53 results about "Mutational analysis" patented technology

Nucleic acids are fixed or immobilized to non-porous solid supports (substrates), and include systems containing such supports and arrays with fixed or immobilized nucleic acids. These compositions are useful for nucleic acid analyses and a host of applications, including, for example, detection, mutational analysis and quantification. The non-porous solid supports can be transparent or translucent, and the surfaces can be treated with agents to fix or immobilize the nucleic acids. Such agents include, for example, amine providing compounds, epoxy compounds and acid solutions. The fixed or immobilized nucleic acids can be unlabeled, or labeled with at least one non-radioactive signaling moiety, such as the case when the nucleic acids are double-stranded.

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

The application relates to a method of a predicting the presence of invasive pancreatic cancer or high grade dysplasia, pre-cancerous pancreatic states and non-neoplastic conditions comprising detailed molecular analysis incorporating DNA quality and quantity, K-ras mutational analysis and a broad spectrum of tumor suppressor gene linked microsatellite LOH. Methods of diagnosing, determining prognosis of and determining a course of treatment for pancreatic cancer or high grade dysplasia, pre-cancerous pancreatic states and non-neoplastic conditions are also provided.

A method of detecting the presence of an analyte, such as a target nucleic acid sequence, protein sequence or small molecule, which can also be employed to detect the formation of duplex structures, is disclosed. The method can comprise nucleic acids, proteins and small molecules, employing photoelectrochemically active nanoparticles, branched polymers or other structures that carry photoelectrochemically active molecules capable of generating a photocurrent when excited by light in the presence of an electric field is disclosed. The method can be employed to detect hybridization on an array and can be employed in sequencing, mutational analysis (for example, single nucleotide polymorphisms and other variations in a population) and for monitoring gene expression by analysis of the level of expression of messenger RNA extracted from a cell. The method is applicable to the detection of antibody binding or other protein binding for analyte detection in an array format. The creation of an array addressable by light is disclosed.

Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14) affecting 26% of colorectal cancers and a smaller fraction of lung, breast and gastric cancers. Fifteen mutations were nonsense, frameshift or splice site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRP) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the tyrosine phosphatase genes are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.

The invention relates to a mutation analysis method and device for cell-free DNA (cfDNA) sequencing data. The method comprises the following steps: 1, preprocessing original sequencing data; 2, comparing the sequencing data with a reference standard genome, identifying and eliminating PCR repetitive sequences, and correcting comparison errors of sequences to obtain an accurate sequence comparisonfile; 3, identifying tumor-related somatic cell variation sites, adopting a Sentieon software TNScope tool, setting parameters to ensure that cfDNA variation sites higher than 5/10000 variation abundance can be detected, and obtaining a potential tumor-related somatic cell variation site table; and 4, analyzing and identifying the highly credible low-frequency variation, and finally obtaining an expected positive variation analysis result. The method can achieve ultrahigh mutation sensitivity detection and high verification accuracy.

Genome-wide analysis of copy number changes in breast and colorectal tumors used approaches that can reliably detect homozygous deletions and amplifications. The number of genes altered by major copy number changes—deletion of all copies or amplification of at least twelve copies per cell—averaged thirteen per tumor. These data were integrated with previous mutation analyses of the Reference Sequence genes in these same tumor types to identify genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations include those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analyses provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that are useful for cancer diagnosis and therapy.

The invention discloses a second-generation sequencing method for dimolecular self-checking library preparation and hybrid capture used for trace DNA ultralow frequency mutation detection. The methodcomprises the following steps: extracting plasma free DNA, performing DNA chemical error repair, preparing a self-checking dimolecular identification code hairpin type joint, repairing plasma free DNA, connecting DNA with the joint, and performing Pre-PCR amplification, excessive hybrid capture, Post-PCR amplification, computer sequencing, data error correction, and mutation analysis and annotation. The method disclosed by the invention can efficiently realize low frequency mutation detection of plasma free DNA. DNA error repair and dual redundancy checking technology can enable the method tohave ultralow false positive rate and high sensitity while detecting trace samples, thus avoiding defects of existing plasma circulating free DNA detection methods, not only realizing cancer mutationdetection and targeted medication guidance, but also realizing early screening of genetic and birth defects of fetus.

The invention provides a tumor mutation site screening and mutual exclusion gene mining method, which comprises the following steps: (1) filtering a vcf file and an output file of ANNOVAR annotation software; (2) carrying out the descriptive analysis of different experimental groups of mutation sites; (3) constructing a mutation gene matrix; and (4) carrying out mutual exclusion and joint mutation analysis on the generated mutation gene matrix on the basis of a Fisher exact test to determine a mutual exclusion and joint mutation gene. The mutation site is filtered by the annotation information of the mutation site and basic parameters including a sequencing read number, site sequencing depth and the like, and then, the obtained mutation site is subjected to the descriptive analysis of different experimental groups of mutation modes and the mining of a mutual exclusion and joint mutation gene set.

Methods and compositions for diagnosing and prognosing neoplasms, particularly malignant melanomas, and for identifying patients at high risk for melanocytic nevi and/or melanomas or other cancers are provided. Methods for distinguishing between nevi at high and low risk for malignant transformation and for characterizing or classifying lesions or nevi are also disclosed. Assays and kits for prognosis of melanoma in a human subject comprising assessment of BAP1 protein and/or BAP1 nucleic acid are provided.

