensitivity and specificity on UTUC is realized, false positive is significantly reduced, and the kit has drug resistance early warning potential.

The invention provides an SNP molecular marker combination for paternity test and individual recognition of dairy cows and application, the SNP molecular marker combination comprises 300 SNP markers on 29 autosomes of the dairy cows, the marker combination can be applied to paternity test and individual recognition of the dairy cows, and an identification method comprises the step of preparing a liquid phase chip of the 300 SNP markers, constructing a high-throughput sequencing library by using the genome DNA of the dairy cow to be detected; mixing the liquid phase chip probe with a high-throughput sequencing library, capturing a DNA fragment containing a target SNP site in the dairy cow DNA high-throughput sequencing library, amplifying and purifying to obtain a genetic typing of a dairy cow individual to be detected, and performing paternity test inference according to the genetic typing. The invention provides a probe and a kit for identifying SNP (Single Nucleotide Polymorphism) site information. According to the invention, the SNP polymorphism is detected through targeted capture sequencing, through high-depth sequencing, the typing result is accurate and reliable, and the accuracy of paternity test and individual recognition is ensured.

The invention provides a target character prediction method suitable for low-depth sequencing and a whole genome selection model suitable for low-depth sequencing, and relates to the technical field of biology. According to the target character prediction method suitable for low-depth sequencing and the whole-genome selection model provided by the invention, the target character of the to-be-detected sample can be accurately predicted under a limited data volume by combining low-depth whole-genome re-sequencing data with a machine learning technology, and the genome selection efficiency can be improved by matching the two; the time and economic cost of breeding or medical research are reduced, and the method is particularly suitable for large-scale genetic analysis scenes needing rapid iteration.

Disclosed herein are methods for profiling a cancerous tumor using a high-throughput sequencing technique.

The invention belongs to the technical field of animal genetic breeding, and provides an application of an SNP molecular marker related to a pig backfat thickness character. The nucleotide sequence of the molecular marker is as shown in SEQ ID NO: 7, wherein the polymorphism of the eleventh basic group is C / T. The key gene SLC26A3 related to the backfat thickness of the large white pig is identified through whole genome deep sequencing, the genotype of the backfat thickness character of the large white pig is further detected through an SLC26A3 gene molecular marker, and the backfat thickness of the CC genotype large white pig is obviously higher than that of a CT / TT genotype pig. Therefore, the breeding of the CT / TT genotype individuals is beneficial to meeting the continuous demand of large-scale production on high-efficiency utilization of feed energy. The detection method provided by the invention is simple and easy to operate, can efficiently and quickly identify the back fat thickness character of the large white pig, improves the uniformity of the back fat thickness of the pig, and provides a scientific basis for early breeding of the pig.

The invention discloses a gene detection system which comprises a sample collection module, a gene extraction module, a sequencing module, a data analysis module and a report generation module. The gene extraction module is used for extracting high-quality DNA (Deoxyribonucleic Acid) or RNA (Ribonucleic Acid) from a sample, and the data analysis module is used for processing, analyzing and explaining original data obtained by sequencing by integrating various bioinformatics algorithms and tools. The game theory is integrated into the whole genome association analysis GWAS model to improve the whole genome association analysis GWAS model, the game theory is combined to enable the SNP sites to be more and more detailed, the relevance between deeper hereditary characters and defective genes can be mined, the false positive probability of the result obtained by the association model is smaller, and the accuracy of the result obtained by the association model is improved. A genetic-defect gene association map is constructed according to a whole genome association analysis GWAS model fused with the game theory thought, a defect gene risk prediction model is trained, and the most possible defect gene type is predicted according to genetic characteristics, so that the accuracy is greatly improved.

