74 results about "Specific mutation" patented technology

The invention discloses a screening method of a gene region set for detecting small residual focuses of ovarian cancer, the gene region set and a detection system of the gene region set, and belongs to the technical field of gene molecular diagnosis. According to the method, a preoperative blood sample, an intraoperative multipoint tumor tissue sample and postoperative daily peritoneal drainage liquid of an ovarian cancer patient on the first to sixth days are taken as detection samples, a novel ovarian cancer nuclear genome hot spot region screening method is developed, a gene region for ovarian cancer tumor DNA detection is constructed, and tumor tissue mutation information is taken as a tracing basis, so that an ovarian cancer tumor DNA detection result is obtained. The characteristics of tumor tissue specific mutation in the free DNA of the peritoneal drainage liquid are analyzed, and the purpose of detecting the free tumor DNA of the peritoneal drainage liquid is achieved. The method can be applied to the postoperative residual focus detection of the ovarian cancer patient, can sensitively and accurately evaluate the postoperative residual focus state of the patient at an early stage, and provides timely prognosis judgment basis for clinic, so as to support the adjustment of clinical decisions.

The present invention provides a computer-implemented method for predicting the treatment response of a subject having a lung cancer to an immune checkpoint inhibitor (CPI) therapy, the method comprising: providing a mutation profile of the subject, said profile comprising the presence or absence of cancer-specific mutations at one or more locations in at least five genes selected from the group consisting of: NF1, STK11, TSC2, BRCA2, BRAF, STAG2, U2AF1, BRIP1, PDGFRA, CTNNA1, PDK1, FGF10, and FLT1; analysing the mutation profile to classify the profile as matching the mutation profile of a response signature or a resistance signature, wherein the subject is predicted to be likely to respond to the CPI therapy if the mutation profile for the subject is classified as matching the mutation profile of the response signature and is predicted to be likely not to respond to the CPI therapy if the mutation profile for the subject is classified as matching the mutation profile of the resistance signature. Also provided are related methods and systems for predicting the treatment response of a subject having a lung cancer to an immune checkpoint inhibitor (CPI) therapy.

The present disclosure provides methods of determining whether a tumour-specific mutation is likely to be clonal in a subject. The method comprise determining, by a processor, a metric indicative of the probability that the mutation is clonal by combining evidence from sequence data obtained from the subject and an indication of whether the mutation is associated with one or more predetermined mutational signatures. The methods may be used to identify clonal mutations and clonal neoantigens in a subject, and to design immunotherapies that target clonal neoantigens. Related methods, systems and products are also described.

The disclosed embodiments concern methods for determining sequences of interest using targeted unique molecular index (TUMI) sequences that are uniquely associated with individual polynucleotide fragments in plants, such as those present in a transgenic event, a site-specific mutation or a wild type variant. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

A new technique for improving the secretion production of a heterologous protein by a coryneform bacterium is developed, and thus a method for the secretion production of a heterologous protein is provided. A coryneform bacterium having a secretion production ability of a heterologous protein and modified to maintain a phoS gene having a specific mutation is cultured to produce a heterologous protein by secretion.

Genetically modified zebrafish, in which mutation combinations frequently identified in human AML are stably expressed in the stem cell population of the fish, are provided. The combination of mutations result in morphologic, cytochemical and molecular changes of its blood cells that are remarkably similar to those in human AML. The zebrafish model provides a foundation for the study of AML initiation and progression and a high throughput in vivo drug screening platform to identify personalized therapies for AML based on specific mutation combinations. The method of drug screening includes contacting embryos or adult fish containing mutations as disclosed herein, with a test agent, at test concentrations and test intervals to determine the therapeutic effect if any, of the test agent.

This disclosure relates to a technique for identifying tumor-specific mutations through integrated analysis of next-generation sequencing data using machine learning models. In certain embodiments, a computer implementation method is provided, comprising: generating sequence reads from one or more samples collected from the same patient; generating variant calling files by analyzing the sequence reads corresponding to each of the one or more samples; generating a list of candidate somatic variants by comparing the variant calling files; generating a score for each of the candidate somatic variants in the list of candidate somatic variants using a classification machine learning model, wherein the score is generated based on a plurality of classifications generated by the classification machine learning model; determining the ctDNA status for the patient based on the score, wherein the ctDNA status is either positive or negative; and generating a report providing the ctDNA status for the patient.

