216 results about "Genomic Segment" patented technology

This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.

The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.

The present invention relates to providing new vaccines and treatments for the diseases related to canine influenza virus. It discloses influenza viral antigens, and methods of presenting these antigens to canines, especially dogs. It relates to attenuated and killed vaccines. The present invention relates to experimentally generated canine and equine influenza viruses. The invention also includes influenza A, including H3, N8, H3N8, H7N7 and viruses which contain at least one genome segment from an canine or equine influenza virus. The present invention also relates to the use of these viruses in therapeutic compositions to protect canines, dogs in particular, from diseases caused by influenza viruses.

The invention belongs to the technical field of biology, and specifically relates to Cas9 nuclease and an application. The Cas9 nuclease (Cas9-R919P) has the activity as Cas9 nuclease, fits to a CRISPR/Cas9 system, and is made by mutating the 919 location arginine of wild Cas9 nuclease to proline. A protruding fracture terminal is generated by cutting a DNA double chain with the Cas9 nuclease (Cas9-R919P), and a basic group complementary to the protruding fracture terminal is added in a filling-in manner, so that accurate addition at a specific position of the genome DNA segment can be carried out.

The present invention relates to DNA-based methods for universal bacterial detection, for specific detection of the common bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Staphylococcus saprophyticus, Streptococcus pyogenes, Haemophilus influenzae and Moraxella catarrhalis as well as for specific detection of commonly encountered and clinically relevant bacterial antibiotic resistance genes directly from clinical specimens or, alternatively, from a bacterial colony. The above bacterial species can account for as much as 80% of bacterial pathogens isolated in routine microbiology laboratories. The core of this invention consists primarily of the DNA sequences from all species-specific genomic DNA fragments selected by hybridization from genomic libraries or, alternatively, selected from data banks as well as any oligonucleotide sequences derived from these sequences which can be used as probes or amplification primers for PCR or any other nucleic acid amplification methods. This invention also includes DNA sequences from the selected clinically relevant antibiotic resistance genes. With these methods, bacteria can be detected (universal primers and/or probes) and identified (species-specific primers and/or probes) directly from the clinical specimens or from an isolated bacterial colony. Bacteria are further evaluated for their putative susceptibility to antibiotics by resistance gene detection (antibiotic resistance gene specific primers and/or probes). Diagnostic kits for the detection of the presence, for the bacterial identification of the above-mentioned bacterial species and for the detection of antibiotic resistance genes are also claimed. These kits for the rapid (one hour or less) and accurate diagnosis of bacterial infections and antibiotic resistance will gradually replace conventional methods currently used in clinical microbiology laboratories for routine diagnosis. They should provide tools to clinicians to help prescribe promptly optimal treatments when necessary. Consequently, these tests should contribute to saving human lives, rationalizing treatment, reducing the development of antibiotic resistance and avoid unnecessary hospitalizations.

The invention discloses a quantitative sequencing and library building method for a fusion gene on the basis of DNA (Deoxyribonucleic Acid). The quantitative sequencing and library building method comprises the following steps: firstly, constructing a genome fragmentation DNA library and purifying the library; secondly, capturing a fusion gene generation region by PCR (Polymerase Chain Reaction) amplification, purifying the captured gene and enriching a sequence containing a specific primer fragment; thirdly, capturing a target fragment containing the fusion gene by nested PCR amplification; fourthly, constructing a DNA sequencing library with high-throughput sequencing. The invention also discloses a quantitative sequencing and detecting method for the fusion gene by using the DNA sequencing library prepared by the quantitative sequencing and library building method, application of the quantitative sequencing and detecting method as well as a detection kit containing the DNA sequencing library. According to the quantitative sequencing and library building method disclosed by the invention, the downstream where a fusion breakpoint occurs is anchored by using a one-way specific primer; a target sequence is obtained by pairing specific primers with universal primers and using a PCR method; the background is further reduced label enriching and nested PCR, so that the specificity is improved, the time for building the library is shortened, and the cost for building the library is reduced; the quantitative sequencing and library building method is suitable for an FFPE (Formalin Fixed And Parafiin Embedded) sample or liquid biopsy.