The invention relates to a method for evaluating and positioning nucleic acid pollution of a nucleic acid extraction kit, which comprises the following steps: 1) taking nucleic acid-free water as a negative sample, and performing nucleic acid extraction on the nucleic acid-free water by using the nucleic acid extraction kit according to nucleic acid extraction steps in the kit, the obtained nucleic acid is presumed as the polluted nucleic acid in the nucleic acid extraction kit; 2) amplifying polluted nucleic acid, purifying a PCR product, enriching double-chain cDNA, and determining the concentration of the double-chain cDNA so as to perform quantification, sample mixing and quality control treatment before library construction; (3) carrying out high-throughput deep sequencing by adopting a platform of the Illumina company, and then carrying out bioinformatics analysis to obtain classification information and gene sequences of polluted nucleic acid; and 4) designing a specific primer based on the gene sequence of the polluted nucleic acid, and carrying out pollution evaluation and positioning verification on each component of the nucleic acid extraction kit through qPCR (Quantitative Polymerase Chain Reaction).

Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand. This method uniquely capitalizes on the redundant information stored in double-stranded DNA, thus overcoming technical limitations of prior methods utilizing data from only one of the two strands.

This invention relates to the field of molecular marker screening technology, specifically to a SNP combination and method for paternity testing in cynomolgus monkeys. The method provided by this invention utilizes 100 selected specific SNP combinations (SNP1~SNP100) combined with low-depth sequencing for paternity testing in cynomolgus monkeys. The cost per sample is only 1 / 5 to 1 / 10 of existing high-depth sequencing and 1 / 2 of SNP chips. For large-scale experimental monkey populations (such as populations of thousands), this can save hundreds of thousands of yuan in testing costs annually, significantly reducing the economic burden of breeding and management of experimental monkeys, demonstrating extremely high economic efficiency. The method provided by this invention is applicable to cynomolgus monkey population pedigree management, kinship tracing, breeding pair optimization, and genetic quality control, and can be widely applied in experimental monkey breeding farms, primate research centers, and biomedical research institutions.

The invention discloses a method for evaluating fetal DNA concentration (cffDNA) in free blood of a pregnant female parent through a polymorphic site linkage region block. The method comprises the following steps: acquiring low-depth WGS sequencing data of a sample; obtaining a mapping relation between the point location and the linkage polymorphic relation; and according to the low-depth WGS sequencing data and the mapping relationship between the point locations and the linkage polymorphic relationship, performing concentration calculation by taking a plurality of sites forming the linkage polymorphic relationship as units. Wherein the mapping relation between the point location and the linkage polymorphism can be obtained by processing public genome WGS data, processing public linkage polymorphism region block data or processing a large amount of high-depth WGS measured data. Based on the low-depth WGS data, the cffDNA concentration in the free blood of the pregnant female parent can be directly calculated through the heterozygosity of the linkage SNP region blocks, the method is not affected by the gender of a fetus in NIPT practical application, a father sample and an additional experiment are not needed, the stability is high, the performance is high, and the cost is low.

The invention discloses a construction, high-throughput sequencing and transcription intensity analysis method of a promoter random library. The invention establishes a process and an implementation method for rapidly researching the relative transcription intensity of a large number of promoters in a random promoter library, the promoter random library is rapidly constructed through a random primer method, and the transcription intensity of a large number of promoters is analyzed through deep sequencing of random tags carried by plasmid DNA and transcribed mRNA. According to the promoter library construction-library construction-sequencing-analysis process disclosed by the invention, the transcription intensity of promoters with different sequences can be quickly obtained with high throughput, and the promoter library with ideal promoter transcription intensity span is obtained. The method is rapid and efficient, and the transcription intensity of massive promoter sequences can be obtained.

The application discloses an analysis method and system for noninvasive prenatal screening, and the method comprises the following steps: obtaining target high-depth sequencing data of a target sample; performing data preprocessing on the target high-depth sequencing data to obtain depth information and SNP site information of a target region; obtaining a test result through global Z test based on copy number information, obtaining a first analysis result through local microdeletion / microduplication analysis by using a forward-backward search algorithm, and obtaining a classification result through a Bayesian classifier; obtaining a second analysis result through SNP analysis based on the SNP site information; and finally comprehensively judging to obtain a target analysis result. The application can effectively reduce the complexity of experimental operation, reduce the complexity of the diagnosis process, reduce the sample error probability caused by multiple sampling, significantly improve the efficiency of clinical testing, has high practical value and application prospect, and can be widely applied to the technical field of data processing.