This invention discloses a sequencing technique for enriching mutations after library construction. The co-priming amplification (Co-PCR) technique of this invention couples a mutation probe to a short P5 / P7 primer. This short primer has a low melting temperature (Tm) and cannot hybridize and amplify on its own at the reaction temperature. Only when the mutation probe hybridizes to the mutation site can it assist the coupled short P5 / P7 primer in hybridizing to the adjacent P5 / P7 sequence at the end of the pre-library, initiating amplification. Therefore, this Co-PCR technique not only amplifies a specific mutation in a specified gene but also amplifies from both ends of the original pre-library, replicating the complete sequence information of the pre-library, including sequencing adapters, indexes, and sequencing primers. The amplified products can be directly sequenced after purification. By optimizing the co-primers, Co-PCR enrichment amplification of five sites in the pre-library was achieved, resulting in nearly 100-fold enrichment.

The invention discloses a construction method and application of a basic group editor of industrial bacteria of cephalosporium acremonium based on CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-associated protein 9), and belongs to the field of gene engineering. The cephalosporium acremonium industrial bacterium base editor provided by the invention can be used for specific mutation of a specific site of the DNA level of the cephalosporium acremonium industrial bacterium. The cytosine base editor CBE constructed by the invention is a plasmid comprising a fusion protein A and an sgRNA expression element. The base editor CBE can successfully mediate C.G-T.A, is suitable for the base editor of the high-yield CPC cephalosporium acremonium industrial bacteria, utilizes the protoplast, is high in conversion efficiency, can mediate specific site mutation in the cephalosporium acremonium industrial bacteria, and has application value.

The present disclosure provides methods of introducing site-specific mutations in a target cell and methods of determining efficacy of enzymes capable of introducing site-specific mutations. The present disclosure also provides methods of providing a bi-allelic sequence integration, methods of integrating of a sequence of interest into a locus in a genome of a cell, and methods of introducing a stable episomal vector in a cell. The present disclosure further provides methods of generating a human cell that is resistant to diphtheria toxin.

The present invention belongs to the technical field of molecular biology, and specifically relates to a xylanase XynZT-2 mutant and its application. The xylanase XynZT-2 mutant is obtained by site-directed mutagenesis of the xylanase XynZT-2 with the amino acid sequence shown in SEQ ID No. 2. The specific mutation sites are as follows: T28I, A33V, M97L, A102C, S148T, A238G, S239P, M241L, T287S or I291V. The optimal temperature and optimal pH of 10 xylanase XynZT-2 mutants have changed, and the obtained xylanase XynZT-2 mutants show application value in the fields of pulp brewing, bioenergy, food manufacturing, etc.

A method of treating a subject having been diagnosed as having cancer with an immunotherapy is described. The method comprises targeting one or more clonal neoantigens selected using a method comprising determining whether a tumour-specific mutation is likely to be clonal in a subject. The method comprises providing sequence data from one or more samples from the subject comprising tumour genetic material, the sequence data comprising for each of the one or more samples, and determining the likelihood that the tumour-specific mutation is clonal as a posterior probability depending on: a prior probability of the mutation being clonal, and the probabilities of observing the sequence data if the tumour-specific mutation is (i) clonal and (ii) non-clonal, in view of a tumour fraction for each of the one or more samples and one or more candidate joint genotypes.

The present technology relates to methods, computing devices, and systems for predicting the fitness of mutant p53 based on the loss of transcription factor function and immunogenicity of a particular TP53 mutation. The fitness of mutant p53 may be used to determine whether a patient will benefit from a particular anti-cancer therapy such as immune checkpoint inhibitor therapy, adoptive T-cell therapy, or prophylactic cancer vaccine therapy.

This invention discloses the application of the VDAC2 gene or VDAC2 protein as a target in screening drugs for the treatment of retinitis pigmentosa, relating to the field of biomedical technology. The drug is one that reduces the expression level of the VDAC2 gene or inhibits the expression level or activity of the VDAC2 protein; the CDS sequence of the VDAC2 gene is shown in SEQ ID NO.1. This invention uses a rod cell-specific promoter to inhibit VDAC2 expression, which can significantly improve the survival rate of local photoreceptor cells. This method intervenes in the early stages of the disease, conforming to the natural course of RP. It strengthens the function of rod cells before a large number of photoreceptor cells die, delaying their degenerative process and indirectly protecting cone cells, thereby prolonging the patient's effective visual retention time. This overcomes the shortcomings of existing gene therapies, which are mainly applicable to late-stage or specific mutation types, and provides a therapeutic basis for retinitis pigmentosa.

