175 results about "Mutation frequency" patented technology

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

The invention discloses a tumor cloning mutation detection method and device based on next-generation sequencing and a memory medium. The method provided by the invention comprises the steps of carrying out mutation detection on a comparison file of paired tumor and normal samples through utilization of mutation detection software, computing a mutation frequency, and selecting segments with high sequencing quality as a statistics result; carrying out copy number and purity detection on the paired tumor and normal samples through utilization of purity detection software; combining small segments into big segments, and annotating the copy number in a mutation area; and computing a proportion of the mutation in a tested tumor tissue through utilization of a beta distribution model according to tumor sample purity and copy number detection results, thereby judging a tumor cloning mutation type. According to the method provide by the invention, influences of the sample purity and multiploidon the detection are avoided, the mutation type detection is relatively accurate, the subcloning mutation with clinical significance can be effectively identified, and the foundation for accurately and deeply researching a tumor cloning evolution process and searching a tumor therapy molecular mechanism is laid.

The present invention provides compositions and improved methods for multi-site directed mutagenesis and DNA shuffling. The present compositions and methods provide increased mutation frequency and increased number of transformants which allow one to sequence only a few clones in order to identify the correct mutants and to obtain the desired mutant by screening large number of transformants in a short time. Moreover, the inclusion of FEN-1, PEF and optimized buffer and cycling conditions provided in the present invention should also facilitate random mutagenized library construction and the mutagenesis of large or difficult templates.

The invention discloses a label joint for detection of ultra-low-frequency gene mutation and an application of the label joint. The label joint comprises a first chain and a second chain, wherein the first chain comprises a first nucleic acid sequence, a second nucleic acid sequence, a third nucleic acid sequence and a fourth nucleic acid sequence from the 5' end to the 3' end sequentially; the first nucleic acid sequence is a universal primer binding target region; the second nucleic acid sequence is a random single-molecular label sequence and used for distinguishing DNA fragments; the third nucleic acid sequence is a sample label sequence and used for distinguishing library samples; the fourth nucleic acid sequence is a sequencing primer binding target region; the second chain is a sequence reversely complementary to the 3' end of the first chain to form double-strand. The label joint is introduced into a tested sample, can effectively improve the mutation detection sensitivity of the tested sample and can even detect mutation sites with mutation frequency as low as 0.1%; besides, the label joint is easy to prepare and has quite high actual application values.

A molecule adaptor having characteristics of high stability, a high sample DNA connection efficiency and correction functions is designed based on illumina sequencing adaptor optimization. The molecule adaptor can detect mutation sites the mutation frequency of which is as low as 0.05%. The molecule adaptor is used for identifying real mutations in a sample sequencing library constructing process and false-positive mutations introduced by an operating process. In addition, a method of constructing a sequencing library for a sample to be detected is provided.

The invention discloses an FFPE reference product for gene detection and a preparation method and application of the FFPE reference product. The preparation method comprises the following steps that S1, cell culture is performed on a tumor cell line, and cell pellets are collected; S2, formalin fixation is performed on the cell pellets, then sepharose gel wraps the cell pellets to form cell aggregates, and the cell aggregate are prepared into cell paraffin blocks; S3, genomic DNA of the tumor cell line in the cell paraffin blocks is extracted, and genetic mutation frequency determination is performed on the genomic DNA of the tumor cell line; S4, the genomic DNA of the tumor cell line containing a target mutation site is mixed into a DNA mixture of a target mutation frequency, and the DNAmixture is the FFPE reference product for gene detection. According to the technical scheme, formalin fixation and paraffin wrapping are performed on the cells cultured by tumor cell line, so that thesituation of clinical samples can be better simulated.

The invention provides a device for detecting somatic mutation. The device comprises an acquisition module, an annotation module, a screening module, a computing module, a mutation type primary judgment module and a mutation type correction module, wherein the screening module comprises a virtual comparison set, and the virtual comparison set contains 561 cases of mutation information of leukocytes. According to the device, detection data is compared with a database including the virtual comparison set through the screening module, so that embryonal system mutation sites are screened; the computing module is utilized to obtain a mean value and a standard deviation of embryonal system mutation frequency of all chromosomes through computing; then the mutation type primary judgment module and the mutation type correction module are utilized to analyze mutation frequency features of all different mutation sites to determine the type of the mutation sites; and the primarily determined mutation type is corrected through the database of the mutation sites of the known mutation type, so that the mutation sites with somatic mutation in samples are screened out. Through the device, detection accuracy of the mutation sites with somatic mutation is improved.