The invention discloses a method and a kit for rapidly constructing a target nucleic acidsequencing library on the basis of probe capture and enrichment. The method comprises following steps and adopts reagents required for the steps: genome DNA is subjected to fragmentation; DNA end repair is performed; a probe and a single-stranded DNA fragment formed through thermal denaturation are subjected to molecular hybridization; biotin-avidinmagnetic bead separation is executed; the probe is taken as a primer for primer extension, and a complementary strand is synthesized; one end of a double-stranded DNA fragment is connected with an linker, and the other end is not connected with the linker; PCR amplification is performed; DNA fragment lengthselection is executed; the reagents are used for completing the reactions of all the steps. Compared withconventionaltarget nucleic acid enrichment technologies, the method has the advantages of good fidelity, good reproducibility, high speed and high universality.

The invention relates to a micro genome segment clustering method based on fuzzy k-mean, and belongs to the technical field of bioinformatics analysis. The micro genome segment clustering method based on the fuzzy k-mean aims at utilizing the self features of micro genome segments under the condition of no assembly of the micro genome segments, and then the micro genome segments are clustered, so the number of contained species and the abundance ratio of species are obtained. The method comprises the following steps of obtaining the micro genome segments, establishing the feature vectors, utilizing the fuzzy k-mean method to cluster, and calculating the number of the contained species and the abundance ratio of the species according to the clustering results. The method has the advantages of directness and convenience.

In one aspect, the present invention relates to a method for selectively capturing and/or amplifying exons or targeted genomic regions from biological samples. In one embodiment, the method includes the steps of obtaining DNA templates for the targeted genomic region, cloning the DNA templates into cloning vectors to form template DNA clones, constructing libraries of the template DNA clones that cover at least the targeted genomic regions, generating hybridization probes from the DNA template clones in the libraries, capturing the targeted genomic DNA regions by hybridizing the targeted genomic DNA samples (fragmented either mechanically or enzymatically) with the generated hybridization probes, and eluting the captured genomic fragments by using conditions for releasing and separating the bound DNA from the hybridization probes.

The present application relates to arenaviruses with rearrangements of their open reading frames (“ORF”) in their genomes. In particular, described herein is a modified arenavirus genomic segment, wherein the arenavirus genomic segment is engineered to carry a viral ORF in a position other than the wild-type position of the ORF. Also described herein are trisegmented arenavirus particles comprising one L segment and two S segments or two L segments and one S segment. The arenavirus, described herein may be suitable for vaccines and/or treatment of diseases and/or for the use in immunotherapies.

Method of processing and/or genome mapping of ditag sequences There is provided a method and system for processing and/or mapping ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment. The method of processing comprises preparing a database or file comprising at least one ditag sequence. The method of mapping comprises preparing a database or file of ditag(s), and mapping the ditag sequence(s) to the genome, comprising matching the 5′ and the 3′ terminal tags of the ditag sequence to at least a portion of the genome.

The invention relates to a method and a device for assembling genomes by utilizing a long transcriptome sequencing result. The method adopts the scheme that transcriptome sequencing reading segments and genome segments of the same species are compared; only one transcriptome sequencing reading segment from a comparison to one genome segment is removed, query blocks of reserved transcriptome sequencing reading segments are filtered under specified conditions; block connection relative to the reserved query blocks are obtained according to the specified conditions; and the genome segments are connected on the basis of the block connection, thereby completing assembling of the genome sequences. According to the method for assembling the genomes by utilizing the long transcription sequence result, long segment sequencing data including a large amount of existing and published Sanger data can be utilized, so that the genome sequences can be assembled by utilizing the long transcriptome sequencing reading sequence.

The present invention provides comparative genomic hybridization methods for detecting and mapping chromosomal or genetic abnormalities associated with various diseases or with predisposition to various diseases, or to detecting the phenomena of large scale copy number variants. The method includes hybridization with one or more probes for detecting balanced translocations. Such probes may be complementary to the moving genomic segment which is translocated or may be complementary to the translocation break point.

The invention discloses a quality control method for detecting human EGFR (Epidermal Growth Factor Receptor) gene variation based on high-throughput sequencing and a kit, and applications thereof. The quality control method comprises the following steps: extracting a plurality of genome DNAs of an EGFR gene variation-positive human tumor cell line; measuring variation positive sites as positive control sites through a Sanger sequencing method; fragmenting the genome DNAs and mixing according to a certain proportion to obtain a quality control product which can be applied high-throughput sequencing detection of human EGFR gene variation. The kit comprises the human EGFR gene variation detection quality control product.

