65 results about "Cancer genome" patented technology

The present invention discloses a cancer-related genes finding method by using miRNA expression data, based on a pan-cancer program PanCancer under The Cancer Genome Atlas (TCGA), and uses statistical analysis and a machine learning algorithm to carry out analysis and processing on the gene expression data, and to identify complex diseases related genes. The method comprises: sorting out sample data; carrying out statistical analysis on the miRNA expression data; sorting miRNA in order of an average change rate; selecting a target gene; extracting a corresponding disease sample and normal sample; and using a Relief algorithm to sort genes in the extracted miRNA sample. The method disclosed by the present invention can find a plurality of risk genes related to cancer and other complex diseases, and has important significance to a biological target therapy, biomedical research, pathogenesis explanation, risk prediction, and the like.

The invention provides a target region enrichment sequencing method for 165 genes. According to the method, 165 group-entering genes are screened according to the cancer genome and medicine data of TCGA, NCCN, FDA and the like. The 165 genes comprise detection genes recommended by NCCN, target genes corresponding to target medicines and important clinical medicines approved by FDA, genes influencing the medication effect of the target medicines, and genes influencing the chemical drug sensibility and toxic and side effects. According to the method, the exon regions of the 165 genes are enriched at once through the probe capturing technology, the multi-gene and multi-target parallel depth high-throughput sequencing is realized, the various variation types (such as point mutation, deletion, insertion, fusion and copy number amplification) of the genes can be simultaneously detected, and the detection depth and accuracy are superior to those of the prior art.

The invention provides methods to monitor cell free nucleic acids. The method comprises obtaining a plasma sample from a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer; isolating cell free nucleic acids from the plasma sample obtained from the subject; measuring the amount a housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the plasma sample to confirm that the amount of housekeeping gene and/or total DNA in the sample is within a selected range; measuring the amount of a first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the plasma sample; and indicating in a report that the subject has the first mutation when (a) the amount of the housekeeping gene and/or total DNA in the cell free nucleic acids isolated from the plasma sample is within the selected range and (b) the amount of the first mutation is increased as compared to a control amount, wherein the control amount is determined by measuring the apparent amount of the first mutation in control cell free nucleic acids isolated from plasma samples obtained from control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first mutation in the cell free nucleic acids isolated from the plasma sample from the subject.

The invention relates to a cancer genome and non-specific gene tag-based large-scale drug relocation method, and discloses a method for expression profile core labels of single human coding gene mutations without organization resource backgrounds through integrating and analyzing large-scale transcriptome data in different cancer types for the first time. On the basis of core labels, the inventionprovides a drug relocation method which aims at the in-vivo environment, is not based on model animals or cells and is capable of comprehensively covering more than 8000 human genome potential targetgenes for the first time, and designs a quantitative index for measuring interaction specificity between drugs and target genes for the first time, so that a drug relocation analysis method for comprehensively analyzing human drug target genes in a large scale is realized and a new way is provided or drug target point design and human disease treatment.

The invention discloses a flow correction method for second-generation cancer genome high-throughput sequencing data; in the method, a series of 32-bit unsigned numbers are used as identification quantities to record corresponding bloodline variation or somatic cell variation data respectively to generate read data embodying purity and different subcloning ratios, somatic cell variation correction data for offspring subcloning and its brother subcloning are acquired according to variation relationship between farther-son subcloning inheritance and brother subcloning mutual exclusion, and the data are used to correct a processing flow of second-generation cancer genome high-throughput sequencing data.

The invention discloses a fusion method for gene expression and methylation data. The fusion method includes the steps of firstly obtaining the gene expression data of a certain cancer and the DNA methylation data measured by a 450K chip from a database of cancer genome maps, then respectively performing pretreatment on the gene expression data and the DNA methylation data to obtain their respective differential gene, then cross-matching the two differential genes to obtain overlapping genes, and finally analyzing the pathways of the overlapping genes by a David online tool, and finding out cancer- and immune-related pathways in the significantly enriched pathways for the expansion of the DNA methylation data to obtain a greater number of genome-wide CpG sites.

