343 results about "Amplicon" patented technology

The invention provides a primer group for targeted simultaneous detection of multiple bacterial pathogens based on multiple amplicons and application of the primer group, and belongs to the technical field of biological detection of pathogenic bacteria. The primer group for targeted simultaneous detection of multiple bacterial pathogens based on multiple amplicons provided by the invention consists of 196 pairs of primers, and the nucleotide sequences of the primers are shown as SEQ ID NO: 1-392. By using the primer group provided by the invention, multiple pathogens can be rapidly and efficiently detected at the same time, and the primer group has the technical advantages of high targeting, strong specificity and the like.

The invention discloses a rapid detection method for fusarium wilt in corn based on an RPA-CRISPR / Cas12b technology, and belongs to the technical field of nucleic acid detection. The invention provides a specific reagent combination, a kit and a detection method in order to solve the problems of high amplicon pollution risk, complicated operation and the like in the existing technologies such as RPA (recombinase polymerase amplification). The reagent combination comprises an RPA (recombinase polymerase amplification) primer pair with sequences as shown in SEQ ID NO.1 and SEQ ID NO.2, and sgRNA (single guide ribonucleic acid) with a sequence as shown in SEQ ID NO.3. The method comprises the following steps: carrying out RPA amplification by taking nucleic acid of a sample to be detected as a template, carrying out mixed incubation on an amplification product, sgRNA, Cas12b protein and fluorescent reporter molecules, and judging a result by detecting a fluorescent signal. The optimized RPA and CRISPR systems are integrated on the centrifugal micro-fluidic chip, so that the full-flow closed tube and automatic detection is realized, the detection can be completed within 30 minutes, the detection sensitivity reaches 1E2 copies / T, the risk of aerosol pollution is greatly reduced, and the centrifugal micro-fluidic chip is suitable for port quarantine and field on-site rapid detection.

The invention relates to a primer probe set for quantifying HIV-1 (human immunodeficiency virus-1), which comprises an internal standard primer probe set for amplification in the same environment and a target primer probe set corresponding to a specific conserved region sequence of HIV-1, and the internal standard primer probe set and the target primer probe set are configured as follows: the difference between the target probe and the internal standard probe does not exceed 5 DEG C according to the fusion degree; the melting temperature of the internal standard probe is 5-10 DEG C higher than that of the internal standard upstream and downstream primers. Through multi-target design, primer probe optimization, amplicon sequence control and interior label universality improvement, the accuracy, sensitivity and universality of HIV-1 detection are remarkably improved, meanwhile, the development cost and the use complexity are reduced, and the kit has important clinical application value.

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 discloses a 26 Multi-InDel genetic marker system for highly degraded sample typing, a detection primer and application of the 26 Multi-InDel genetic marker system, and belongs to the technical field of forensic medicine identification. According to the invention, through bioinformatics screening and experimental verification, a multi-InDel genetic marker system of which the lengths of 26 amplicons do not exceed 125 bp is constructed. The problem that degradation detection material detection and high system efficiency are difficult to consider at the same time is solved. The random matching probability of the system in Han population in Hunan reaches 2.25 * 10 <-17 >, the cumulative paternity exclusion rate is 0.999925, complete typing of highly degraded DNA can be achieved, triad paternity test can be completed, and a new technical scheme which is efficient and compatible with a capillary electrophoresis platform is provided for forensic practice.

The invention provides a comprehensive 16S automatic analysis method and process based on Web, and from upstream sequencing data processing to downstream data analysis, the most common analysis items at present and 16S advanced analysis are included. And meanwhile, the analysis content is modularized, the data mining method and the like are diversified and deep, and different analysis modules can be selected according to individual needs. The method not only can help researchers without any biological information background to carry out 16S research on flora micro-ecology, but also can overcome the defects of some existing 16S analysis processes, can obtain an accurate and comprehensive analysis result, and meets various analysis requirements.

The invention provides a bay water health status evaluation method, device and product, and the method comprises the following steps: S1, determining a sampling site and collecting a zooplankton eDNA sample to obtain amplicon sequence variant information; s2, annotating amplicon sequence variant information to obtain species composition information and abundance data; s3, obtaining a first evaluation candidate index according to the species composition information and the abundance data; constructing a co-occurrence network and determining a second evaluation candidate index according to the network topology parameters; combining the first evaluation candidate index with the second evaluation candidate index to obtain a third evaluation candidate index; s4, selecting a reference point and a damaged point, and obtaining key evaluation candidate indexes through an artificial neural network model; and S5, constructing a zooplankton integrity index based on the key evaluation candidate indexes, and evaluating the water quality health grade according to the zooplankton integrity index. By utilizing the technical scheme, the precision of evaluating the ecological health condition of the severely polluted bay water body can be improved, and meanwhile, the complexity of an evaluation index system is reduced.

