102 results about "Hybridization capture" patented technology

The invention relates to the technical field of crop genetic breeding and plant molecular design breeding, in particular to a pakchoi whole genome liquid phase chip and application. The pakchoi breeding gene chip disclosed by the invention comprises a target capture probe which is designed by taking 1000 core SNP (Single Nucleotide Polymorphism) molecular markers positioned on 40KSNP sites on a pakchoi reference genome version V4.0 as templates. The pakchoi whole genome liquid phase chip provided by the invention comprises a 40K site targeted capture probe mixed solution and a hybridization capture reagent. The pakchoi 40KSNP targeted capture probe can rapidly and effectively track genetic materials of pakchoi, and is suitable for different application scenes such as accurate identification of pakchoi germplasm resources, genetic relationship analysis between materials, variety authenticity identification, QTL gene positioning and mining, molecular marker-assisted breeding, variety improvement and whole genome selective breeding application. Therefore, the method has good application prospect and important social value.

The invention relates to the technical field of high-throughput sequencing, and discloses a kit and a library construction method and a target variation detection and analysis method thereof, the kit comprises a pre-library construction reagent and a target region liquid phase hybridization capture reagent; wherein the pre-library construction reagent comprises a repair reagent, a joint, a connection reagent, an amplification reagent and purified magnetic beads; the target area liquid phase hybridization capture reagent comprises a hybridization reagent, a cleaning reagent, an amplification reagent, a purification magnetic bead, a target gene probe and a CNV / LOH probe. The invention provides a rapid, accurate and low-cost construction method of a library containing a targeting gene probe and a CNV / LOH probe and application of the library, through one-time library construction and sequencing, the advantages of a high-throughput targeting sequencing technology and a CNV-Seq technology are integrated; multi-gene point mutation, insertion and deletion, gene copy number variation, large-fragment copy number variation and heterozygosity deletion can be detected at the same time.

The invention provides a capture probe for detecting a human parainfluenza virus whole genome and a kit and application thereof, and relates to the technical field of gene sequencing. The capture probe composition disclosed by the invention comprises probes of which the sequences are shown as SEQ ID NO. 1 to SEQ ID NO. 947. The capture probe composition disclosed by the invention can fully cover the full-length genome of the human parainfluenza virus type 1-4, and has the characteristics of uniformity, specificity and high capture efficiency on a captured region. According to the method, the whole genome sequence of the human parainfluenza virus can be more economically and efficiently obtained through probe hybridization capture and next-generation sequencing technologies, and the purposes of human parainfluenza virus variation monitoring and virus type traceability can be achieved depending on sequence information.

The present invention discloses a capture probe combination for detecting thyroid cancer-related genes, including at least one of the sequences shown in SEQ ID NOs 1 to 101. A kit comprising the capture probe combination is disclosed to detect thyroid cancer-related genes using the kit. The present invention can detect 8 thyroid cancer-related genes RET, TERT, BRAF, TP53, NRAS, HRAS, KRAS, and PIK3CA at one time using a hybrid capture method. The capture probe and kit provided by the present invention have a wide coverage, a high sequencing depth, a starting amount of samples required for library construction as low as 20 ng, a short experimental process, and the advantages of high efficiency and high precision, and have great application potential and market value.

The invention discloses a congenital agomphosis gene detection panel and application thereof, and belongs to the technical field of gene detection. The congenital odontia gene detection panel comprises probes for detecting or hybridizing 104 congenital odontia related genes shown in a capture table 1, a sample DNA and the panel are subjected to solution / chip hybridization, sequencing is carried out after DNA enrichment of a target area is completed, harmful sites or genes related to congenital odontia are screened / predicted according to a determination result, and the congenital odontia gene detection panel is used for detecting or hybridizing the 104 congenital odontia related genes. The expansibility, speed and resolution required for evaluating the target gene can be met, multiple genes in multiple samples can be evaluated at the same time, time is saved, and cost is reduced. Besides, the panel sequencing is high in coverage rate, strong in pertinence, high in detection sensitivity, higher in effectiveness, easier to manage and capable of more accurately, comprehensively and effectively detecting the related genes of the congenital odontoprisis and mutation conditions of the related genes, and accurate diagnosis and risk assessment of the congenital odontoprisis are achieved.

