84 results about "Nucleotide variation" patented technology

The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set of patient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the set of amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.

The invention relates to methods of in situ detection of a nucleic acid variation of a target nucleic acid in a sample, including single nucleotide variations, multi-nucleotide variations or splice sites. The method can comprise the steps of contacting the sample with a probe that detects the nucleic acid variation or splice site and a neighbor probe; contacting the sample with pre-amplifiers that bind to the nucleic acid variation probe or splice site probe and neighbor probe, respectively; contacting the sample with a collaboration amplifier that binds to the pre-amplifiers; and contacting the sample with a label probe system, wherein hybridization of the components forms a signal generating complex (SGC) comprising a target nucleic acid with the nucleic acid variation or splice site, the probes and amplifiers; and detecting in situ signal from the SGC on the sample. The invention also provides samples, tissue slides, and kits relating to detection of nucleic acid variations, including single nucleotide variations, multi-nucleotide variations or splice sites, of a target nucleic acid.

The invention relates to data related to influences of different kinds of fat intake on obesity and influences of different types of sports on weight reduction and blood glucose reduction in disclosed human genome single nucleotide polymorphism (SNP) data. According to genetic differences between individuals, a method suitable for determining main reasons of obesity and making personalized diet schemes or giving suggestions about lifestyles is built, and the method is applied to development of wearable mobile devices and application software. The invention further relates to preparation and application of genetic chips related to detection. The personalized weight losing and body building schemes can reasonably, efficiently and selectively use modern sports exercise means and diet regulation according to personal gene characteristics, so that individuals achieve the aims of diet regulation and exercise planning more scientifically and more quickly.

Methods and reagents for determining a nucleotide variation at position 937 of the HCV-1a NS5A gene useful in predicting an individual's response to interferon treatment are presented.

The invention belongs to the field of tumor purity detection, and especially relates to a model construction method for identifying a tumour purity sample and application thereof. The method comprisesthe steps of: based on targeted capture sequencing data of a tumor sample with known tumor purity, acquiring index data including a somatic cell copy number variation amplitude, heterozygote germlinemononucleotide variation and a somatic cell allele variation fraction; and associating the index data with the tumor purity of the tumor sample with known purity to construct an identification model.In the method, somatic mutation and germ cell variation are combined, the index data such as the somatic cell copy number variation amplitude, the heterozygote germline mononucleotide variation, themodel constructed by integrating the index data such as the somatic cell allele variation fraction and the like is used to solve the problem that the purity of tumors is difficult to identify due to few mutation sites in interval chip capture sequencing such as panel sequencing is solved, low-purity samples can be accurately identified, multiple cross confirmation among different indexes is achieved, and the reliability is high.

The invention discloses a method and a device for detecting gene mutation and expression quantity. The method comprises the following steps: S1, extracting RNA, interrupting, and carrying out reversetranscription to obtain cDNA; S2, constructing a gene library by adopting cDNA; S3, capturing and enriching a target gene from the gene library by utilizing specific hybridization of a capture probe and the target region; S4, sequencing by using a high-throughput sequencer to obtain RNA targeted sequencing data; S5, analyzing changes of gene mutation and expression quantity in the RNA targeted sequencing data, wherein the step S5 specifically comprises the following substeps: S51, analyzing the gene expression quantity; S52, analyzing gene overexpression; S53, carrying out gene fusion analysis; S54, carrying out the fusion mutation expression quantity analysis; S55, carrying out the single nucleotide variation analysis; S56, analyzing the expression quantity of the mononucleotide variationmutation. RNA transcripts expressed by tumor-related genes can be efficiently enriched, and the expression quantity and mutation conditions of the tumor genes in tumor tissues are analyzed.

The invention discloses a method for functional prediction of single nucleotide genomic variation in a non-coding region, which comprises the following steps: 1) identifying a chromatin open region; 2) identifying transcription factor bin sites; 3) assessing the role of single nucleotide variations: Based on the site-specific frequency matrix of transcription factors, the effect of single nucleotide variations in the transcription factor binding site region on transcription factor binding is calculated, and the single nucleotide variations that significantly change the binding capacity of transcription factors are identified; the role of single nucleotide variations is further evaluated by viewing the biological pathway of the target gene of the transcription factor. The method recognizesa variety of transcription factors and their binding sites at one time through chromatin open region information and gene expression information, and realizes the functional annotation of non-coding region genomic mutation.

The present invention discloses a method for detecting multiple single nucleotide variations or polymorphisms in a single reaction tube, and the oligonucleotide, the probe, the set of probes, the kit used, as well as the use thereof. Specifically, it relates to a method for identifying the genotype of multiple single nucleotide variation or SNP sites from the melting temperature of a kind of artificial melting temperature tag sequence (AMTS) and the type of fluorescence labels.

The invention discloses a gene data system for clinical diagnosis and prediction. The system comprises a source data processing module, a data warehouse and a data application module, wherein the source data processing module is used for receiving original sequencing data, conducting sort processing on the original sequencing data according to a preset rule, and generating single nucleotide variation genome data and copy number variation genome data; the data warehouse is used for storing the single nucleotide variation genome data and the copy number variation genome data; the data application module is used for receiving control commands, acquiring related data from the data warehouse according to the control commands and disposing and outputting the related data; the system further builds the data architecture of normal variation and pathogenicity variation of the human gene, can conduct analysis and management on the data and provides reliable data support for clinical diagnosis and prediction.

