75 results about "Exome sequencing" patented technology

The invention discloses a whole-exome sequencing data analysis system. The system comprises a quality control module which is used for assessing single base quality in an original sequencing data file and read quality; a genome mapping module which is used for finishing a read to genome mapping process by employing an aln algorithm of a BWA; a genome variation module which is used for finding variation sites in a genome by employing a Unified Genotyper method of a GATK packet; and a variation site annotation module which is used for annotating variation candidate sites or a genome interval. According to the system, large-scale data analysis is finished through simple parameter submission; the analysis comprises quality detection of original data, data denoising and sequencing upstream to downstream original sequencing data of genome mapping of the read; the sequencing data is analyzed through a parameter automatic submission and analysis module; the candidate pathogenic mutation sites and related genes are output; and the basis is provided for later experiment verification.

The invention relates to an identification method for a genetic disease-related gene, comprising the following steps: 1) obtaining a sample of DNA in genetic disease gene family; 2) carrying out preliminary positioning of chromosomes of related genes; 3) optionally, further carrying out accurate positioning and haplotype analysis of the chromosomes of the related genes; 4) according to chromosomal localization results, taking a certain amount of DNA samples and identifying the related genes with the technology of human genome exome sequencing. The invention also relates to an identification method for related genes of hereditary spinocerebellar ataxia and a kit for the analysis of the related genes of hereditary spinocerebellar ataxia.

The invention provides a whole-exome sequencing data analysis method. The method comprises the following steps of 1) quality control of sequencing data; 2) genome mapping of the sequencing data; 3) seeking of high-confidence genome mutation by the sequencing data; and 4) annotation of mutation sites. According to the method, the analysis of large-scale data is finished through simple parameter submitting, wherein the analysis of the large-scale data comprises quality detection of original data, data denoising and genome mapping of sequencing read; an upstream part takes over original sequencing data of a lower machine; the analysis of the sequencing data is finished through a parameter automated submitting and analysis module; and candidate pathogenic mutation sites and related genes are output, thereby providing a basis for later experimental verification.

The invention provides an exome potential pathogenic mutation detection method based on a family line. The detection method comprises the following steps: 1) reading a result file of an exome sequencing data processing flow, and conducting function filtering; 2) reading the file obtained in the last step, extracting mutations in all samples, calculating a union set, and then combining all samples, so that a matrix is constituted; 3) extracting mutation information in the matrix obtained in the last step, enumerating and assessing pathogenicity of single mutation and pathogenicity of combined dual-site mutation, so that a potential pathogenic mutation list is obtained; and 4) in accordance with the list obtained in the last step, calculating the appearance situations of sites in various samples and target genes. According to the method disclosed by the invention, data integration and basic filtration are completed by taking an output result of the common exome sequencing processing flow as an input condition; by virtue of a special mutation screening algorithm, a candidate set of the potential pathogenic mutations is provided; and the method focuses on solving a problem on potential pathogenic mutation mining of sequencing data with high heterogeneity, high mutation rate and high noise.

The invention relates to a kit of extracting a whole genome DNA (Deoxyribonucleic Acid) from blood and a using method thereof. The kit is characterized by comprising a red blood cell lysate, a white blood cell scrubbing solution, digestive juice, proteinase K, a purifying liquid, gDNA salting out liquid, a gDNA scrubbing solution, a gDNA eluant and the like. The using method of the whole genome DNA extraction kit for blood is characterized by comprising the following steps: washing the red blood cell split to obtain the white blood cell; splitting the white blood cell by the digestive juice containing the proteinase K; and further purifying by an improved lithium chloride purifying liquid, salting out the liquid layer, and carrying out chromatography to obtain the high purity whole genome DNA. When the kit provided by the invention is used to extract the whole genome DNA in blood, plasma and serum in blood are not separated in advance but fresh or frozen anti-freezing whole blood is taken, wherein the lowest blood volume required reaches 20 microliters or blood cakes are required. According t the kit provided by the invention, the whole genome DNA with high purity can be fully unlinked and the PCR (Polymerase Chain Reaction) amplification is efficiently carried out, so that the kit is used for scientific research or clinical diagnostic analysis such as PCR amplification, gene expression, gene sequencing, whole genome sequencing, exome sequencing, gene mutation and single nucleotide polymorphism.

The invention provides a kit for guiding human mental disease medication and a detection method thereof. The kit can simultaneously type 16 gene loci through one reaction, and comprises 16 pairs of amplification primers for amplifying 16 gene segments; the sequences of 16 pairs of the amplification primers are specifically SEQ ID No.1-SEQ ID No.32; the kit also comprises 16 extension primers, andthe sequences of the 16 extension primers are specifically SEQ ID No.33-SEQ ID No.48. According to the kit and the detection method thereof, through typing based on multiple PCRs and a mass spectrum sequencing technology, human genome mutation related to mental disease medication can be accurately detected; relative to whole genome re-sequencing and whole-exome sequencing, and through the kit andthe detection method of the kit, the experiment cost is also greatly reduced, the period is shortened, and therefore the kit and the detection method of the kit have the all-important practical application value.