The present invention relates to a method for the ex vivo molecular diagnosis of gastrointestinal stromal tumors, comprising the steps of: providing at least one isolated tissue sample comprising at least one nucleic acid and the subsequent extraction of the at least one nucleic acid. The method according to the present invention further comprises a step of quantifying the at least one previously isolated nucleic acid. Furthermore, the method according to the present invention comprises preparing at least one amplicon library of said previously isolated nucleic acid, which comprises sequences obtained from the FGFR1, NF1, SDHA, SDHB, SDHC and SDHD genes. This step is followed by the step of purifying the at least one amplicon library and the step of simultaneously sequencing the amplicons themselves. The present invention also relates to a multi-gene panel for ex vivo molecular diagnosis of gastrointestinal stromal tumors and a kit comprising such a panel.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

The invention discloses a fiveleaf virus GI.2 whole genome sequencing primer based on an amplicon sequencing technology and application thereof, and belongs to the technical field of virus gene sequencing. The primer group composed of 18 pairs of primers is preferably obtained according to an amplicon sequencing technology, the primer group can effectively improve the primer amplicon coverage degree, it is guaranteed that the primer amplicon coverage degree is 1.5-1.8 times that of a virus sequence, the amplification time is shortened, the amplification difficulty is reduced, the primer amplicon coverage degree and the whole genome capture efficiency are improved, and the primer amplification efficiency is improved. And the method has important significance on epidemic situation traceability and propagation trend of the fiveleaf virus GI.2.

The present disclosure relates to proteomics, including the detection of immune cell target proteins as examples that the disclosed methods can be used for protein detection. Methods, compositions, and systems are described for identifying the presence of proteins, including detecting immune cell proteins from a sample using a combination of multiplex immuno-PCR with antibodies conjugated to oligonucleotides comprising an antibody-specific barcode flanked by PCR priming sites; detection of barcoded amplicons obtained from immuno-PCR with encoded padlock probes comprising codes specific for the barcodes / target protein; rolling circle amplification (RCA) of the circularized padlock probes; and determination of the sequence of the codes amplified by RCA by next generation sequencing or using fluorescently labeled hybridization probes.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Provided herein are multi-modal methods and systems of diagnosing one or more disease, as described elsewhere herein.

The invention provides an oligonucleotide set and a multiple amplicon library building method, and belongs to the technical field of biology. According to the method provided by the invention, a connection product or an extension product can be generated from a gene-specific multiple amplification primer and a library amplification primer in a system in a connection or complementary extension manner, and then the construction of the amplicon library is completed in one step by taking the connection product or the extension product as a long primer. Compared with a traditional multiple amplicon library building method, the method provided by the invention has the advantages that the uncovering operation step can be reduced, and the risk of cross contamination is avoided.

The invention belongs to the field of intelligent medical treatment, and particularly relates to a multi-target pathogen detection primer group design method, equipment, a medium and a program product. The method comprises the following steps: acquiring a target gene bank of various pathogens; performing single primer design on the basis of the target gene bank to obtain a single primer set, extracting amplicons of primer pairs in the primer set, and screening to obtain a first layer of primer pair set after specific verification consisting of primer pairs corresponding to the amplicons conforming to species specificity; extracting a sequencing product of the primer pair subjected to the first-layer specific verification, and screening to obtain a second-layer primer pair set subjected to the specific verification, wherein the second-layer primer pair set consists of primer pairs corresponding to the sequencing product conforming to the species specificity of the pathogen; and screening the primer pair set subjected to the second-layer specific verification to obtain an optimized primer group, wherein Panel specificity is taken as a screening condition in the screening process. According to the invention, through the synergistic effect of three-layer verification, better optimization of the design of the multi-target multiple primer is realized.

The application provides a STR typing method applied to second-generation sequencing data, and relates to the technical field of biology.The method specifically comprises the following steps: customizing an STR locus configuration file; constructing a k-mer index library of a flanking sequence of the STR locus; extracting STR allele sequences from each READ of a sequence alignment file in combination with a CIGAR value and the k-mer index; constructing a PCR ghost peak model of the STR locus, and estimating parameters of the PCR ghost peak model by using a maximum likelihood estimation method; estimating candidate allele frequencies by using a second-generation sequencing sample data set; calculating posterior probabilities of all candidate alleles by using an allele set extracted from a given sequence alignment file, and inferring the most possible allele.The STR typing method has higher detection rate and typing accuracy, and has faster typing speed, and can be used for whole genome sequencing data, high-coverage targeted sequencing data or amplicon sequencing data.