The present teachings disclose methods for evaluation of sequence information to characterize putative heterozygous indel mutations. The mutation analysis methods utilize sequence and trace information to identify mixed-base presence resulting from allelic differences. These methods may be applied to identify and resolve single nucleotide polymorphisms, insertions, deletions, and other mutational events.

The invention discloses an algorithm for the automatic generation module of the HGVS (Human Geome Variation Society) name of gene mutation. The algorithm comprises the following elements: 1) describing a mutation site by a ''gene(R/M)Sz/c'' format, wherein the meaning of the gene(R/M)Sz/c is a gene name, one segment of sequence after a (mutation site reference sequence/ mutation site mutation sequence) mutation site and whether the mutation site is a homozygotic type or a hybrid type, and the three parts are separated by a space so as to describe mutation discovered by sequencing; 2) the format is input into a mutation analysis system, a gene information database, a gene inheritance pattern way database, an HGMD database and the like are called through an HGVS calculation program for calculation; and 3) the HGVS name of the gene mutation and relevant information based on the HGVS information are obtained. Through tests, a human gene mutation system based on the algorithm can analyze of mutation of more than 6000 human genes so as to meet the analysis requirements of gene mutation including common genetic diseases, cancers and the like.

Long QT Syndrome (LQTS) is a cardiovascular disorder characterized by prolongation of the QT interval on electrocardiogram and presence of syncope, seizures and sudden death. Five genes have been implicated in Romano-Ward syndrome, the autosomal dominant form of LQTS. These genes are KVLQT1, HERG, SCN5A, KCNE1 and KCNE2. Mutations in KVLQT1 and KCNE1 also cause the Jervell and Lange-Nielsen syndrome, a form of LQTS associated with deafness, a phenotypic abnormality inherited in an autosomal recessive fashion. Mutational analyses were used to screen 262 unrelated individuals with LQTS for mutations in the five defined genes. A total of 134 mutations were observed of which eighty were novel.

A method for determining mutation load in a somatic cell is determined by mutation analysis of the p53 gene. The p53 gene has been found to be a useful indicator of predisposition to spontaneous mutations or prior carcinogen exposure. Cells that contain mutated p53 tend to accumulate the mutant protein. Thus, DNA from a cell identified by p53 accumulation is amplified and the amplification product further analyzed for mutations in the p53 gene.

The invention relates to the field of gene engineering and cytology, in particular to an AAV receptor knocking out method, an HEK293 cell strain with an AAV receptor being knocked out and an application. The knocked-out AAV receptor is KIAA0319L. The knocking out method comprises the following steps: establishing a sgRNA carrier of a targeted AAVR genome sequence; carrying out transfection for a 293 T-cell, and culturing to obtain each clonal cell; carrying out Suveyor gene mutation analysis test; selecting AAVR mutant monoclone; then selecting an AAVR mutant cell strain with high yield of AAV; identifying a mutation condition of other potential mutant site; and enlarging the cell strain without other mutant sites, and establishing a library for production. The final yield of the AAV produced by the HEK293 cell strain of the knocked-out AAV receptor is about 50 percent higher than the yield of the conventional HEK293.

A method for analysing genetic mutations, and in particular single nucleotide polymorphisms (SNPs) and/or somatic mutations, is described, as well as methods for preferentially amplifying one allelic form compared with another form. The methods use an oligonucleotide probe which hybridises to a first allele with a lower melting temperature (Tm) than that with which it hybridises to a second allele, together with amplification primers which flank the oligonucleotide probe binding site and which bind to the sample with a higher Tm than that of the probe and the first allele. An amplification reaction may be carried out at a temperature such that the probe is preferentially hybridised to the second allele, thereby amplifying the first allele. The amplified sequences may be detected using the same probe as acted as the blocking probe during amplification.

The invention presents a method for examining genetic material (deoxyribonucleic acid, DNA) to detect the presence of pre-known mutations, especially single nucleotide polymorphisms (SNP), using mass spectrometry with ionization by matrix-assisted laser desorption (MALDI). The invention uses nucleoside triphosphates with modified sites for the method of primer extension in a duplicating, enzymatic reaction and at least partially removal of primers from the extension product, in combination with product neutralization by chemical treatment of the modified sites, so that the resulting DNA products can be, by using special matrix materials, preferredly ionized in an adduct-free form over other constituents in the reaction solution without any further cleaning. The method is particularly suitable for simultaneous identification of several mutations by multiplexing.

The present disclosure is directed to methods for typing and characterizing sperm. The technology employs a sequencing-based method for detecting and measuring RNA transcripts from single sperm cells and the analysis of the sequencing data for the prediction of male parent contribution to autism.

A method of simultaneously analyzing RNA and DNA in a sample, the method comprising the step (a) contacting the sample with a reverse primer from a first primer pair directed to a target RNA region to effect reverse transcription of RNA into cDNA with a reverse transcriptase; (b) subsequently contacting the sample with (i) a forward primer from the first primer pair directed to a second cDNA region, (ii) a forward and a reverse primers from a second primer pair targeted to a DNA region, and (ii) a DNA polymerase to simultaneously amplify the target cDNA and target DNA region; and (c) analyzing the amplified target cDNA region and/or amplified target DNA region. Also encompassed are uses of the method to analyze gene expression and mutations, kits comprising primers, enzymes, buffers.