32 results about "Mutational hotspot" patented technology

The functional interpretation of somatic mutations remains a persistent challenge in the interpretation of human genome data. Systems and methods for detecting significantly mutated regions (SMRs) in the human genome permit the discovery and identification of multi-scale cancer-driving mutational hotspot clusters. Systems and methods of SMR detection reveal differentially mutated genetic regions across various cancer types. SMR detection and annotation reveals a diverse spectrum of functional elements in the genome, including at least single amino acids, compete coding exons and protein domains, microRNAs, transcription factor binding sites, splice sites, and untranslated regions. Systems and methods of SMR detection optionally including protein structure mapping uncover recurrent somatic alterations within proteins. Systems and methods of SMR detection optionally including differential expression analysis reveal previously unappreciated connections between recurrent and somatic mutations and molecular signatures.

The invention discloses a novel chromosome microdeletion/microduplication syndrome detection system which mainly comprises 643 pairs of probes, multiplex PCR (polymerase chain reaction) amplification primers and correlation detection reaction reagents. The detection process comprises the following steps: hybridizing a probe set with target nucleic acid in the sample; connecting the hybridized probe; amplifying the connecting probe; and detecting the amplification product to determine the existence or quantity of the target nucleic acid in the sample. The platform can implement systematic screening and detection on 24 chromosome aneuploids, 24 chromosome telomere abnormities, more than 70 chromosome microdeletion/microduplication syndromes and multiple monogenic disease mutation hot spots at one time by using the optimized probe set and reaction system. Compared with the existing like detection techniques (such as MLPA and the like), the detection system covers nearly all definite pathogenic regions with abnormal number of copies in the DECIPHER database, has the advantages of wide detection range, high detection precision and low cost, and is simple to operate.

The invention discloses a primer for detecting IDH1 and IDH2 gene polymorphism mutation sites, a method and a kit. According to the primer, (1) an amplified IDH1 gene comprises a primer body of a 132nd amino acid sequence, and (2) an amplified IDH2 gene comprises primer bodies of 140th and 172nd amino acid sequences. A common PCR technique is adopted, the primer can be used for quickly detecting mutation situations of IDH1 and IDH2 gene polymorphism hot spots in the body of a patient suffering from acute granulocytic leukemia (AML). According to the primer, the method and the kit, the automation degree is effectively improved, complicated procedures and large detection expenses for expressed region sequencing of IDH1 and IDH2 are eliminated, the patient can be diagnosed quickly and precisely and expenses are low.

The invention relates to a design method and application of a probe combination for cancer detection. The design method comprises the following steps: extracting a mutation set of cancer in a database, dividing the mutation set into a training set and a verification set, and combining mutations with reference genome distance less than or equal to 80 in the training set so as to obtain a plurality of mutational hotspot intervals; and sequentially screening the multiple mutation hotspot intervals on the basis of the regional mutation density, and taking the mutation hotspot intervals meeting the following conditions as targets of the probe combination. The probe combination designed by the invention has excellent coverage on common cancers, a Gene+ database and MSK database verification set is adopted to simulate the coverage condition of the panel on nine cancers, and the result shows that the coverage degrees of nine cancer types are all greater than 93%; the early cancer detection based on the probe has high sensitivity and specificity, and the detection rate of liver cancer reaches 85%; and a ctDNA positive judgment method based on the probe can effectively perform prognosis layering on a patient.

The invention relates to the technical field of bioinformatics and biological medicine, in particular to a screening method of SARS-CoV2 potential mutation sites. The method comprises the following steps of: 1) downloading to obtain a gene sequence of SARS-CoV2, carrying out rapid file annotation and sequence comparison on the downloaded sequence, and extracting sequences of all coding genes from a whole genome sequence; (2) calculating the mutation frequency of each site, screening out high-frequency mutation hot spots, and screening out mutation sites with remarkable selection advantages in a population by combining the sampling time and geographical distribution information of strains; 3) downloading tertiary structure information of proteins corresponding to existing coding genes; and 4) according to the predicted B cell and T cell epitopes, screening mutation sites on or near the immune epitopes, evaluating the possible influence of the mutation sites on the host immune response, and identifying the potential key mutation sites possibly related to virus infection and host adaptation of the SARS-CoV-2 on the genome in epidemic propagation.

The invention discloses a primer composition, a kit and a method for detecting EGFR gene mutations, which aim to improve the convenience and the flexibility of EGFR gene mutation detection. The primer composition comprises a first composition A, wherein the first composition A comprises a first primer pair for amplifying a No.18 exon and a second primer pair for amplifying a No.19 exon; the first primer pair comprises A_E18-CS1-TS_1F as shown in SEQ ID NO:1 and A_E18-CS2-TS_1R as shown in SEQ ID NO:2. The primer composition simultaneously comprises the primer compositions for amplifying the No.18 exon and the No.19 exon, and the length of each amplicon obtained through amplification is smaller than 150bp, so that mutational hotspot areas in the two exons can be detected conveniently at the same time, an appropriate sample source is conveniently selected according to a sample state, and the convenience and the flexibility of EGFR gene mutation detection are improved.