Blood and lung infection is a worldwide health problem, and about five millions of cases of death each year. Early treatments can help rescue life but require better tests to identify these infections. The invention recognizes pathogens, in particular those having antibiotic resistance, more quickly. The invention allows appropriate antibiotic treatment to be performed at an earlier point in time. Data from deep RNA sequencing of human blood is used to create a faster diagnostic test against infection and related antimicrobial resistance.

The invention relates to the technical field of nucleic acid molecule detection, and discloses a pre-amplification detection method of a low-abundance fusion gene. According to the invention, a high-sensitivity SNT-MRD platform technology and the specificity of a qPCR primer probe system are combined, and a two-stage PCR amplification strategy and an optimized primer probe design are adopted, so that effective enrichment and detection of trace fusion genes in plasma ctDNA are realized. Compared with the existing qPCR detection method, the method disclosed by the invention has the advantages that the target sequence is firstly enriched, and then specific detection is performed, so that the problem of non-specific amplification caused by a large number of cycles in single PCR is avoided; compared with a method purely depending on NGS deep sequencing, the method has the advantages that the dependence on sequencing depth and complex biological information analysis is reduced, sensitive detection can be realized on a conventional qPCR instrument, the cost is lower, and the speed is higher.

The invention discloses a method for detecting monophilic disomes and application of the method. According to the method, on the basis of given family whole genome low-depth sequencing data, a sliding window is set in a whole genome to count and compare contribution rate differences of male parents and female parents to fetal (subline) genetic materials in the window, so that UPD detection is realized. According to the method, the UPD abnormity of the whole chromosome can be accurately identified, local UPD (segment UPD) in the chromosome and the breakpoint position of the UPD can be identified, and the parent source of the UPD can be automatically judged.

The application discloses a method for simulating high-depth sequencing TSS characteristics. The method comprises the following steps: (1) obtaining reference genome captured free DNA sample sequencing data and sequence coverage of the upstream and downstream regions of the TSS of each gene; (2) obtaining features for constructing TSS values of simulated high-depth sequencing results based on the low-depth sequencing results of free DNA; and (3) constructing a TSS value model of simulated high-depth sequencing results based on the features of the low-depth sequencing results of free DNA. According to the application, the features are extracted based on the low-depth sequencing results, a model is constructed, the TSS characteristics equivalent to high-depth sequencing can be obtained, the number of analyzable gene TSS regions can be effectively increased, the stability of the sequencing fragment coverage of the analyzable gene TSS regions is increased, the sequencing cost is greatly reduced while the calculation accuracy of the TSS values is ensured.

Methods and systems provided herein address current limitations of bisulfite-based methylation sequencing by improving the quality and accuracy of nucleic acid methylation sequencing and uses thereof for detection of disease. Methods that include minimally-destructive conversion methods for methylation sequencing as well as specialized UMI adapters provide for improved quality of sequencing libraries and sequencing information. Greater accuracy and more complete methylation-state information permits higher quality feature generation for use in machine learning models and classifier generation.

Methods and systems provided herein address current limitations of bisulfite-based methylation sequencing by improving the quality and accuracy of nucleic acid methylation sequencing and uses thereof for detection of disease. Methods that include minimally-destructive conversion methods for methylation sequencing as well as specialized UMI adapters provide for improved quality of sequencing libraries and sequencing information. Greater accuracy and more complete methylation-state information permits higher quality feature generation for use in machine learning models and classifier generation.

The application provides a general avian infectious bronchitis virus whole genome deep sequencing method and application. The method realizes efficient amplification of long fragments of whole genomes of different genotype IBV epidemic strains by designing and applying a set of combinations containing 24 pairs of specific primers. The specific sequences of the primer combinations are shown in SEQ NO:1 to SEQ NO:48. Compared with a traditional sequencing method, the application significantly reduces the sequencing cost. Only two PCR reactions are needed, and more than 27 kb of IBV full-length genome sequence can be successfully obtained, which provides a more economical and efficient solution for IBV related scientific research and molecular epidemiology monitoring, and helps to promote the development of related field scientific research.