Synthetic Southern Phaseoloviridae satellite RNA molecules and satellite particles containing the same are disclosed. Synthetic Southern Phaseoloviridae satellite RNA molecules containing an internal heterologous RNA virus (HRV) amplicon are also disclosed. Also disclosed are methods of using Southern Phaseoloviridae satellite RNA molecules and satellite particles containing the same to alter plant phenotypes, improve stress resistance in plants, and improve pest and pathogen resistance in plants.

The present invention generally relates to systems and methods for imaging or determining nucleic acids in cells or other samples. In some cases, the transcriptome of a cell may be determined. Certain embodiments are generally directed to determining nucleic acids and other targets in a sample at relatively high resolutions. For instance, nucleic acid probes may be applied to sample, and binding of the nucleic acid probes to a target may be amplified using primary and secondary amplifier nucleic acids. In some cases, there is a maximum number of amplifier nucleic acids that can be bound to a target, e.g., the binding is saturatable, and cannot grow indefinitely, even in the presence of abundant reagents. This may be advantageous, for example, for controlling the brightness of each binding event, controlling the size of the amplified regions (e.g., during imaging), and / or for limiting the degree of amplification noise (i.e. the final variation in amplified signal from molecule to molecule), etc. In addition, in some embodiments, the primary and / or secondary amplifier nucleic acids may be formed from only 3 of the 4 naturally-occurring nucleotides, which may result in less secondary structure, faster binding rates, etc. These properties can in some cases facilitate the rapid design of multiple orthogonal amplification sequences, allowing the extension of such an approach to many distinct molecular targets.

The invention relates to the technical field of high-throughput gene sequencing, and discloses a method for one-tube one-step construction of an amplicon library for detecting gene fusion, and the method for one-tube one-step construction of the amplicon library for detecting gene fusion comprises the following steps: carrying out joint connection on total cDNA of a sample in a connection system to obtain a connection product; the connecting system contains ligase and a short Y joint. According to the one-tube type one-step amplicon library construction method for detecting the gene fusion, in order to comprehensively detect the gene fusion and reduce the omission ratio, the gene fusion detection of known and unknown fusion partners is realized by using multiple single-ended anchoring PCR (Polymerase Chain Reaction) to construct a library and designing a specific primer aiming at a specific gene exon; by means of the method, all gene sequences of main gene exon fusion participating in fusion can be amplified without difference, and the problems that an existing detection method is prone to missing detection, and unknown fusion cannot be detected are effectively solved.

A hand-held molecular diagnostic test device includes a housing, an amplification (or PCR) module, and a detection module. The amplification module is configured to receive an input sample, and defines a reaction volume. The amplification module includes a heater such that the amplification module can perform a polymerase chain reaction (PCR) on the input sample. The detection module is configured to receive an output from the amplification module and a reagent formulated to produce a signal that indicates a presence of a target amplicon within the input sample. The amplification module and the detection module are integrated within the housing.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

The invention discloses a fiveleaf virus GII.3 whole genome sequencing primer based on an amplicon sequencing technology and application thereof, and belongs to the technical field of virus gene sequencing. According to the whole genome sequencing primer and the sequencing method for the fiveleaf virus GII.3, interference of other microorganisms on sequencing can be avoided, the gene sequencing depth is high, the advantages of being wider in whole genome coverage, high in detection accuracy and high in specificity are achieved, the sequencing result can reflect mutation characteristics of main epidemic strains of the fiveleaf virus, and the sequencing result can be used for detecting the mutation characteristics of the main epidemic strains of the fiveleaf virus GII.3. And a powerful tool is provided for rapid diagnosis and full prevention of the fiveleaf akebia viruses.

A method of performing a digital polymerase chain reaction (dPCR) includes performing an amplification reaction on a reaction mixture including a crude lysate sample to generate amplicons of a target nucleic acid of a pathogen, wherein the crude lysate sample includes biological tissue. Fluorescence is detected from a probe hybridized to the amplicons. A method of detecting pathogen in a subject includes performing the above amplification reaction. The crude lysate sample includes biological tissue from the subject. The fluorescence detected from the probe hybridized to the amplicons is used to determine if the pathogen is present in the subject. Compositions, PCR systems, and kits are also provided.