The invention discloses primers for detecting mutation of human B-raf gene V600E, primer probe composition and a kit. The kit comprises a B-raf gene V600E mutation detection primer pair and detectionprobe, an internal quality control primer pair and a quality control probe. A forward primer of the detection primer pair comprises three parts arranged in the following order from the 5' end to the 3' end: 1) a first sequence: the first sequence is used for identifying mutation hot spots, is a peptide nucleic acid PNA sequence hybridizing with a wild type template, is completely matched with thesequence of the wild type template and has a base mismatched with the sequence of a mutant template; 2) Spacer: the Spacer is connected with the 3' end of the first sequence and the 5' end of a secondsequence; 3) the second sequence: the second sequence is bound with a sequence upstream of a mutation site, 3-6bp of the sequence of the 3' end of the second sequence overlaps with the 5' end of thefirst sequence, Tm value of the first sequence is 6.3-11.3 DEG C higher than that of the second sequence. The kit is simple and quick, has sensitivity up to 1 permillage, and has high specificity, and the false positive rate is greatly reduced.

The embodiment of the invention provides a detection kit for APL drug resistance gene mutation and a detection method using the kit. The kit contains specific primers designed respectively for a PML/RARalpha fusion gene and protein mutational hotspot regains of PML and RARalpha, the primers are used for amplification of the PML/RARalpha fusion gene through PCR first and then respectively for amplification of the mutational hotspot regains of the PML and RARalpha, and finally sequencing analysis is carried out on target fragments in the APL sample amplification product to obtain the gene mutation condition of the APL sample. The kit and detection method provided by the invention can realize detection of mutation of three kinds of isomer PML/RARalpha fusion genes once, prevent S type and V type isomers from being undetected, and save the reagent cost at the same time; and by analyzing the gene mutation detection result acquired by the detection method provided by the embodiment of the invention, the suppression resistance caused by PML/RARalpha gene mutation to medicines such as As2O3 can be clinically revealed.

The invention relates to a detection method and a kit for detecting U2AF1 gene mutation based on drop-ffdPCR. Primers and probes of the detection method are designed according to a U2AF1 gene DNA sequence, two wild probes are designed for two mutation hotspots Q157 and S34 of a U2AF1 gene respectively, one wild probe is located on the mutation hotspot, the other wild probe is located outside the mutation hotspot, and when mutation such as insertion, replacement and deletion exists in the mutation hotspot, the wild-type probe located at the mutation hotspot cannot be tightly combined with the template, so that the kit can detect multiple mutations of the two mutation hot spots Q157 and S34 of the U2AF1 gene only by using two pairs of primer probes, and the kit is high in sensitivity and can be used for MRD monitoring.

The invention relates to a detection method and a kit for detecting NPM1 gene mutation based on drop-offddPCR; primers and probes thereof are designed according to an NPM1 gene DNA sequence; two wild probes are designed aiming at a 12th exon mutation hot spot of an NPM1 gene; one wild probe is located on the mutation hot spot; the other wild probe is located outside the mutation hot spot; when mutation such as insertion, replacement and deletion exists in the mutation hot spot, the wild probe located at the mutation hot spot cannot be tightly combined with a template, so that the kit can detect various mutations of the mutation hot spot of the 12th exon of the NPM1 gene only by using two pairs of primer probes; and the kit is high in sensitivity and can be used for MRD monitoring.

The invention relates to a gene mutation detection kit for a human glucose-6-phosphate dehydrogenase deficiency disease. The gene mutation detection kit comprises probes with sequences represented bySEQ NO.1-382. By carrying out distribution analysis on positive mutation sites of 500 G6PD genes in the China area and combining with Human Gene Mutation Database (HGMD) and gene mutation hotspot dataof the European and American areas, gene mutation hotspots are more comprehensively summarized, so that the problems of genetic mutation detection of nearly 99% of patients with a G6PD deficiency disease are solved, and rapid and effective execution of genetic diagnosis of the G6PD deficiency disease is realized.

The invention discloses a PCR primer group, a kit and application thereof. The total number of the PCR primer group is 65. The primer pairs are uniformly distributed in the full length of the RB1 gene, and meanwhile, extra densification is carried out on a mutation hot spot region. The primer pair of the invention can be used for full-length amplification of exons which are short in part of the RB1 gene and are close to each other, and deletion in the amplification region can be found. For an intron region with a relatively long span, a primer pair design is additionally added, aiming at a relatively conserved sequence of an intron, a large-section repetitive sequence and a high-GC-ratio sequence are avoided, and a PCR reaction is easy to carry out. By using the method, the breakpoint of RB1 gene exon deletion can be simply and conveniently positioned with extremely low price, basic molecular biology experiment conditions and relatively low labor hours. The PCR primer group can be used for primary screening of RB1 gene exon deletion of small-scale tumor samples, and can also be used for accurately positioning breakpoints of RB1 gene exon deletion in combination with WES results.

A rat with a disrupted Apc (adenomatous polyposis coli) gene is provided. The mutation can include an A to T transversion changing a lysine to a stop codon at codon 1137. Methods of generating the knockout rat are provided. Also provided is the offspring or progeny of that rat. In addition, methods of using these rats are provided, including methods for screening a carcinogen or a promoter of carcinogenesis, and methods for screening preventive and inhibitory agents of carcinogenesis.