The invention belongs to the technical field of biochips, and particularly relates to a reusable genetic typing chip and a detection method thereof, the reusable genetic typing chip provided by the invention is prepared from polystyrene microspheres, capture probes and a silicon substrate, and depends on competitive hybridization of DNA in an SNP recognition stage, and the detection result is more accurate. The recognition sequence of the capture probe is converted into the sequence of the target object, and the added detection probes are hairpin probes with a self-protection function, so that the generation of false positive signals is remarkably reduced, and the detection specificity is remarkably improved. And no enzyme participates in the whole process, so that the detection process is remarkably simplified, and the detection cost is reduced.

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.

Disclosed is a single-cell exon sequencing method and a use thereof, the method comprising: S1, tumor single cell sorting; S2, performing MDA amplification of sorted tumor single cells to obtain a genome library; S3, measuring the uniformity of MDA amplification products, selecting multiple sites located on different chromosomes and designing corresponding amplification primers, and testing the amplification effect of the multiple sites of the MDA product of each single cell by means of qPCR, thereby determining whether the genome has been uniformly amplified; S4, gDNA library preparation: breaking the amplified DNA into 150-200 bp fragments, and obtaining a gDNA library by means of end repair, tailing, adding adapters, and amplification; S5, exon capture and library construction: hybridizing the prepared gDNA library with a specific probe, capturing a specific region, and then adding an index tag via PCR amplification to obtain an exon library; and S6, sequencing the exon library.

The present disclosure provides a novel hybrid capture probe for enrichment of a target nucleic acid sequence. Its principle is that a probe sequence is divided into three segments: a middle segment is a target sequence binding segment; a 5′ end segment of one probe can be complementarily paired with a 3′ end segment of another probe, and a 3′ end segment of one probe can be complementarily paired with a 5′ end segment of another probe. This novel probe can bind more robustly to a target sequence, and has better effects in hybrid capture and targeted enrichment at low starting amounts or small target regions (Panels) compared with traditional hybrid capture probes.

The present disclosure provides a method for detecting the methylation and mutation status of a DNA sample, specifically, a method for simultaneously detecting the methylation and mutation status of DNA molecules in a sample, the method comprising treating the sample with a methylation-sensitive restriction enzyme, performing hybrid capture on amplification products of the restriction enzyme-treated sample and a sample that has not been subjected to enzyme cleavage treatment with a probe set including a mutation capture probe and a methylation capture probe, and sequencing the captured products.

The invention discloses a probe combination for detecting genetic susceptibility genes of prostatic cancer. The probe combination comprises at least one of sequences as shown in SEQ ID NO 1-89. The invention also discloses a kit comprising the probe combination and a method for detecting the genetic susceptibility gene of the prostatic cancer by using the kit. According to the present invention, the prostatic cancer genetic susceptibility related genes such as ATM, ATR, BRCA1, BRCA2, BRIP1, CHEK2, EPCAM, FANCA, HOXB13, MLH1, MRE11A, MSH2, MSH6, NBN, PALB2, PMS2, RAD51C, RAD51D and TP53 can be detected at one time by using the hybrid capture method; the probe provided by the invention is wide in coverage, high in sequencing depth and capable of detecting embryonic line variation of all exon regions of a target gene. All related diseases of the related genes of the genetic susceptibility of the prostatic cancer can be reported, genetic modes corresponding to the diseases are provided, and the application potential and the market value are large.

According to the library building kit, the library hybridization capture method, the library building method and the application of the X-linked dyspepsia-related genes, the library building kit comprises a probe pool containing a capture probe, and the capture probe is used for hybridizing and capturing the X-linked dyspepsia-related genes. According to the kit, firstly, a DNA library is constructed, the initial quantity of a template can be as low as 10 ng, enzyme digestion breaking, terminal filling and A tail adding are completed in one system, the consumed time is short, and the efficiency is high; secondly, as many as 384 pairs of UDI probes are arranged in the library building kit, and 384 libraries can be simultaneously built and can be loaded on a machine for sequencing together; in addition, according to a rapid hybridization system of the library building kit, the hybridization time can be as short as 15 min, and the efficiency of common overnight hybridization can be achieved. The size of the finally obtained library fragment is about 300-500bp, and the library fragment can be compatible with various sequencing platforms of illumina for sequencing.