The invention belongs to the technical field of agricultural biology, and particularly discloses a grape germplasm innovation method based on X-ray gradient mutagenesis and an LD50 precise prediction model, and the method comprises the following steps: selecting an annual grape branch for vernalization treatment, and trimming the annual grape branch into a single-bud stem segment; setting an irradiation time gradient, accurately calculating an LD50 value through a cubic spline interpolation model, and carrying out X-ray irradiation on the single-bud stem segment according to the LD50 value; after irradiation, performing cutting and liquid paraffin sealing, and then performing cuttage, potting and field planting treatment; performing secondary vernalization on mutagenesis plant branches, trimming the mutagenesis plant branches into single-bud stem segments, collecting tender leaves after cutting survival, extracting genome DNA, performing whole genome sequencing, and accurately distinguishing mutagenesis specific variation and natural variation. By establishing a complete technical system of standardized vernalization, gradient irradiation, LD50 accurate calculation and whole genome verification, the problems of inaccurate irradiation parameters, nonstandard material treatment, low mutation screening accuracy and the like in the prior art are solved.

The application provides a pyroglutamic acid transaminase mutant and application thereof, the mutant is obtained by mutation on the basis of wild-type pyroglutamic acid transaminase, and specific mutation includes at least one of the following sites: (1) the 13th isoleucine is mutated into arginine; (2) the 35th valine is mutated into arginine; (3) the 183rd asparagine is mutated into aspartic acid; and the mutant is suitable for industrial enzymatic production of L-aspartic acid and the process of amino acids taking L-aspartic acid as a precursor; especially, the I13R / V35R / N183D mutant obtained by modification has high positive catalytic activity and strict direction selectivity, and completely loses the reverse reaction activity of decomposing L-aspartic acid; the mutant is overexpressed with phosphoenolpyruvate carboxylase in L-threonine production strain THRS-6, and a high-efficiency L-threonine synthesis metabolic pathway is constructed, and the yield of L-threonine is significantly improved when glucose is used as a substrate.

The invention relates to norcoclaurine synthases and substrate binding sites having one or more site-specific mutation which increase the activity, when compared to the wild type synthase, of the condensation of 4-HPAA and dopamine to (S)-norcoclaurine and / or 3,4-DhPAA and dopamine to (S)-norlaudanosoline. The inventors both identified specific mutations corresponding to at position 73, 75, 77, 82, 99, 114, 141, 142, 147, 152, 174 and / or 178 in the count according to SEQ ID No: 1, and sites corresponding to the binding domains defined in SEQ IN NO: 4 and 5, where the mutated increase of the activity may be positioned within these norcoclaurine synthases. These domains are conserved regions.

The application discloses a kind of identification Pinb The primer sequence for amplifying the dCAPS molecular marker is shown in SEQ ID No.10-SEQ ID No.11.The application uses a strong wheat variety as a transgenic receptor, edits the variety by gene editing Pinb Gene to make it produce specific mutations and lose function, and creates a new wheat germplasm with greatly improved grain hardness and improved flour quality. Pinb The effect is stronger than that of reported single knockout of the gene, and the resistance to wheat scab does not decrease after knockout, and the content of DON toxin in flour is actually reduced.

The invention provides a primer and probe combination, a kit and a method for quantitatively detecting the JAK2V617F gene mutation rate, and the primer and probe combination comprises a primer and probe set targeting JAK2V617F mutation sites and a primer and probe set of reference genes GPI, according to the primer probe set targeting JAK2V617F mutation sites, the nucleotide sequence of an upstream primer of a specific mutation site is any one of SEQ ID NO.1-7, the nucleotide sequence of an upstream primer of a specific wild type site is any one of SEQ ID NO.9-14, the nucleotide sequence of a universal downstream primer is SEQ ID NO.8, and the nucleotide sequence of a probe is SEQ ID NO.15. The invention further discloses a kit for detecting the JAK2V617F mutation sites. According to the invention, the JAK2V617F mutation rate can be economically, simply, efficiently, sensitively, accurately and quantitatively detected, and the detection mutation rate is as low as 0.1%.