A method for determining adfuwei tolerance variation of hepatitis B virus includes designing specific primer, carrying out amplification by set of PCR means, using BgII and BseDI to carry out enzyme cut reaction electrophoresis on amplified product then carrying out restrictive section length polymorphism analysis.

The present invention is related to a method for a simultaneous determination of the relative amounts of more than one target polynucleotide sequence and nucleotide variations in said targets. The method is carried out by separating and recording single-stranded probes, which have hybridized to the targets and which are determined and distinguished by their defined properties including size and optional detectable label. The probes are complementary to a region in the target that has a sequence being contiguous to the nucleotide variations to be determined. After being hybridized with affinity-tagged targets, the probes are attached to a solid support and purified. The target probe hybrids are elongated using enzyme-assisted elongations. The elongated probes are recorded after release from the solid supports and the amount of each of the targets and their nucleotide variations and the ratio of modified and modified target polynucleotide sequences are calculated from the recorded results. Also disclosed is a test kit, which kit comprises in a packaged form devices equipments and reagents as well as instructions for carrying out the method. The method is useful for several diagnostic purposes.

The invention discloses an SNP mark related to the weight of eriocheir sinensis and application of the SNP mark. The SNP mark related to the weight of the eriocheir sinensis is located on the5'- side wing area of an MIH gene, the specific position is the 372bp part of the MIH gene, and nucleotide variation information is SNP g.372T>C. Obvious relevance exists between the SNP position point and the weight trait of the eriocheir sinensis species, and the average weight of the CC gene type individual is obviously higher than the average weight of the TT gene type individual. SNP g.372T>C genetic typing is carried out on a river crab breeding colony and morphology characteristic analysis is combined so that the individual with the gene type of CC can be preferably selected as a breeding parent, and the research has the significant guiding meaning on breeding of a novel large-specification river crab variety.

The invention discloses an SNP locus significantly relevant to the precocious puberty trait of eriocheir sinensis and the application. The SNP locus is positioned in a Vg gene 5'-flanking region-437bpposition of the eriocheir sinensis, and nucleotide variation information is SNP g.-437T) G. PCR primer used for detecting the SNP locus is SEQ ID NO.1 and SEQ ID NO.2, and restriction enzyme is MboI.The SNP locus has significant correlation with precocious puberty of the eriocheir sinensis, and the risk of precocious puberty trait of GG gene eriocheir sinensis individual is obviously smaller than that of precocious puberty trait of TT gene individual. The SNP locus and the PCR primer used for genetic typing are applied to the predication of the risk of precocious puberty of the eriocheir sinensis and/or the variety breeding of the eriocheir sinensis.

Provided is a variety identification-encoding system, including: a chromosome-decoding module decoding a chromosome of a reference genome variety and a chromosome of a target variety; a variation region-detecting module detecting a variation region in the decoded chromosome through single nucleotide variation dense region analysis; an amplification result-acquiring module setting an indel marker in the detected variation region and amplifying the indel marker by a polymerase chain reaction (PCR) to acquire an amplification result; and an encoding module encoding the amplification result.

The invention discloses an epitaxial probe type qPCR detection method for single nucleotide variation (SNV). Four primers are designed according to known single nucleotide variation sites, two of the four primers are outer side primers, the other two primers are specific primers, bases at the 3' ends of the specific primers are respectively complementary with bases of a mutation template and a normal template, mismatch can be introduced or not introduced into bases near the 3' ends, epitaxy of a segment of artificial sequence is carried out from the 5' end of each specific primer, a homodromous affiliated primer is designed on the 5' segment of each artificial sequence, an affiliated probe is designed on the 3' segment of each artificial sequence, and in the amplification of the specific primers and downstream primers, the affiliated probes on the specific primers are degraded and emits light in the extension of the affiliated primers so as to indicate the amplification efficiency of the specific primers. If only one genotype of the single nucleotide variation sites is detected, the two outer side primers, one specific primer, the affiliated primer of the specific primer and the probes can be used. The method still has a plurality of implementation modes, and compared with probe type AS-PCR, the method has higher sensitivity and lower cost.

The present invention discloses a genomic characteristic mutation fingerprint related to hHRD type homologous recombination repair defects and comprises a combination characteristic of a single nucleotide variation (SNV) and insertion deletion (Indel) genomic fingerprint, and an identification method thereof. The fingerprint characteristics can be subjected to high-throughput whole-genome resequencing, bioinformatics software analysis and statistical correlation analysis and are used to identify infectious diseases or tumors with the characteristic mutation fingerprints, especially hepatitis Bvirus infection and related diseases, including liver cirrhosis, liver fibrosis and liver cancer. The mutation fingerprint can also be used to guide methods and uses of treatments of targeted drugs targeting the homologous recombination defects on a variety of the various tumors with the hHRD homologous recombination repair defects, including but not limited to breast cancer, ovarian cancer, endometrial cancer, endometrioid carcinoma, ovarian clear cell carcinoma, prostate cancer, gastric cancer, skin cancer, hepatitis B virus infection or related liver cirrhosis, liver cancer and bile duct cell cancer.