The invention provides a phosphorylated probe capture amplification method. The method comprises the following steps: hybridizing a phosphorylated probe to genome DNA to form a hybridization probe, extending and connecting the hybridization probe to form a closed loop by using a bridging primer to form a closed loop PCR product, and carrying out PCR amplification on the obtained PCR product to obtain an amplified product which is an enriched target area. According to the application, phosphorylation is carried out by taking the probe as a skeleton, a sequence on an Illumina Tru Seq joint and a bridged complementary sequence are added, by adopting a mode of increasing primer bridging, products after probe amplification are connected end to end to form cyclization, and by adopting a mode of increasing EXO1 / EXO3 enzyme digestion, the formation of a dimer is reduced, so that the detection sensitivity is improved, and the detection sensitivity is improved. According to the invention, small-volume hybridization and small-volume amplification modes are adopted, so that the molecular collision probability is increased. The method has ultrahigh specificity and accuracy, each target site is independently amplified, the PCR preference is avoided, the coverage uniformity is superior to that of multiple PCR and hybrid capture, the operation is simple and convenient, the period is short, and the experimental process only needs several hours.

A DNA methylation library construction method and a library obtained with same, a DNA hybridization capture method and a kit. The construction method comprises: providing a test sample comprising a plurality of double-stranded DNA fragments; degenerating the double-stranded DNA fragments into single-stranded DNA; carrying out ligation reaction on the single-stranded DNA and a double-stranded linker sequence to obtain single-stranded DNA linked with the double-stranded linker sequence; carrying out extension reaction on the single-stranded DNA linked with the double-stranded linker sequence to form an extended fragment, the extended fragment being linked with the double-stranded linker sequence of the single-stranded DNA; carrying out oxidation reaction on cytosine having methylation modification in double-stranded DNA linked with the double-stranded linker sequence to obtain double-stranded DNA having protected cytosine; removing the extended fragment in the double-stranded DNA having the protected cytosine to obtain single-stranded DNA having protected cytosine; carrying out deamination reaction on cytosine having no methylation modification in the single-stranded DNA having the protected cytosine to obtain single-stranded DNA having uracil; and carrying out amplification reaction on the single-stranded DNA having uracil to obtain a DNA methylation library.

The invention discloses a 20K liquid phase chip for precise identification and efficient breeding of local goose germplasm resources and application of the 20K liquid phase chip, and relates to the technical field of biology. The method comprises the following steps: S1, genome DNA breaking; S2, whole genome library construction; and S3, probe hybridization capture. By developing the 20K liquid phase chip, a plurality of genetic markers are integrated together in a high-density manner, the number of the markers is greatly increased, the coverage range of the markers is greatly expanded, efficient and comprehensive genetic analysis can be performed in the whole genome range, the problems of insufficient number of the markers and narrow coverage range in the prior art are solved, and the breeding accuracy is improved; the method can effectively improve the precise identification capability of local goose germplasm resources, optimize the breeding strategy and accelerate the local goose breeding process, thereby providing powerful technical support for genetic improvement and efficient breeding of local goose varieties.

Provided are a method and a combination for one-tube simultaneous detection of tumor-specific gene mutation and methylation, and the use thereof. The method comprises searching a database to select mutation and methylation sites of a cancer driver gene and a cancer suppressor gene, synthesizing capture probes correspondingly paired with a target interval, performing hybrid capture on an amplification product of a sample treated with a restriction endonuclease by using a probe set comprising tumor-specific gene mutation and methylation capture probes, constructing a high-throughput sequencing library containing a target region, and performing high-throughput sequencing to obtain the sequence of a target fragment, so as to obtain the results of methylation, point mutations and indel variation of a cancer-associated gene. The provided method enables one-tube simultaneous detection of mutation and methylation states of a cancer-associated gene in one assay, requires a low content of a gene to be detected, can be used for methylation and mutation detection of a tumor-specific DNA, and has low detection costs and high efficiency.

The invention provides a chlamydia whole genome detection method and application thereof, and further provides a probe for capturing a chlamydia whole genome, and the probe is designed according to a chlamydia genome sequence as a reference sequence; the probes are 3-10 layers of probes designed in an imbricated manner, the length of each probe is 90-120nt, and the total number of the probes is 50,000-200,000. A probe for capturing a chlamydia whole genome is used for performing hybrid capture and high-throughput sequencing analysis on a to-be-detected sample to obtain a whole genome sequence. According to the detection method developed by the invention, a whole genome sequence can be directly obtained from a clinical sample, the problem that the chlamydia is difficult to detect is solved, the detection efficiency and typing accuracy of the chlamydia are greatly improved, and the method has an important application prospect in clinical detection.