The invention discloses a colorectal cancer judgment model for distinguishing cancer tissue of colorectal cancer from paracancerous normal tissue and an establishing method of the colorectal cancer judgment model. The method includes: selecting 107 genes related to colorectal cancer with methylation differences in the promoter region of the genes; verifying the expression of the 107 genes and the level of methylation in the promoter region by the aid of patients with both methylation and gene expression data in a TCGA (the cancer genome atlas) database, wherein a total of 37 genes are successfully verified, and 371 CpG sites are located in the promoter regions thereof; screening the 371 CpG sites by the aid of the data in the TCGA database, wherein a total of 78 CpG sites is selected; for the 78 CpG sites and on the basis of the data in the TCGA database, establishing the colorectal cancer judgment model by the aid of the elastic network algorithm. With the method, a theoretical basis is provided for blood screening of colorectal cancer in the future.

The invention provides a specific cancer coregulatory network establishment method and device and belongs to the technical field of regulatory network establishment. The method comprises the followingsteps: according to a public databank, acquiring TF regulatory information and miRNA regulatory information of TF and miRNA upon target genets; according to the TF regulatory information and the miRNA regulatory information, establishing a ternary regulatory network; recognizing FFLs in the ternary regulatory network, and acquiring FFLs recognition results; according to the FFLs recognition results and cancer genome expression information, screening, thereby obtaining a specific cancer miRNA-TF coregulatory network. According to the method, the ternary regulatory network of TF, miRNA and target genes is established, together with gene expression information, the miRNA-TF coregulatory network is obtained, and the accuracy of miRNA-TF coregulatory relationships is improved.

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 the technical field for detecting influence of mutation to an RNA secondary structure, and particularly to a method for predicting an element being rich in riboSnitch or with lost riboSnitch in a cancer genome and related equipment. The invention provides software which is named as SNIPER. The software can be used for predicting the riboSNitch and identifying a non-coded element which is rich in riboSNitch or has lost riboSnitch in a tumor. The content of the invention includes introduction to the software SNIPER and firstly analyzes the riboSnitch in somatic cell mutation in a cancer.

The invention provides a method for predicting the influence degree of mutation on an RNA secondary structure based on a Mean Diff value and related equipment. The present invention also provides methods of predicting the enrichment or deletion of riboSNitch elements in a cancer genome. The invention also provides software named as SNIPER, and the software can be used for predicting riboSNitch andidentifying a non-coding element which is rich in riboSNitch or lacks riboSNitch in a tumor.

The invention relates to a kit for detecting gene mutation related to an anti-oxidative stress pathway of lung adenocarcinoma. The kit contains detection reagents for detecting the expression quantity of the following genes: RP11-539L10.2, AKR1C2, RP11-572H4.1, TRIM16L, RARA, SESN2, RP5-827L5.2, CTD-2139B15.5, Metazoa_SRP, snoU13, RP11-545H22.1, KRT8P30, TALDO1, TRAPPC13P1, GS1-388B5.2, RP11-267L5.1, TRAV11, RP11-699A7.1 and AL132671.1. Compared with the prior art, the kit has the advantages that the genes related to the anti-oxidative stress pathway are screened through RNA sequencing, LASSO and binary classification Logistic regression, the score Score is constructed, the cut-off value of the corresponding score in the lung adenocarcinoma is obtained through ROC curve analysis, and the kit can be used for predicting mutation of the genes (KEAP1, NFE2L2 and CUL3) related to the anti-oxidative stress pathway in the lung adenocarcinoma. The specific gene mutation of the lung adenocarcinoma is predicted by utilizing the expression quantity of the gene composition, the prediction method has the advantages of high accuracy and good specificity through verification of a TCGA (The Cancer Genome Atlas) database, an experiment and a multi-omics database, and the kit has a very good application prospect.

