344 results about "Tandem repeat" patented technology

Oligonucleotides for genotyping the thymidylate synthase gene are provided. The number of tandem repeats in the promoter region of the thymidylate synthase gene can be identified based on the hybridization of an oligonucleotide of the invention to the genomic DNA of a subject. Therefore, the genotype of the thymidylate synthase gene can be identified based on the number of tandem repeats. The genotype relates to the responsiveness of a subject towards an antitumor agent.

The present invention is directed to the simultaneous amplification of multiple distinct genetic loci using PCR or other amplification systems to determine in one reaction the alleles of each locus contained within the multiplex.

The present invention provides devices and methods for detecting or characterizing a nucleic acid analyte without requiring electrophoresis or the direct sequencing of analyte samples or analyte fragments. The device includes a panel or array of double stranded oligonucleotide probes immobilized on a solid support. each probe comprising a nucleotide sequence having a hypervariable number of tandem repeat sequences. Desirably, the specificity of the probes is varied with the location on the panel or array. One strand of each probe is preferably anchored at one terminus to a solid support and the opposite terminus of a second strand is not so anchored. The probes and / or the analyte are labeled by one or more reporter moieties, designed, for example, to allow for visual or instrument based detection of hybridization events.

This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

Methods, devices, and compositions are described that provide for amplification of nucleic acid sequences without reliance upon temperature cycling, thus freeing the methods from conventional benchtop thermal cycling devices. Denaturation of double stranded nucleic acids, primer annealing, and precision control over primer extension by polymerase can be accomplished by applying stress to a nucleic acid. These methods can provide one ore more benefits over conventional PCR methods including: precision control over the PCR process; generally improved fidelity; improved accuracy over problematic sequences such as GC-rich or tandem repeat regions; greater sequence length; increased reaction yield; reduced experimental time; greater efficiency; lower cost; greater portability; and, robustness to various environmental parameters, such as temperature, pH, and ionic strengths.

The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and / or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and / or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.

Disclosed are compositions and methods for amplification of RNA molecules. The disclosed method involves synthesizing first strand cDNA molecules from RNA molecules, circularizing the first strand cDNA molecules and replicating the circularized first strand cDNA molecules using rolling circle replication. The method can be aided by the use of specialized primers for cDNA synthesis and specialized probes for circularizing the first strand cDNA molecules. The method can be used to replicate and amplify multiple RNA molecules, such as all RNA molecules in a sample or all mRNA molecules in a sample, or be used to replicate and amplify specific RNA molecules. Rolling circle replication of the circularized first strand cDNA molecules results in long DNA strands containing tandem repeats of the cDNA sequence. The tandem sequence DNA can be used directly (for detection of sequences, for example), further amplified, or used any other purpose. Double-stranded tandem sequence DNA can be used to produce unit lengths of the cDNA sequence. Tandem sequence DNA can also be transcribed to produce transcripts having sequence complementary to or matching the sequence of RNA molecules.

A system and method for genotyping tandem repeats in sequencing data. The invention uses Bayesian model selection guided by an empirically-derived error model that incorporates properties of sequence reads and reference sequences to which they map.

Spectrogram extraction from DNA sequence has been known since 2001. A DNA spectrogram is generated by applying Fourier transform to convert a symbolic DNA sequence consisting of letters A, T, C, G into a visual representation that highlights periodicities of co-occurrence of DNA patterns. Given a DNA sequence or whole genomes, with this method it is easy to generate a large number of spectrogram images. However, the difficult part is to elucidate where are the repetitive patterns and to associate a biological and clinical meaning to them. The present disclosure provides systems and methods that facilitate the location and / or identification of repetitive DNA patterns, such as CpG islands, Alu repeats, tandem repeats and various types of satellite repeats. These repetitive elements can be found within a chromosome, within a genome or across genomes of various species. The disclosed systems and methods apply image processing operators to find prominent features in the vertical and horizontal direction of the DNA spectrograms. Systems and methods for fast, full scale analysis of the derived images using supervised machine learning methods are also disclosed. The disclosed systems and methods for detecting and / or classifying repetitive DNA patterns include: (a) comparative histogram method, (b) feature selection and classification using support vector machines and genetic algorithms, and (c) generation of spectrovideo from a plurality of spectral images.

The invention relates to a compound amplification system for simultaneously analyzing a plurality of STR (short tandem repeat) loca, which is characterized by being used for carrying out compound amplification on 20 locas: Amelogenin, vWA, D21S11, D18S51, D5S818, D7S820, D13S317, D16S539, FGA, D2S1338, D19S433, D6S1043, D12S391, D8S1179, D3S1358, CSF1PO, Penta D, Penta E, TH01 and TPOX. The invention also relates to a method and a kit for simultaneously analyzing DNA (deoxyribonucleic acid) samples and other applications of the loca.

