17 results about "Hybrid capture" patented technology

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 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.

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 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 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 invention relates to an NGS detection kit for gene variation related to targeted medication of gastric cancer and application of the NGS detection kit. The kit provided by the invention comprises a capture probe for detecting related genes and a corresponding reagent based on a next-generation sequencing technology, and variation conditions of six genes (BRAF, NTRK1, NTRK2, NTRK3, RET and ERBB2) of gastric cancer targeted medication related genes can be detected at one time by utilizing a hybrid capture method. The probe provided by the invention has the advantages of wide coverage and high sequencing depth, and can detect all variations in the capture area of the designed gene probe. According to the method, all variations of genes related to gastric cancer targeted medication can be reported, the specificity on gastric cancer patients is high, compared with multi-gene solid tumor large panel detection, resource waste caused by irrelevant gene detection is reduced, the detection cost is reduced, and the detection efficiency is improved.

The invention relates to the technical field of gene detection, in particular to an IKBKG gene mutation detection probe group and a kit for liquid phase hybridization capture of a Pacbio sequencing platform. The probe group comprises sequences as shown in SEQ ID NO. 1 to SEQ ID NO. 329; by designing an IKBKG gene specific probe and combining the advantages of long reading length and high accuracy of Pacbio sequencing, synchronous detection of IKBKG gene point mutation, insertion and deletion and large-fragment structure variation is realized. The invention overcomes the interference of pseudogene IKBKGp1, is suitable for clinical diagnosis of pigment disorder and other related diseases, and has important clinical transformation value.

The invention discloses a site, a primer, a kit and a method for detecting cervical cancer DNA methylation, a DNA methylation site LRFN5 is obtained through library construction, hybrid capture, high-throughput sequencing and qMSP detection on a cervical cancer tissue sample through screening, and it is found that the LRFN5 site has differentiated expression in the early stage (1-2 stages) of CIN compared with cervical cancer samples in other stages, so that the DNA methylation site LRFN5 can be used for detecting cervical cancer DNA methylation. Therefore, the site can be used for early recognition of the cervical cancer, and early diagnosis and early treatment of the cervical cancer are facilitated.

The application discloses a probe and a method for detecting micro residual lesions. The probe for detecting micro residual lesions is a four-layer encrypted imbricated hybrid capture probe, wherein two layers of probes are wild-type probes, and two layers are mutant probes. The nucleic acid sequence of the wild-type probe comprises the sequence described in SEQ ID NO. 1-SEQ ID NO. 74, and the nucleic acid sequence of the mutant probe comprises the sequence described in SEQ ID NO. 75-SEQ ID NO. 149. The four-layer encrypted imbricated hybrid capture probe for detecting micro residual lesions is designed, a micro residual lesion molecular detection method with high sensitivity and good specificity is provided, the low-frequency mutation capture efficiency is high, and the detection limit of the ct DNA mutation frequency containing micro residual lesions can be as low as 0.005%.

The application discloses a mutation background noise filtering calculation method based on second-generation sequencing data, and relates to the technical field of high-throughput sequencing data analysis, to solve the problems that the prior art depends on a baseline, has poor adaptability and high false positives. The algorithm first preprocesses sequencing data to obtain a pileup file, classifies sites according to sequence context and calculates error rates, constructs a hierarchical background noise model to test mutations, combines sample types to qualitatively determine real mutations and background noise, and simultaneously evaluates sample quality. The algorithm does not need to construct a baseline in advance, is suitable for hybrid capture and amplicon sequencing, can improve mutation detection specificity and consistency of repeated samples, guarantees reliable results, and is suitable for tumor gene detection and other scenes.

According to the kit for detecting the inherited metabolic disease related genes based on the hybridization capture method, the hybridization capture method and the application, the kit comprises a probe pool of capture probes, and the capture probes are used for hybridizing and capturing the inherited metabolic disease related genes. The kit disclosed by the invention has the beneficial effects that when the kit is used for constructing a DNA library, the initial quantity of a template can be as low as 10ng, and enzyme digestion breaking, terminal filling and A tail adding are completed in one system, so that the consumed time is short, and the efficiency is high; secondly, the number of index pairs of the kit is up to 384, and 384 libraries can be constructed at the same time and can be used for sequencing on a machine together; in addition, according to a rapid hybridization system of the kit, the shortest hybridization time can reach 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.