The present application relates to the technical field of gene detection, in particular to a SNP molecular marker for detecting donor cfDNA of a pregnant organ transplant patient, a detection method and device. The SNP molecular marker for detecting donor cfDNA of a pregnant organ transplant patient is shown in Table 10. The present application uses free DNA in peripheral blood of a pregnant patient and genomic DNA in peripheral blood of a biological father of a fetus as detection objects, adopts liquid phase hybridization capture and high-throughput sequencing technology, uses thousands of SNP sites, obtains the genotype of the fetus through the genotype of the couple, eliminates the influence of cfDNA from the fetus on the content of cfDNA from the transplanted organ, accurately determines the concentration of cfDNA from the transplanted organ, has higher detection sensitivity, can be detected multiple times only by using peripheral blood of the patient, and achieves the purpose of long-term dynamic monitoring.

The invention belongs to the field of medical detection, and particularly provides a solid tumor molecule residual focus detection method which comprises tissue baseline detection, probe design, peripheral blood MRD detection and result analysis and interpretation. According to the present invention, the technical steps such as optimized pre-library construction and hybridization capture process, customized probe design, unique fusion gene probe design and the like are improved, such that the problems of low detection sensitivity, low specificity, low accuracy and the like in the prior art are solved.

The present invention discloses a capture probe-based amplicon library construction method and its application, which belongs to the field of medical technology. The present invention realizes a library construction technology that performs probe capture and multiple primer amplification in the same process: using probe hybridization capture to perform non-directional enrichment of DNA / RNA templates and using primers to perform specific enrichment of target fragments to construct libraries, respectively, to achieve DNA and RNA co-construction of libraries. The above method is suitable for detection technologies such as MRD that require trace sample library construction and mutation information amplification, and can simultaneously analyze DNA-level variation SNV / INDEL / fusion variation and RNA-level fusion variation, thereby improving detection sensitivity, while reducing clinical biological background noise caused by the probe method and improving clinical specificity.

This application provides a method and system for infectious disease risk prediction based on a large language model and wastewater monitoring. The method includes: acquiring a multimodal time-series dataset of a target area in a first time period, wherein the multimodal time-series dataset includes wastewater epidemiological data sequences of the target disease, vaccination data sequences of the target disease, clinical monitoring data sequences of the target disease, environmental data sequences, and demographic data sequences obtained based on technologies such as multipathogen hybridization capture sequencing and PCR; converting the multimodal time-series dataset into a text time-series data sequence; inputting the text time-series data sequence into a preset risk prediction model to generate corresponding feature vectors, and predicting the trend of hospitalization rate changes of the target disease based on the feature vectors; and predicting the risk level of the target disease in the target area based on the trend of hospitalization rate changes and the wastewater epidemiological data sequence, thereby improving the accuracy of infectious disease area risk prediction.

Provided herein are systems, kits, compositions and methods for sequencing library preparation and sequencing workflow (e.g., for the identification of mutations). In certain embodiments, provides herein systems and methods to identically barcode both strands of templates, and PCR-based enrichment of each strand that does not require hybridization capture.

The invention discloses a library construction method for non-HPV (human papillomavirus) related cervical tumor and precancerous lesion molecular subtypes thereof based on high-throughput sequencing, which comprises the following steps: ultrasonically breaking genome DNA (deoxyribonucleic acid) of a detected sample to obtain a DNA fragment, modifying the tail end, connecting a joint, and performing purification and pre-amplification reaction, namely performing hybridization reaction on a pre-amplification sequence by using a hybridization capture reagent, according to the method, a hybridization capture reagent is adopted, DNA fragments combined through non-specific capture are enriched and removed, then an amplification reaction is carried out, a library is obtained, next-generation sequencing is carried out, original data are subjected to bioinformatics analysis, variation information is obtained, and the hybridization capture reagent comprises specific primers with the sequences shown as SEQ ID NO: 1-175. According to the present invention, the integration of the non-HPV-related cervical tumor and precancerous lesion molecule detection is achieved, the detection can be completed in one experiment, and the sequencing depth is improved by specifically enriching the target region so as to improve the sensitivity of the non-HPV-related cervical tumor and precancerous lesion molecule detection.

The invention discloses a mutation back noise filtering algorithm based on next-generation sequencing data, relates to the technical field of high-throughput sequencing data analysis, and aims to solve the problems that the prior art depends on a baseline, and is poor in adaptability and high in false positive. The algorithm comprises the following steps: preprocessing sequencing data to obtain a pileup file, classifying sites according to a sequence context, calculating an error rate, constructing a layered back noise model to check mutation, qualitatively determining real mutation and back noise by combining a sample type, and evaluating sample quality. The method does not need to construct a base line in advance, adapt to hybrid capture and amplicon sequencing, can improve mutation detection specificity and repeated sample consistency, guarantees result reliability, and is suitable for scenes such as tumor gene detection.