This invention provides a method for detecting genome-wide ROH based on ultra-low depth sequencing. The method first acquires the raw PGT-A sequencing data of the sample, extracts high-frequency SNP loci from the population, and screens out loci on autosomes with sequencing depths of 2-4X to construct a locus set. Then, the heterozygosity index (HetRR) and its standard score (Z) are calculated. Based on thresholds, the results are judged as follows: HetRR < 0.1 and Z ≤ -3.0 indicates genome-wide ROH; 0.1 ≤ HetRR < 0.5 and Z ≤ -3.0 indicates ROH chimerism; HetRR ≥ 1.05 and Z ≥ 3.0 suggests triploidy or DNA contamination; the rest are normal. This method can utilize sequencing data as low as 0.01X and can be simultaneously detected in the routine PGT-A process without additional operations or costs, improving the accuracy of embryo screening and possessing high clinical application value.

Disclosed are methods and systems for detecting methylation of the promoter of O-6-methylguanine-DNA methyltransferase gene (MGMT). In particular, the methods and systems may be utilized to detect methylation in the MGMT promoter in a DNA sample from a glioblastoma and optionally in order to predict whether a subject having the glioblastoma will respond to treatment with an alkylating agent. The methods and systems typically include a step of deep-sequencing the DNA sample after the DNA sample has been treated with a reagent that converts unmethylated cytosine to uracil such as a bisulfite reagent.

The invention discloses a method for separating cochlea related cells in situ based on a patch clamp system. The method comprises the following steps: contacting an electrode with a target single cell under a microscope, and carrying out in-situ grabbing on the target single cell through negative pressure adsorption; the target single cell and surrounding cells are kept in a connection state before in-situ grabbing; before the electrode approaches the target single cell, positive pressure is continuously applied, and when the electrode is in contact with the surface of the target single cell, the positive pressure is instantly stopped and switched to negative pressure. According to the method provided by the invention, high-quality cochlea related cells can be obtained in situ for deep sequencing analysis, and the method can be used for basic research and accurate diagnosis and treatment of clinical hearing impairment, and has a good application prospect.

The application discloses a methylation marker combination for detecting early esophageal cancer and application thereof. The marker combination comprises 178 methylation sites of 12 specific DNA regions and a specific internal marker region, and the methylation levels of the regions in plasma of patients with early esophageal cancer and healthy people are significantly different. The application also provides a primer combination and a kit for detecting the marker combination, and supports high-throughput deep sequencing. A detection system is used to extract plasma free DNA, perform bisulfite conversion and amplification, calculate a prediction value by using a logistic regression model, multiply the average methylation rate of each region by a corresponding weight coefficient, and compare the result with a threshold value to make a positive judgment. The application greatly improves the detection sensitivity of non-invasive screening for early esophageal cancer under the premise of ensuring high specificity, and has a wide clinical application prospect.

The present disclosure provides methods and systems for capturing and enriching nucleic acid sequences. Probes or primers may be used to capture or enrich nucleic acids. Characteristics of the probe or primer may be adjusted or tuned to produce a sequencing depth for a given region. The sequencing depth may be non-uniform between genomic regions.

The invention provides an ITK-SYK fusion gene detection kit and detection method based on ultra-high depth sequencing, the ITK-SYK fusion gene detection kit comprises a plurality of primers, the detection method uses obtained cf-RNA as a template to amplify a target sequence and build a library, the obtained library is sequenced, offline data is analyzed, and the detection result of the ITK-SYK fusion gene detection kit based on ultra-high depth sequencing is obtained. And calculating the relative proportion of the ITK-SYK fusion gene. According to the detection method, the limit of digital PCR is broken through, the designed amplified fragment is shorter, the detection sensitivity is further improved, an SE50-SE75 short read length mode is used during sequencing, ultrahigh sequencing depth is achieved under the condition of extremely small data volume, 10 <-6 > low-frequency fusion mutation can be detected, the time required by the overall experimental process is as short as 1 day, and the report period is greatly shortened. The method is high in specificity, high in sensitivity, simple, convenient and rapid to operate and rigorous and reliable in result, provides a reliable method for related research of ITK-SYK gene fusion diseases, and is a convenient and non-invasive detection technology.