The invention provides methods for the detection of molecular targets by digital PCR (dPCR) using a set of universal probes and target-specific tailed primers. Each target is amplified by a unique mixture of primers. The tailed amplicons anneal to a universal set of probes to detect the associated targets. Some targets are amplified using more than one tailed primer. Some targets are amplified using the same multiple tailed primers. In these embodiments, the primers are concentrated to produce a different number of amplicons for each tailed primer, resulting in a different probe-amplicon balance for each target. Two colors of fluorescence intensity are read and plotted as a 2D plot. In the plot, different targets contribute well-resolved clusters. Each cluster in the plot essentially lies a long its own radius allowing for radial multiplexing. The use of a universal set of probes in multiple assays provides for greater flexibility and throughput.

The invention discloses a Crohn disease identification system, which comprises a data acquisition module, which is used for obtaining a fungus ITS amplicon sequence variant data set based on the results of microorganism DNA extraction and fungus ITS sequencing on respectively acquired fungus sample data of ileum end mucous membranes of healthy personnel and target patients; the model construction module is used for carrying out first training on a constructed Crohn disease recognition model by using a fungus ITS amplicon sequence variant data set based on a random forest algorithm, and determining a model characteristic strain type based on an initial Crohn disease recognition model obtained by the first training; performing second training on the initial Crohn disease recognition model according to the model characteristic strain type to obtain a target Crohn disease recognition model; and inputting the ITS amplicon sequence variant of the model characteristic strain of the individual to be identified into the Crohn disease identification model to obtain an identification result. The recognition system provided by the invention is high in recognition accuracy, good in robustness and simple and efficient in operation.

The invention discloses a megalurothrips megalurothrips methylamino abamectin benzoate resistance molecule detection method which comprises the following steps: (1) collecting megalurothrips megalurothrips female adults in a plurality of regions, and extracting DNA (deoxyribonucleic acid) in a single region in a mixed manner; (2) designing glutamic acid gated chloride ion channel gene specific primers of the megalurothrips megalurothrips, respectively adding specific tags at the front ends of the primers in all regions, and carrying out PCR (Polymerase Chain Reaction) amplification; mixing the PCR products of each region to obtain a library; (3) performing second-generation amplicon sequencing on the library to obtain off-machine data; and (4) analyzing offline data, merging the data in the same region, calculating the mutation frequency of each region by taking the ratio of the mutation (G232S) of the target sequence as an index, and judging the resistance of the megalurothrips usitatus to the emamectin benzoate. The method can be used for rapidly and massively monitoring the emamectin benzoate resistance condition of the field megalurothrips megalurothrips, and an important basis is provided for high-level emamectin benzoate resistance early warning and megalurothrips megalurothrips chemical treatment.

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.

Disclosed are synthetic Marivirus eye satellite RNA molecules and satellite particles containing the same. Also disclosed are synthetic mateur virus satellite RNA molecules containing an internal heterologous RNA virus (HRV) amplicon. Also disclosed are methods of altering plant phenotypes, improving stress resistance in plants, and improving pest and pathogen resistance in plants using the Marivirus eye satellite RNA molecules and satellite particles containing the same.

The present disclosure generally relates to cartridge-based methods and devices for preparing a sequencing nucleic acid library from a sample. In embodiments, a cartridge-based method comprises placing a sample in a self-contained cartridge having a plurality of chambers, a reaction vessel, and a filter disposed in a fluidic path between the plurality of chambers and the reaction vessel, utilizing the filter to isolate the nucleic acid from the sample; forming a library prep reaction mixture; causing the library prep reaction mixture to flow into the reaction vessel and preparing the sequencing nucleic acid library comprising the tagged nucleic acid fragments, amplicons, and / or adapter labeled nucleic acid; isolating the tagged nucleic acid fragments, amplicons, and / or adapter labeled nucleic acid from the library prep reaction mixture on to the filter and eluting each from the filter; and purifying and optionally size selecting the sequencing nucleic acid library on the filter.

Sequencing methods for sequencing populations of nucleic acid molecules in which sequencing reads of amplicons are grouped into families according to the nucleic acid molecule of origin by partitioning, sample indexes and information from the sequencing reads, such as start and end points. The methods described herein provide many advantages over other sequencing analysis methods, including the identification of sequencing reads deriving from the same nucleic acid in the original sample while minimizing the number of aliquots that are processed.