The invention discloses a preciseness-adjustable probe hybridization capture method which is characterized in that a hybridization resolution enhancing probe is added into a system of a probe hybridization capture target area, a potential non-specific capture area is competitively combined, and the hybridization capture resolution of the probe to the target area is improved. The binding strength of the hybridization resolution enhanced probe and a potential non-specific capture region is higher than that of the probe and the potential non-specific capture region, and the binding strength of the hybridization resolution enhanced probe and a target region is far lower than that of the probe and the target region, so that the detection sensitivity of the target region is not influenced. The method realizes local fine control of hybridization capture preciseness of the nucleic acid target area, and simultaneously achieves high-sensitivity and high-specificity detection of the nucleic acid target area compared with a traditional method.

The invention belongs to the technical field of genotyping, and particularly relates to a Tan sheep 50K liquid phase chip based on targeted capture sequencing and application thereof, the Tan sheep 50K liquid phase chip is composed of independently packaged probe mixed liquid and a hybridization capture reagent, the independently packaged probe mixed liquid comprises a Tan sheep 50K probe, and site information of the Tan sheep 50K probe relates to 50000 SNP sites. The prepared Tan sheep 50K liquid chip is mixed with a Tan sheep high-throughput sequencing library, a target site is captured and amplified and purified, and after a product is subjected to high-throughput sequencing, a sequencing result is compared with a sheep reference genome, so that the genetic typing of the Tan sheep to be detected is obtained. The method is applicable to resource evaluation, genetic identification and genome selection of the Tan sheep variety, can break through key technical evaluation restricting genome selection breeding, lays a foundation for building a Tan sheep genome selection sharing platform, and accelerates the realization of the Tan sheep from phenotype selection to genome selection.

The invention belongs to the technical field of gene sequencing, and particularly relates to a library building kit and probe for detecting blood tumor related fusion genes. According to the library building kit, only a trace amount of total RNA is needed to be used for cDNA synthesis, the initial quantity of a template can be as low as 10 ng, so that a cDNA library is built, then the library is subjected to hybrid capture and enrichment by using an autonomously designed probe hematologic tumor fusion gene Panel (RA Panel), the time consumption is short, the efficiency is high, and simultaneous building and on-machine sequencing of 384 libraries can be realized. According to the rapid hybridization system of the library building kit, the shortest hybridization time can reach 30 min, the size of a finally obtained library fragment is about 200-400 bp, and the rapid hybridization system can be compatible with various Illumina sequencing platforms for sequencing. According to the invention, through a simple and easy-to-use solution of NGS sequencing while synthesis, rapid and accurate typing of fusion genes which may affect blood tumor diagnosis is realized.

Described herein are methods and compositions for improved hybridization capture for enriching for target nucleic acid sequences from a population of nucleic acids. In one aspect, the methods and compositions are useful for Next Generation Sequencing (NGS) applications. The methods and compositions include combining in solution capture probes and target nucleic acid and permitting hybridization of the target nucleic acid to the capture probes under conditions to promote efficient hybridization. Following hybridization, the probe / target complex is immobilized to a capture material while simultaneously incubating at an optimum hybridization temperature. The incubation denatures unwanted nucleic acids from the capture probes further enriching for target nucleic acid.

The invention belongs to the technical field of library construction, and particularly relates to a DNA targeted library construction kit and application thereof. The kit comprises a hybridization capture reagent combination, the hybridization capture reagent combination comprises a hybridization reaction solution, and the hybridization reaction solution comprises a hybridization reaction solution 1 and a hybridization reaction solution 2; the hybridization reaction solution 1 is prepared from betaine, tetramethylammonium chloride, Mg < 2 + > and Triton X-100; the hybridization reaction liquid 2 is prepared from formamide and N-methyl pyrrolidone; hybridization of the probe and the library is facilitated, the capture efficiency is superior to that of an existing hybridization reaction solution, and Panel with different sizes and different hybridization durations can be compatible; a small panel can also achieve relatively high and relatively stable capture efficiency, the hybridization time is selectable within 1-20 h, fast and slow hybridization reagents are unified, and production and simultaneous operation of multiple products are facilitated.

The present application belongs to the field of medical detection, and specifically provides a detection method for solid tumor molecular residual lesions, which comprises tissue baseline detection, probe design, peripheral blood MRD detection and result analysis interpretation. Through the improvement of technical steps such as optimized pre-library construction and hybridization capture process, customized probe design and unique fusion gene probe design, the present application solves the problems of low detection sensitivity, low specificity and low accuracy in the prior art.