424 results about "Amplicon" patented technology

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 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 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 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 relates to the field of high-throughput sequencing, in particular to an amplicon library building primer pool as well as a preparation method and application thereof. It is found that the uniformity of the sequencing depth value of the corresponding amplicons is improved by adjusting the primer dosage, the uniformity among the amplicons is optimized, and amplification deviation is reduced. Meanwhile, the method is short in consumed time, and does not need to specially design primers, so that the sequencing cost is favorably controlled.

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.

Various embodiments relate generally to the field of nucleic acid amplification and detection, in particular loop-mediated isothermal nucleic acid amplification and the detection of amplicons using designed detection probes. Moreover, various embodiments also relate to methods and kits for determining the presence or quantity of point mutations in a target nucleic acid molecule in a sample using loop-mediated isothermal amplification, which may be used for identifying genetic variants. In one aspect, the detection probe is a single-stranded probe comprising a nucleotide sequence fully complementary to a nucleotide sequence of the probe binding site comprising the point mutation. In another aspect, the detection probe comprising a nucleotide complementary to the point mutation at the penultimate base relative to the 3′ end of the detection probe.

The invention provides a multi-modal soil microorganism classification method based on deep learning. The method comprises the following steps of: cleaning and formatting two types of modal data by using a data preprocessing technology to ensure the quality and consistency of the data, then constructing an efficient feature extraction module, respectively performing feature extraction on the image and amplicon sequencing data in combination with a Transform network and a self-normalization network (SNN) suitable for the sequencing data, and then performing feature extraction on the image and the amplicon sequencing data to obtain a feature extraction result; according to the method, a common attention fusion module is introduced to effectively integrate image features and gene sequence features and capture correlation among different modals, in addition, a multi-modal feature alignment strategy is adopted, feature representation is optimized through a contrast learning method, and therefore the recognition capacity of the model for microbial species is enhanced.

The invention discloses an application of intestinal bacteria in an ulcerative colitis prediction technology, and belongs to the technical field of biology, and the intestinal bacteria are Alistipes finegoldii; the method comprises the following steps: detecting the relative abundance of Alistipes finegii in an excrement sample of a patient, and using the low relative abundance of Alistipes finegii to predict the disease activity of ulcerative colitis; according to the application disclosed by the invention, not only is the association between the Alistipes finegili and the UC disease activity verified, but also the potential action mechanism of the Alistipes finegili is further explored. By means of 16s amplicon sequencing and transcriptomics combined analysis, it is found that the Alistipes finegili plays an anti-inflammatory role through an Hsp90 / AMPK / ACC signal channel, and the intestinal barrier function is maintained. The invention verifies that a new view angle is provided for the effect of the Alistipes finegili in the UC pathogenesis, and provides a theoretical basis for developing a treatment strategy based on the strain.

Methods are provided for amplifying microbial cell free DNA (mcfDNA) in blood samples. In contrast to amplicon sequencing, in which regions between two conserved sequences are targeted for PCR amplification, the methods herein use a single conserved sequence as the primer annealing site to initiate PCR amplification. Enrichment PCR (E- PCR) is performed using a degenerate primer complementary to a conserved region in a microbial phylogenetic marker gene and an additional primer to the opposite end of the mcfDNA. The conserved region is adjacent to a hypervariable region. Amplification PCR is performed on the enriched mcfDNA fragments using a modified degenerate primer having a 3 '-end extension relative to the degenerate primer, and the additional primer, thereby generating enriched amplified mcfDNA fragments. Sequencing the amplified mcfDNA enables identification of microbial species, which is useful for diagnosing and monitoring inflammatory diseases and cancer, including stratification of cancer by stage, type, and tumor subtype.

The invention discloses an internal reference composition, a kit and a method for detecting the absolute content of microorganisms based on high-throughput sequencing, the internal reference composition comprises quantitative internal references P1-P12 and an indication internal reference P0, and the sequences of the quantitative internal references P1-P12 are shown as SEQ ID NO: 1-12; the sequence for indicating the internal reference P0 is as shown in SEQ ID NO: 13. The method comprises the following steps: adding an internal reference composition consisting of internal references with different concentration gradients into a detection sample for amplification together, carrying out gel leakage detection on amplicons by adopting agarose gel, carrying out gel electrophoresis analysis on a gel chart by using software, carrying out concentration comparison on PCR products, pre-estimating the internal reference proportion according to the concentration of a gel leakage strip, and determining the content of the internal reference in the PCR products. According to the method, samples with the internal reference pre-estimation proportion being 8%-50% are conveniently selected, the method is wide in application range, low in cost and high in accuracy, different types of samples can be covered, and the applicable sample concentration range is 1 ng / mu L-50 ng / mu L.

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 invention discloses a microsatellite instability detection method and device based on a next-generation sequencing technology, and belongs to the technical field of biological detection. The method comprises the following steps: selecting MSI sites, and carrying out capture probe design and / or amplicon primer design based on any combination of the sites; selecting a plurality of samples, and calculating the missing fragment proportion and the normal fragment proportion of each sample at each MSI site; selecting a plurality of samples which are judged to be in an MSI-L or MSS state by a PCR method as baseline samples, and setting different depth levels for each baseline sample to construct a baseline; carrying out MSI state detection; selecting a sample of which the MSI state is MSI-H, and judging whether the sample is an abnormal sample or not through a Spearman rank correlation coefficient; and if yes, adjusting the base line and re-judging the MSI state. The method has high stability and high accuracy, does not need a control sample, and can be simultaneously applied to microsatellite instability detection of hybridization capture and amplicon sequencing data.

The invention discloses a method for detecting gene copy number variation based on an amplicon sequencing technology, which can accurately calculate the input molecule number of a target area based on the amplicon sequencing technology by introducing a correction template into a PCR amplification reaction system for correcting the amplification efficiency and amplification preference of a to-be-detected sample. The variation condition of the copy number of the target area of the to-be-detected sample can be accurately judged according to the comparison condition of the copy number of the to-be-detected sample and the number of the input molecules of the internal reference area.

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.