The invention discloses a biomarker detection method for predicting a tumor immune treatment effect. The method comprises the following steps: detecting a plurality of biomarkers on the basis of second-generation sequencing detection tissue whole exome sequencing (WES) data, and constructing a prediction model for comprehensively predicting a tumor immune treatment effect. Compared with a traditional method capable of only detecting a single biomarker, the method provided by the invention effectively improve the accuracy and applicability of predicting the curative effect of the inhibitor at the immune checkpoint.

The invention relates to a cloud computing-based method for quality control and management of gene sequence data. The method includes sample clinical information management, experimental data management, data whole process quality control and analysis result management. Testing items of the sample clinical information management includes genomic analysis and transcriptomics analysis, and the genomic analysis includes whole genome sequencing, whole exome sequencing and whole exome sequencing; the transcriptomic analysis includes gene fusion, variable splicing and differential expression analysis. Experimental links are closely connected with analytical links, an analyst can comprehensively understand clinical information, sample information and experimental results, subsequent analysis is facilitated, the accuracy of the analysis result is improved, and the method can help experimenters to understand the quality of sequencing data and thus reflect on shortcomings in the experimental process, the experimental quality is thus improved, and the need of practical use can be applied well.

In the invention, two new mutations of two disease-causing genes relative to Alport syndrome are identified through an exon sequencing method. The inventor, by employing two ATS families as research objects, particularly performs exon sequencing and comparison respectively to diseased individuals and non-diseased individuals in the two ATS family and finds a frame shift deletion mutation (c.3213delA,p.Lys1071fs*5) on a COL4A4 gene of one family and a frame shift deletion mutation (c499delC,p.Pro167Glnfs*36) on a COL4A5 gene of the other family, wherein the two frame shift deletion locus are actual disease-causing locus of the two families. On the basis of above, the invention provides a mutant COL4A4 gene and a mutant COL4A5 gene, encoded protein and application thereof and includes carriers, host cells and kits of the mutant COL4A4 gene and/or the mutant COL4A5 gene. By means of the mutant COL4A4 gene and/or the mutant COL4A5 gene, molecular diagnosis and diseasing risk evaluation of the Alport syndrome can be carried out. The two mutant genes and the encoded proteins thereof also can be used as medicine targets for treating the Alport syndrome.

The invention discloses a method and a device for extracting a gene fusion immune treatment neoantigen by integrating deep sequencing data of DNA and RNA. The method comprises the following steps: S10, acquiring a genome gene fusion sequence of a sample; S20, acquiring a transcriptome gene fusion sequence of the sample; S30, constructing a gene fusion proteome; and S40, obtaining a sample neoantigen. The tumor specific neoantigens discovered by the scheme of the invention are all from gene fusion, so that the screening range of the neoantigens is expanded, and an ammunition library of an immune treatment method based on the neoantigens is enriched. Through analysis and integration of tumor sample whole exome sequencing data and transcriptome sequencing data, gene fusion events in tumor tissues are comprehensively detected, the false positive rate of neoantigens generated by fusion is reduced, the effectiveness of neoantigen vaccine is improved, and the method is of great significance to improvement of the clinical immune treatment effect.

The invention discloses an evaluation method for judging rare hereditary diseases, which comprises the steps of deep phenotype analysis, whole exon group sequencing, gene mutation identification and filtration, mutation optimization combined with a genetic pattern and a disease phenotype, whole exon group sequencing and human phenotype ontology. Clinical doctors can be assisted to judge and evaluate pathogenic factors of rare hereditary diseases in time, the evaluable rate of the rare hereditary diseases is increased, a basis is provided for determining appropriate treatment measures and clinical management strategies, genetic counseling and prenatal evaluation are provided for families, birth of similar child patients is reduced, and economic burdens of the families and the society are relieved. Therefore, the method has important significance for judging the hereditary diseases with high phenotypic heterogeneity and low morbidity.

The invention discloses a kit for screening susceptible gene of atrial fibrillation disease, and belongs to the technical fields of medicine and molecular biology. The kit comprises the following detection gene: KCNQ1, SCN5A and KCNJ2, and comprises reagents for performing whole exome sequencing on KCNQ1, SCN5A and KCNJ2. By performing whole exome sequencing on KCNQ1, SCN5A and KCNJ2 of a subject,whether the subject carries mutation sites is found, so that the atrial fibrillation disease is determined. The kit screens sporadic atrial fibrillation virulence gene in a crowd, and effectively improves the early detection rate of fibrillation disease, thereby realizing early treatment, reducing the burden of patients, and providing reference for the medication of patients with atrial fibrillation.