The present invention provides methods and compositions for analyzing compromised nucleic acid samples. The present invention also includes methods of selecting panels and panels of single nucleotide polymorphisms that are selected so as to be outside of tandem repeat regions, and are not genetically linked.

The present invention provides methods of determining the size of a particular nucleic acid segment of interest in a sample of nucleic acids through fragmentation of DNA, size fractionation, an optional second fragmentation, and identification using a marker sequence. In particular aspects, an expansion or reduction of tandem repeat sequences can be detected. In further aspects, carriers and individuals afflicted with fragile X syndrome or other diseases associated with tandem repeats can be distinguished from normal individuals.

Allelic ladders of short tandem repeat (STR) loci selected from the group consisting of D16S539, D7S820, D13S317, and D5S818; methods for their use in analyzing STR polymorphisms, and kits containing the allelic ladders are disclosed.

The present invention relates to the detection of a cell proliferative disorder associated with alterations of microsatellite DNA in a sample. The microsatellite DNA can be contained within any of a variety of samples, such as urine, sputum, bile, stool, cervical tissue, saliva, tears, or cerebral spinal fluid. The invention is a method to detect an allelic imbalance by assaying microsatellite DNA. Allelic imbalance is detected by observing an abnormality in an allele, such as an increase or decrease in microsatellite DNA which is at or corresponds to an allele. An increase can be detected as the appearance of a new allele. In practicing the invention, DNA amplification methods, particularly polymerase chain reactions, are useful for amplifying the DNA. DNA analysis methods can be used to detect such a decrease or increase. The invention is also a method to detect genetic instability of microsatellite DNA. Genetic instability is detected by observing an amplification or deletion of the small, tandem repeat DNA sequences in the microsatellite DNA which is at or corresponds to an allele. The invention is also a kit for practicing these methods.

The invention discloses a method for extracting purified DNA from human exfoliative cells. The method comprises the following steps: 1) pretreating: contacting the human exfoliative cells with pretreating lysate to remove the solid matters adhering to the biological cells to obtain coarse lysate; 2) nucleic acid adsorbing: mixing the coarse lysate obtained in the step 1) with lysis integrated liquid and magnetic bead suspension to form a solution system containing a magnetic nano microsphere-DNA compound and collecting the magnetic nano microsphere-DNA compound in the solution system; and 3) washing: washing the magnetic nano microsphere-DNA compound obtained in the step 2) with washing liquid I and washing liquid II respectively and then dissolving out the DNA with eluent. The efficiency of extracting DNA by the method can reach 90% and the extracted DNA can be applied to such downstream analysis operations as STR (short tandem repeat) multiplex amplification, DNA sequencing, DNA quantifying and the like.

A method of detecting and outputting tandem repeats in a sequence of symbols comprising a) mapping the symbols to quaternions; b) constructing a Quaternionic Periodicity Transform (QPT); c) computing the QPT of the sequence to determine the tandem repeats of the sequence; d) post-processing of the QPT; e) outputting a list of tandem repeats obtained from step d) to a computer's memory. In embodiments, the sequence of symbols is a sequence of letters representing nucleotides in a DNA or RNA sequence.

A kinship analysis program for missing persons and mass disasters for kinship and missing persons analyses. The inventive device includes consensusG, Kinship Indices, Matching, cross-checking, pedigree that performs the following: Extract a list of unique victims' genotypes from the remains or missing persons database, make perfect matches to personal effect, identify next-of-kin related to a victim, make matches through parentage trios, confirm consistency of family pedigrees, exclude nearly all fortuitous hits on the basis of the SM scoring performance of the entire family of the relative that triggered the fortuitous hit, make matches despite the known existence of errors in sample names and reported relationships, flag samples with inconsistent reported relationships, display matches in their context, so that “close-calls” are brought to the attention of the data reviewer. An algorithm which reduces very large collections of complete / partial STR (Short Tandem Repeats) genotypes derived from the remains down to a restricted number of consensus genotypes believed to reflect the many different victims. An algorithm which calculates Kinship Indices through a segregated score approach and likelihood ratio calculations through a linkage to the KinTest software. An algorithm which contrasts the consensus genotypes against the data set of genotypes from next-of-kin and personal effects for direct matches to personal effects, for evidence of genetic relatedness to kin through the Kinship Indices, or for successful production of a parentage trio with any two members of the next-of-kin cohort. An algorithm which cross-checks matches to parentage trios against other kinship scoring results between the victim and other members of the same family to confirm that the purported family structure is consistent with Mendelian inheritance rules. A schematic diagram describing the relationship of the relatives to a matched victim. A user interface that is accessible to a broader range of users.