A method of improving DNA repair and reducing DNA damage and for reducing mutation frequency in skin for the purpose of reducing consequences of exposure to solar or ultraviolet radiation is disclosed. The methods comprise administering to the skin a composition containing deoxyribonucleosides in concentrations sufficient to enhance DNA repair or reduce mutation frequency in a vehicle capable of delivering effective amounts of deoxyribonucleosides to the necessary skin cells.

The invention relates to a device for detecting somatic cell mutation by circulating tumor DNA (deoxyribonucleic acid) samples. The device comprises a data acquisition module, a mutation frequency statistics module, a comparison module, a judgment module and a detection result output module. The device for detecting the somatic cell mutation by the aid of the circulating tumor DNA samples has the advantages that system errors can be accurately differentiated from the real somatic cell mutation by the device, accordingly, the sensitivity can be improved, and false positive and false negative can be reduced.

The invention provides a biological information quality control method and device based on next-generation sequencing and a storage medium. The method comprises the steps that sequencing data of a to-be-detected tissue sample and control sample which are from the same individual source is obtained, wherein the control sample is a sample other than the to-be-detected tissue sample; the sequencing data is compared with a reference genome, a locus serving as a homozygous locus in the control sample while serving as a non-homozygous locus in the to-be-detected tissue sample is detected and regarded as contamination, and the contamination degree of the to-be-detected tissue sample is obtained through detection; it is judged whether or not the contamination degree is larger than a contaminationthreshold, if yes, it is determined that contamination exists, and a contamination source is found in the sequencing data in the latest several batches; if the contamination source is found, all mutations of the contamination source are removed from mutation detection results of the sequencing data of the to-be-detected tissue sample; if the contamination source is not found, mutations having themutation frequency less than the contamination degree and belonging to a known population high-frequency reproductive mutation database are removed. The biological information quality control method based on next-generation sequencing can judge the quality state of the sample, and remove false positive mutations caused by the quality problem from the detection results.

The invention relates to a statistics verification method for high-throughput sequencing mutation detection results. The method comprises the steps that firstly, a feminine background mutation frequency library of interested mutation is established; based on the feminine background mutation frequency library, the mutation detection results of a mononucleotide replacing type in the high-throughput sequencing mutation detection results are verified through Z detection, and the mutation detection results of a continuous polynucleotide missing type in the high-throughput sequencing mutation detection results are verified through chi-square detection. By means of the method, the high-throughput sequencing mutation detection results can be verified without any cost, and high correctness and sensitivity are achieved.

The invention provides a preparation method of a tumor sample sequencing reference, and belongs to the technical field of high-throughput sequencing. The method comprises the following steps: performing monoclonal culture on a tumor cell line to obtain a monoclonal cell line and extracting a whole genome; determining an allele frequency; determining a dilution multiple according to an allele mutation frequency and a target allele mutation frequency; diluting the monoclonal cell line with negative cells in multiple proportion to obtain mixed cells; extracting a whole genome of the mixed cells,and determining an allele mutation frequency; and according to the comparison between the allele mutation frequency and the target allele mutation frequency of the mixed cells, refining the multiple of multiple-proportion dilution, and diluting the monoclonal cell line with negative cells to obtain the reference. According to the method disclosed by the invention, the gene background of a cell line is determined by combination of cell strain monoclone and high-throughput sequencing; and a multiple-proportion dilution method with multi-step gradual refinement is combined with a flow cytometry to accurately count cells so as to ensure high repeatability of reference preparation.

The invention discloses a novel deafness related gene mutation detection system, for detecting whether deafness gene mutation sites have mutation or not by using multiple PCR primers and a detection probe. The deafness gene mutation sites comprise a newly found CEACAM16 gene (NM_001039213.2)c.418A>C mutation site. The 32 sites selected by the detection kit are screened according to the latest human genetic deafness related gene mutation information and firsthand information accumulated by the inventor in clinical detection, and the selected sites are sites with relatively high mutation frequency in people of China and other countries and sites which are newly found in clinical detection by the inventor. Compared with deafness related gene mutation detection products available in the market, the kit covers relatively more detection sites so that the mutation detection rate is increased.

The invention belongs to the field of plant biotechnology, and in particular relates to rice thousand kernel weight gene TGW6 guided RNA target sequences and application thereof. The oligonucleotide sequences of the rice thousand kernel weight gene TGW6 guided RNA target sequences are as shown in SEQ ID NO.1-6. The group of the target sequences is applicable to the editing of rice genome, and has the advantages of being convenient, efficient and the like. When the rice thousand kernel weight gene TGW6 guided RNA target sequences provided by the invention are used for editing the rice genome, the mutation frequency of rice thousand kernel weight gene tgw6 is 90% or above, including more than 50% of fragment-deleted homozygous mutants and around 40% of diallelic heterozygous mutants. The invention provides an important reference for the rapid establishment of high-quality new rice germplasm having an important application value on rice quality and like production, and is expected to provide a safe and efficient new way for the innovation of rice germplasm resources; and the invention has important theoretical and practical significance.