The invention discloses a novel Fc effect eliminated framework flow antibody, and belongs to the technical field of biological medicine. The antibody comprises a mutation combination of L234A, L235A, P238S and D265A in a heavy chain CH2 region, and can further comprise S267E and L328F mutations, so that the Fc receptor binding capacity is effectively reduced. The type of the antibody can be selected from multiple forms of scFv-Fc, (scFv) 2-Fc, scFv / scFv-Fc, Fab / scFv-Fc and the like. The invention also provides a nucleic acid sequence for coding the antibody and a preparation method of the antibody. The preparation method comprises the following steps: introducing specific mutation into a CH2 region of recombinant rabbit IgG, and expressing and purifying in a mammal expression system to obtain the antibody. When the antibody is applied to a flow cytometry detection reagent, a non-specific background signal caused by Fc receptor combination can be effectively eliminated, and the detection specificity and accuracy are improved.

The invention discloses a soybean FAD2 gene mutation site, a specific identification primer and a method for increasing the content of oleic acid in soybean, the soybean provided for the first time after the specific mutation sites of FAD2-1A and FAD2-1B genes are mutated can significantly increase the relative content of oleic acid in soybean seeds, the relative content reaches 70% or above, and meanwhile the content of linoleic acid is reduced to 20% or below. When the specific primer is used for detecting the corresponding mutant gene, a specific band exists, the efficiency reaches 100%, and the accuracy is high. The mutation does not influence the normal growth and development and other agronomic characters of the soybeans while obviously improving the oleic acid content, ensures the yield and other comprehensive properties of the soybeans, and is beneficial to large-scale popularization and planting. The mutation site and related technologies have wide application prospects in soybean breeding and soybean product production, can be used for cultivating different types of high oleic acid soybean varieties, meet various market requirements, and also can be used for improving the quality of various soybean products.

This invention relates to the fields of molecular biology and human genetic disease detection; specifically, it relates to a reference standard for methylmalonic acidemia and its application. The reference standard comprises positive reference cells with MMACHC gene mutation sites. The genome of the positive reference cells contains one or more combinations of specific mutation sites of the following MMACHC genes: c.609G>A, c.567insT, c.658_660delAAG, c.482G>A, c.1A>G, c.80A>G, c.217C>T, c.315C>G, and c.394C>T. This reference standard provides reliable technical support for the accurate detection of methylmalonic acidemia, especially MMACHC gene-related mutations, and is of great significance in improving detection accuracy and promoting detection standardization.

The invention discloses a liver cancer gene mutation detection method and application, and belongs to the technical field of liver cancer gene detection. The invention finds that deletion mutation of the No.7 exon of the TP53 gene is closely related to the occurrence of liver cancer for the first time, and the research result of the invention can make the early screening sensitivity of liver cancer reach 93.33%, and has important significance for the early detection and intervention of liver cancer. The specific primer pair and the fluorescent probe for digital PCR detection are designed for deletion mutation of the No.7 exon of the TP53 gene, and accurate recognition of specific mutation sites of the TP53 gene is ensured by combining high-fidelity polymerase. According to the invention, the designed detection specific primer is combined with a digital PCR technology, so that the sensitivity of liver cancer gene mutation detection is improved, and the accuracy and reliability of experiments are ensured.

To provide cancer vaccines based on a replication-defective vaccinia virus such as an MVA expressing antitumor neopeptide fusions, and to provide methods for preparing the same.SOLUTION: The present invention relates to a personalized cancer vaccine comprising a recombinant poxvirus encoding one or more neopeptides, or to a composition comprising such a recombinant poxvirus and a pharmaceutically acceptable vehicle, and to use of the personalized cancer vaccine to treat a cancer subject in need thereof. A particular embodiment is a method for providing the vaccine or composition, comprising the steps of: a) extracting DNA from tumor and non-tumor samples; b) selecting a target region, preferably the entire coding region of the genome (exome); c) sequencing the target region (e.g., the exome) from the extracted DNA; and d) identifying one or more tumor-specific mutations by comparing the DNA sequences obtained from the tumor and non-tumor samples.SELECTED DRAWING: None