The invention relates to application of human cartilage glycoprotein (YKL-40) as a glioblastoma biomarker. The glioblastoma (Glioblastoma, GBM) patient is low in survival rate and poor in prognosis. Effective biomarker and monitoring method are absent at present. The invention finds that the overall YKL-40 meso-position expression is obviously increased (Fold change=9.483, P<0.0001) by analyzing the YKL-40 mRNA gene expression data of the glioblastoma patient in a TCGA (The Cancer Genome Atlas) database. 45 IV-stage Chinese people glycoprotein clinic samples are further collected, and after qPCR process is adopted for quantitatively analyzing the YKL-40 expression and the prognosis correlation analysis is performed, the YKL-40 mRNA transcriptional level of 41 patients is obviously increased and the patients are short in lifetime and poor in prognosis. The invention analyzes and verifies that the YKL-40 is closely related to the lifetime and poor prognosis, the YKL-40 can be used as a potential glioblastoma biomarker, and a qPCR or protein quantitative monitoring method can be utilized to indicate the lifetime and prognosis of the glioblastoma patient.

The embodiment of the invention provides a cancer genome Hi-C data simulation method and device and electronic equipment, and relates to the technical field of genomics. According to the method, a specified variation mode can be adopted to simulate chromosome structure variation of a cancer genome and the interaction frequency matrix and the gene information of the reference enzyme digestion fragment are taken as templates; the simulated Hi-C data of the cancer genome is obtained in combination with the chromosome structure variation characteristics, various variation conditions of the chromosome are simulated, and the interaction characteristics of different positions of the cancer genome can be reflected, so that the accuracy of simulating the Hi-C data of the cancer genome is improved.

The invention relates to an analog cancer genome sequencing data generating device. The device comprises a human reference genome sequence position information acquiring module, a capturing area reference genome sequence acquiring module, a cancer genome variation data analog module, an analog cancer genome sequencing data generating module and an analog cancer genome sequencing data output module. The invention provides an algorithm and a device which can simulate various kinds of variations so that the generated analog sequencing data is suitable for evaluation of properties of various kindsof detection software.

In the invention, aiming at tumor heterogeneity, the difference of cytodynamics and molecular characteristics between conventional osteosarcoma and normal cancellous bone is compared, and the obvious differentiation direction of osteosarcoma cells is detected based on a single-cell RNA sequencing (scRNA-seq) technology or gene detection kit and gene detection chip technologies or an immunohistochemical method, and the possible interaction between each cell type in the tumor microenvironment is researched. According to the differentiation direction of the osteosarcoma cells, the conventional osteosarcoma can be divided into three types, microenvironment characteristics of each type are described, and prognosis of each type is verified according to The Cancer Genome Atlas (TCGA) data.

The invention provides a reagent kit for diagnosing oral squamous cell carcinoma. The reagent kit comprises specific antibodies for detecting HOXA10, specific antibodies for detecting HOXA11, specific antibodies for detecting HOXC6 or compositions with more than one or two optional specific antibodies for detecting the expression quantities of HOXC8. The reagent kit has the advantages that sequencing results for mRNA [messenger RNA (ribonucleic acid)] of the oral squamous cell carcinoma and normal oral tissues in TCGA (the cancer genome atlas) databases are statistically analyzed, data of 32 cases of normal oral tissues and 341 cases of oral squamous cell carcinoma tissues are incorporated, obvious difference of expression of partial genes in HOX families in the oral squamous cell carcinoma and the normal tissues is discovered, and accordingly the reagent kit is suitable to be applied to diagnosing the oral squamous cell carcinoma; expression of genes in the HOX families is detected in oral squamous cell carcinoma tissue pathological sections by the aid of immunohistochemical processes, and accordingly positive expression of the genes in the oral squamous cell carcinoma and application values of the genes in diagnosis can be determined.