The invention provides preparation of a circulating tumor free DNA (deoxyribonucleic acid) standard product for a simulating plasma matrix. The preparation comprises the following steps of A, purchasing a natural cell line carrying gene mutation, or editing the gene to obtain a cell line carrying the gene mutation; B, cracking a wild cell line and a gene mutation cell line, and obtaining fragmented DNA by a nucleosome enzyme digestion or ultrasonic intercepting method; mixing the fragmented DNA of the wild cell line and one or multiple fragmented DNA of the gene mutation cell line according toa ratio, so that the mixture has the required gene mutation points and mutation frequency; D, preparing simulating plasma; E, feeding the mixture in step D into the simulating plasma, fully and uniformly mixing, and verifying the property. The preparation has the advantages that a standard product of a ctDNA sample approximate to a natural sample of the human body is provided, and a standard reference substance is provided for a circulating tumor free DNA detection platform, development of detection reagents, and evaluation on laboratory detection ability.

The invention provides a standard product for detection of clinical drug-resistant genes in intestinal cancer and application thereof. The standard product comprises a minimum detection limit reference product, the minimum detection limit reference product at least comprises a DNA mixture of two different levels of mutation frequencies, the DNA mixture of each level of mutation frequency comprises mutation sites shown in the following table 1. By using a DNA mixture containing multiple gene mutation sites related to the mutation of the intestinal cancer as a minimum detection limit reference product, and the standard product comprises the DNA mixture of at least two levels of mutation frequencies, which can be able to detect whether mutations can be detected and the frequencies of mutation can be detected or not when kits from different manufactures are used for corresponding gene mutation, thus the accuracy and reliability of detection results of each kit can be verified, and thereby relatively accurate guidance for clinical medication can be provided.

The invention provides a drug relocation method based on gene mutation and gene expression. The method is used for solving the technical problem that in the prior art, a location result is low in accuracy. The method comprises the implementation steps that SNP mutation data is processed to obtain mutation frequency data of all genes; gene expression data is processed to obtain standard gene expression matrix data, and all gene expression change values and statistical significance values are calculated; secondary classification is performed on the mutation frequency data of all the genes in the SNP mutation data and the genes in the standard gene expression matrix data; correlation values of diseases and all drugs are acquired; absolute values of the correlation values of the diseases and all the drugs are calculated, and all the drugs are ordered according to a descending rule of the absolute values to obtain rankings of all the drugs; and candidate drugs with potential treatment effects on the diseases are acquired. The method can be used for predicting the candidate drugs with potential treatment effects on cancers.

The invention provides a verifying method of a high-throughput sequencing mutation detection result and a method for mutation searching through the high-throughput sequencing result. According to the verifying method, mathematical calculation and statistical formulas are combined, whether interested single-locus special base substitution exists in a high-throughput sequencing sample or not is determined by calculating the mutation frequency of the interested single-locus special base substitution, and whether interested continuous-locus base deletion or interested continuous-locus special base substitution exists or not is determined by calculating the variation coefficient of the interested continuous-locus base deletion or the interested continuous-locus special base substitution.

The present invention discloses a technique for making tobacco NaN3 mutation germplasm innovation and selecting-breeding variety. Said technique includes the following steps: (1), mutagenic material selection, selecting air-dried seed of tobacco cultivated variety with good comprehensiveness and strong adaptability; (2), preparing NaN3 solution; (3), seed treatment, using NaN3 solution whose concentration is 4mmol/L to treat seed for 6h at 25deg.C; (4), planting and management of M1; (5), planting and selection of M2; and (6), M3 and next-treatment. Said method can greatly raise mutation frequency, and its beeding effect is high.

The invention discloses a rapid and high-efficiency transgenic method for indica rice. The method comprises the following steps of: exposing indica rice mature seeds to Agrobacterium tumefaciens 5 to 15 days after callus induction, co-culturing, performing resistant callus screening for 10 to 20 days, performing differentiation culture for 10 to 20 days, performing rooting culture for 5 to 10 days, and performing resistance screening again. The transgenic plants of indica rice can be produced within 40 to 50 days, and the conversion efficiency reaches 20-30%. In the conversion process, the culture conditions are as follows: the temperature ranges from 30 DEG C to 33 DEG C and the light is continuously supplied with the intensity of 80 to 120 mu mole/m<-2>s<-1>, except that the co-culture stage is carried out at 25 DEG C in the dark. The method provided by the invention greatly shortens the in vitro culture time of calli, increases the differentiation efficiency, reduces the mutation frequency of somatic cells, simplifies the operation procedure and saves a large amount of labor and material resources.