Two or more peptides or polypeptides and an adjuvant for use in a method of inducing a tumor specific immune response, wherein the peptides or polypeptides have been identified by a method comprising: identifying a plurality of neoantigenic peptides for preparing a subject-specific immunogenic composition, each neoantigenic peptide comprising a tumor-specific neoepitope comprising a tumor-specific mutation, the method comprising: a. identifying a plurality of subject-specific tumor mutations in expressed genes of a subject having cancer by whole genome or whole exome nucleic acid sequencing of tumor and normal tissue samples from the subject, wherein the mutations are present in the genome of cancer cells of the subject but not in normal tissue from the subject; b. wherein when a mutation identified in step (a) is a point mutation: i. identifying a mutant peptide having the mutation identified in step (a), wherein said mutant peptide comprises a tumor-specific neoepitope which binds to a class I HLA protein with a greater affinity than a wild -type peptide; and has an IC50 less than 500 nm; c. wherein when a mutation identified in step (a) is a splice-site, frameshift, read-through or gene-fusion mutation: i. identifying a mutant polypeptide encoded by the mutation identified in step (a), wherein said mutant polypeptide comprises a tumor-specific neoepitope which binds to a class I HLA protein.

Provided in the present invention are a fatty-acid-chain-modified GLP-1-FGF21 fusion protein, and a preparation method therefor and the use thereof. In the fusion protein, after a specific mutation site is introduced at the C-terminus of FGF21, the terminus of GLP-1-FGF21 is subjected to a fatty-acid-chain modification by using a Sortase-A enzyme-mediated molecular modification technique. The fatty-acid-chain modification can achieve: extended half-life of GLP-1-FGF21; slowed terminal degradation of FGF21 by fibroblast activation protease (FAP); and low-cost operation and rapid preparation of the GLP-1-FGF21 fusion protein in an aqueous solution at room temperature. The enzyme-mediated molecular modification technique is used on the GLP-1-FGF21 fusion protein of the present invention, thereby providing significant advantages.

The invention relates to a recombinant antigen aiming at Zika / dengue virus as well as a vaccine composition and application thereof. The recombinant antigen is obtained by introducing specific mutation into an FL fusion loop region and optionally a non-FL fusion loop region of an E protein of the wild type Zika / dengue virus; by introducing specific mutation, the FL epitope of the recombinant antigen is destroyed, and the generation of an induced FL epitope antibody can be avoided, so that the aim of reducing or eliminating an ADE effect is fulfilled; moreover, the recombinant antigen has correct E protein conformation, has protein expression quantity similar to or higher than that of a wild type, and can induce relatively high specific binding antibody titer and neutralizing antibody titer in animal bodies, so that effective immune protection can be provided, and the recombinant antigen has relatively good clinical application value and industrialization prospect.

To provide IL-2 muteins and IL-2 mutein Fc fusion molecules that preferentially expand and activate cells and are amenable to large scale production.SOLUTION: Disclosed are human IL-2 muteins having specific mutations. The IL-2 muteins have a relatively low likelihood of inducing an immune response against the IL-2 mutein and / or endogenous IL-2, and enable preferential proliferation and activation of Treg. Also disclosed are methods for producing and using the compositions of the present invention.SELECTED DRAWING: Figure 1

This invention discloses a radiotracer targeting pan-KRAS mutant proteins, its preparation method, and its applications. The tracer uses small molecule ligands that specifically recognize multiple KRAS mutant proteins as targeting modules, and is coupled to diagnostic radionuclides through an optimized linkage system. This tracer is independent of specific mutation sites and can broadly and specifically bind to multiple high-frequency KRAS mutant subtypes, including G12C, G12D, and G12V. Based on PET / SPECT imaging, this tracer enables rapid, non-invasive, systemic, visualized, and quantitative assessment of KRAS mutant protein expression load in living tumors, overcoming the invasiveness, spatiotemporal limitations, and tumor heterogeneity challenges of traditional biopsies. It provides a novel molecular imaging tool for accurate companion diagnosis of KRAS-mutant tumors, screening of patients benefiting from pan-KRAS inhibitors, and monitoring efficacy, possessing significant clinical translational value.

The invention relates to a method for detecting low-frequency mutation in cfDNA and application of the method, a mutation detection method with high sensitivity and high specificity is established through a TARGET directional enrichment technology, and the problems that traditional NGS is high in false negative rate, inaccurate in quantification and the like in ultralow-frequency mutation detection are solved. The technical breakthrough not only provides a new tool for early screening and drug resistance monitoring of lung cancer, but also lays a methodological foundation for liquid biopsy application of other tumors.