The invention provides a standard substance for extensive oncogene detection. The standard substance includes 13 mutation sites verified by Droplet Digital PCR (ddPCR) and 500X high-throughput whole exome sequencing verified site information, has more than 700 variation sites of over 330 genes, also includes common structural variations of cancer genomes, such as common gene SNV, base insertion deletion and the like, has corresponding mutation site frequencies within a range of 1% to 100%, and is wide in application scene and platform. The standard substance can be used for evaluating stability, specificity and sensitivity of the working flow from sample extraction to biological information analysis, evaluating each sample treatment method and detecting performance differences among platforms. The standard substance belongs to a major innovation in the industry, and has wide application prospect and great industrial application value.

The invention relates to markers for multiple morphological abnormalities of the sperm flagella and their application, in particular to a novel MMAF (multiple morphological abnormalities of the sperm flagella) pathogenic gene and application thereof. More particularly, the novel MMAF pathogenic gene CFAP43 is discovered for the first time via large-scale whole-exome sequencing screening. In the case of using multiple families and individuals with MMAF as study subject, the individuals in the families are subjected to exome sequencing and comparing, and it is discovered that the different patients show different gene mutations in the gene CFAP43. By using these mutations, it is possible to detect multiple morphological abnormalities of the sperm flagella.

The invention belongs to the technical field of biomedicine, and particularly relates to an application of a substance for detecting a genetic marker to preparation of a kit for risk early warning andearly diagnosis of rectal cancer. Tumor tissue samples of three Chinese Han family sCRC patients are sequenced and analyzed by utilizing an exon group sequencing technology, and specific low-frequency function deletion mutation of screened tumor tissues is determined by genotyping large-sample tumor tissues and normal control tissues of the large-sample tumor tissues. Finally, functional geneticmarkers of new candidate genes BMP5, RASSF6, DDI2 and SARDH which can be used for early-stage sCRC risk early warning.

The invention discloses an autosomal dominant Dnajc17 gene mutant as well as application, a diagnostic kit and a diagnostic gene chip thereof. The mutation site of the autosomal dominant Dnajc17 genemutant is that the 401st nucleotide A of a Dnajc17 gene coding region on the human fifteenth chromosome is mutated into C (c.401A>C), so that the 134th amino acid of the protein sequence is mutated into alanine A (p.E134A) from glutamic acid E. Exome sequencing analysis and animal experiment verification are carried out on deafness family members; the Dnajc17 is found to have obvious correlation with the deafness occurrence, and is an important precipitating factor of hereditary hearing loss. The invention provides the diagnostic kit and the diagnostic gene chip for early diagnosis and early intervention treatment of deafness diseases, the diagnostic kit and the diagnostic gene chip have great clinical application value, and the diagnostic kit and the diagnostic gene chip can be used for screening high-risk groups with deafness diseases.

The invention relates to a novel azoospermia pathogenic gene and an application thereof and relates to a marker for azoospermia disease and the application thereof. The novel azoospermia pathogenic gene BRDT is firstly discovered in the manner of screening in a consanguineous marriage family. After patient individuals in the family are subjected to exome sequencing and comparison on the basis of one azoospermia consanguineous marriage family as a research object, the patients are proved as carrying BRDT gene mutations. These gene mutations can be utilized to detect the azoospermia.

The invention discloses a transcriptome sequencing method based on RT-WES (reverse transcription-whole exome sequencing) technology. The method comprises the following steps: 1) extracting total RNA of a sample; 2) synthesizing cDNA with total RNA as template; 3) constructing a cDNA fragment library; 4) capturing whole exons of the fragment library and enriching transcriptome fragments of functional genes; 5) sequencing the transcriptome fragments and analyzing sequencing data. The RT-WES technology is adopted, RNA is first converted into DNA through cDNA synthesis process, and then exon information is enriched through whole exon capture, transcriptome sequencing data with less interference between rRNA and genomic DNA, high expression enrichment of functional genes and low background is obtained, accordingly, requirements on RNA quality and initial amount are reduced, the step of removing rRNA interference is eliminated, and a more accurate and efficient way is provided for expressionchange analysis of mutant gene transcripts.

The invention provides an Imatinib-drug-resistance KIT and PDGFRA wild type GIST cell strain which is named as GIST-FR and preserved in the China Center for Type Culture Collection with the preservation number being CCTC NO:C2017111. The invention further provides an establishment method of the cell strain and application of the cell strain as a cell model for discussing the human GIST drug resistance mechanism and researching relevant signal channels thereof. A tissue block culture method is adopted to obtain GIST primary cells, immortalization is carried out, and a GIST-F cell line is established; then Imatinib drug resistance induction is carried out on the GIST-F cell line, and the Imatinib-drug-resistance GIST cell strain GIST-FR is established. The GIST-FR cells are subjected to in-vitro passage for more than 40 generations, growth is slow compared with GIST-F cells, IC50 of Imatinib is remarkably increased, and the drug resistance index is 3.52 (P is less than 0.01); and a wholeexon group sequencing result shows that KIT and PDGFRA of the GIST-FR cells are negative. The GIST cell line is successfully built from human GIST primary tissue, and further induction is carried outto obtain the Imatinib-drug-resistance cells thereof, so that a foundation is laid for the GIST pathogenesis and drug resistance related research.