The invention relates to a composite amplification system for simultaneously analyzing multiple Y-STR loci. The composite amplification kit is characterized by compositely amplifying the following 26 Y chromosome loci: DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, DYS460, DYS481, DYS533, DYS549, DYS570, DYS576, DYS643, DYS449 and Y-GATA-H4. The invention also relates to a method and a kit for simultaneously analyzing DNA samples, and applications thereof.

To provide a nucleic acid encoding a receptor protein kinase, wherein the nucleic acid has tandem duplication in a nucleotide sequence of a juxtamembrane and is useful for diagnosis of leukemia; a polypeptide encoded by the nucleic acid; an antibody capable of specifically binding to a region encoded by the nucleic acid having tandem duplication occurring in a nucleotide sequence of a juxtamembrane; a nucleic acid capable of specifically binding to the nucleic acid having tandem duplication occurring in a nucleotide sequence of a juxtamembrane; a method for detection of the nucleic acid encoding a receptor protein kinase; and a kit therefor. A nucleic acid encoding a receptor protein kinase, wherein the nucleic acid has tandem duplication in a nucleotide sequence of a juxtamembrane; a polypeptide encoded by the nucleic acid; an antibody capable of specifically binding to the portion of the polypeptide; a nucleic acid capable of specifically binding to the nucleic acid; a method for detection of the nucleic acid; and a kit for detection.

Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

The invention discloses application of a high-pass DNA (Deoxyribonucleic Acid) sequencing method on determination of a short tandem repeat gene locus in human genome and a method, belonging to the technical field of biology. The method comprises the following steps of: preparing a multi-sample gene locus proliferation sublibrary; sequencing high-pass DNA; and analyzing data and reporting the result. According to the application and the method disclosed by the invention, the high-pass DNA sequencing technology is applied to determination of the human short tandem repeat (STR) gene locus for the first time and the resolving power and the sensitivity of the STR locus as individual human recognition are remarkably improved; and meanwhile, the detection pass of the STR is greatly improved.

A collagen-binding MSCRAMM entitled Ace from enterococcal bacteria is provided which was homologous to the ligand-binding region of Cna, the collagen-binding MSCRAMM from Staphylococcus aureus, and which can be utilized to inhibit adhesion of enterococcal bacteria to extracellular matrix proteins. The N-terminal region of Ace contained a region (residues 174-319), or A domain, contains several 47-residue tandem repeat units between the collagen-binding site and cell wall-associated regions. The Ace protein can be utilized in methods of preventing and / or treating enterococcal infection, and in addition, antibodies raised against Ace, or its A domain, can be used to effectively inhibit the adhesion of enterococcal cells to a collagen substrate.

The invention relates to a composite amplification system of 23 short tandem repeat sequences and a kit, is used for detecting heredity mark gene of polymorphism in a mankind genome, and belongs to the biology technical field. The invention relates to a scheme that a plurality of short tandem repeat sequences are simultaneously amplified in a PCR system; a specific gene locus comprises 22 short tandem repeat sequences with high level heredity polymorphism and 1 gender determination locus; primers are respectively designed and a fluorophore is marked; the system has very high individual recognition rate and non-father elimination rate; the system and kit can be used for legal medical individual recognition, paternity tests, and colony genetics analysis, is high in accuracy, and good in sensitivity.

The present application discloses a method for detection of insertion deletion mutation based on second generation sequencing, a device and a storage medium. The method comprises the following steps:comparing a sample to be tested with a file of a reference genome to extract a set of candidate mutation sites with mutation allele frequency being greater than or equal to a threshold; filtering to remove sites in a short tandem repeat region; making detail statistics of comparison information of the mutation sites and comparison information surrounding the mutation sites, wherein the comparisoninformation includes InDel site and reference base support number, comparison quality, coverage depth, surrounding non-reference base and other insertion deletion mutations, surrounding read quality;and filtering to remove sites that do not reach the set threshold according to statistical information to obtain mutation results. The method does not require partial assembly, and filters second-generation sequencing data in advance to quickly eliminate most of false positive results caused by the comparison, reduces detection running time and computing resources, improves detection efficiency, has strong sensitivity and specificity, and can quickly and accurately detect InDel mutations.