Provided are a micro-satellite instability detection method and apparatus based on a next-generation sequencing technology, belonging to the technical field of biological detection. The method comprises: selecting MSI sites, and designing capture probes and / or amplicon primers on the basis of any combination of the sites; selecting a plurality of samples, and calculating the proportion of deletion fragments and the proportion of normal fragments at each MSI site for each sample; selecting a plurality of samples that are determined to be in an MSI-L or MSS state by a PCR method as baseline samples, and setting different depth levels to construct baselines for each baseline sample; performing MSI state detection; selecting samples with an MSI state of MSI-H, and determining whether the samples are abnormal samples by using a Spearman rank correlation coefficient; and if yes, adjusting the baselines and re-determining the MSI state. The provided method has high stability and high accuracy, does not require a control sample, and can be simultaneously applied to micro-satellite instability detection for hybrid capture and amplicon sequencing data.

The invention discloses a library construction method for detecting gastrointestinal stromal tumor molecular typing and a gastrointestinal stromal tumor molecular typing method, and belongs to the technical field of biology. Comprising the following steps: fragmenting a DNA (Deoxyribonucleic Acid) extract of a gastrointestinal stromal tumor patient specimen, modifying a terminal, connecting a joint, purifying and pre-amplifying, and carrying out hybridization reaction on a hybridization capture enrichment probe and a pre-amplified sequence to enrich a target sequence; the hybridization capture enrichment probe comprises a sequence as shown in SEQ ID NO: 1-109; the method comprises the following steps of: performing amplification after non-specific capture and binding DNA fragments are eluted and removed, performing nucleic acid concentration and fragment length quantification on a product to obtain a library, and performing bioinformatics analysis on gastrointestinal stromal tumor patient specimen data by next-generation sequencing to obtain gastrointestinal stromal tumor molecular typing information. According to the invention, in-vitro non-diagnostic gastrointestinal stromal tumor molecular typing joint detection is realized, multi-gene variation form identification is completed in one experiment, the detection cost is saved, and the sensitivity is high.

The invention provides a method and a device for detecting exogene deletion. The method comprises the following steps: S1, obtaining sequencing data; s2, carrying out partition on the hybridization capture region, and respectively obtaining a log2 value of the sequencing coverage degree in each bin partition; s3, calculating the median of the log2 values of all bin partitions obtained in the step S2 as a median value; s4, based on the log2 values obtained in the step S2, calculating the median of the log2 values of all bin partitions corresponding to the to-be-detected gene as a logR value; and S5, judging the deletion state of the to-be-detected gene of the to-be-detected sample according to the difference value between the logR and the median and the threshold value of the logR. According to the method, whether the target gene is subjected to heterozygous deletion or homozygous deletion can be accurately detected.

The invention relates to an endometrial cancer molecular typing, medication and genetic susceptibility related gene detection kit and application thereof. The detection kit comprises a probe group for targeted medication related genes, genetic susceptibility related genes, immunotherapy related genes and molecular typing related genes. On the basis of a next-generation sequencing technology, more than 100 genes highly related to development of endometrial cancer can be detected at a time by utilizing a hybrid capture method, and the genes comprise genes related to targeted medication, genes related to genetic susceptibility, genes related to immunotherapy and genes related to molecular typing. The probe is wide in coverage, high in sequencing depth and capable of detecting germline variation of all exon regions of related genes. The invention can report endometrial cancer targeted medication related variation and immunotherapy related variation, also can report all related diseases of genetic susceptibility related genes, and provides genetic modes corresponding to the diseases.

The invention discloses a method and a probe group for detecting EGFRvIII mutation based on DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) levels. The method comprises the following steps: firstly, designing a probe group of DNA level and RNA level EGFRvIII mutation, then constructing an intermediate library by a DNA sample, and carrying out fragmentation, reverse transcription and library construction on the RNA sample to obtain an RNA sample intermediate library; the DNA sample library and the DNA level probe group are subjected to hybrid capture, the RNA sample library and the RNA level probe group are subjected to hybrid capture, and libraries enriched with target sequences are obtained respectively. Sequencing data is obtained through high-throughput sequencing, and EGFRvIII variation information of a DNA level and an RNA level can be obtained after analysis of corresponding information analysis software. Compared with a traditional method for detecting EGFRvIII mutation, the detection method provided by the invention is more sensitive and higher in accuracy.