The present invention provides new and improved assay for detection of genomic methylated CpG islands. This new method is termed the methylated-CpG island recovery assay (MIRA). In accordance with one embodiment, MIRA comprises the steps of: (a) incubating genomic DNA fragments with a methylated CpG island binding protein in the presence of a binding partner for the binding protein to produce bound DNA containing methylated CpG islands, (b) isolating the bound DNA, and (c) detecting CpG island methylation by gene-specific amplification reactions. In accordance with a preferred embodiment, MIRA comprises the steps of: (a) incubating sonicated genomic DNA with a matrix containing a fusion protein of glutathione S-transferase (GST) and MBD2b (GST-MBD2b) in the presence of MBD3L1 to produce bound DNA containing methylated CpG islands, (b) eluting bound DNA from the matrix, and (c) detecting CpG island methylation by gene-specific amplification reactions.

Various methods and systems for processing at least some of genome sequences and at least some of associated information, for an individual, may be described and disclosed herein. A purpose of such processing may be to prevent, minimize, and/or mitigate against (1) identification of the individual from such genome sequence information and/or from associated information; and/or (2) using such genome sequence information and/or associated information as a basis for discriminating against the individual. In some embodiments, such processing may comprise one or more of: segmenting genome sequences for at least a purpose of anonymizing genome information; using anchor segments for a purpose of minimizing storage space in storing of genetic sequence information; generating at least one linkage record; generating at least one anonymized linkage record; processing a request for genetic study results; processing genetic study results received; and/or generating personalized information of interest pertaining to the individual.

The invention discloses a recombinant influenza virus vector carrying foreign genes in an NA segment, which can be rescued in cells by a virus rescue method and can be amplified in chick embryos in large quantities. The invention also discloses a preparation method thereof, comprising the following steps: firstly constructing plasmids used for rescuing influenza viruses and introduced with the foreign genes on the NA genome segment of the influenza virus and carrying out rescue on host cells. The foreign gene is connected with the NA genome segment by a 2A segment. The foreign gene comprises EGFP reporter genes and adopts a CMV/huPolI bidirectional influenza virus rescue system. The recombinant influenza virus vector overcomes capacity limit of the foreign genes in the influenza virus genome, enjoys stable passage in chick embryos, can be applied to vaccine and drug development and tumor treatment and can produce recombinant cell factor drugs in cheap chick embryo bioreactors.

The present disclosure provides a method for assembly of genomic DNA using multiplex end-tagging amplification of genomic fragments.

The invention relates to the field of diagnosis of and vaccination against Streptococcal infections and to the detection of virulence markers of Streptococci. The invention discloses a method for modulating virulence of a Streptococcus comprising modifying a genomic fragment of Streptococcus wherein the genomic fragment comprises at least a functional part of a fragment identifiable by hybridization in Streptococcus suis to a nucleic acid or fragment thereof as shown in FIG. 5.

The invention discloses a DNA based fusion gene quantitative sequencing database foundation method. The method comprises (1) carrying out genome DNA fragmentation; (2) sorting DNA fragments; (3) carrying out unidirectional specific PCR amplification to obtain an amplification product with fusion sites; (4) connecting a single chain general library linker sequence to the 3' terminal of the amplification product; and (5) carrying out PCR amplification, enriching fusion gene regional fragments, and carrying out purification and quantification to obtain sequencing database. The invention also discloses a method of using a DNA library established by the provided method to carry out fusion gene sequencing detection, an application thereof, and a fusion gene unidirectional specific primer set forthe database establishment method. By unidirectionally specifically amplifying the DNA segments, capturing fusion sequences, and obtaining a DNA library for NGS sequencing through enrichment, the ratio of captured effective database is increased, the database establishment and detection speed is accelerated, and the method is suitable for FFPE sample or liquid state biopsy.

Disclosed are methods and compositions for the selective manipulation of gene expression through the preparation of retroviral expression vectors for expressing antisense sequences, such as K-ras oncogene antisense sequences, or sequences encoding a desired product, such as wild type p53 sequences. Preferred retroviral vectors of the present invention incorporate the β-actin promoter in a reverse orientation with respect to retroviral transcription. Preferred antisense RNA constructs of the present invention employ the use of antisense intron DNA corresponding to distinct intron regions of the gene whose expression is targeted for down-regulation. In an exemplary embodiment, a human lung cancer cell line (NCI-H460a) with a homozygous spontaneous K-ras mutation was transfected with a recombinant plasmid that synthesizes a genomic segment of K-ras in antisense orientation. Translation of the mutated K-ras mRNA was specifically inhibited, whereas expression of H-ras and N-ras was unchanged. A three-fold growth inhibition occurred in H460a cells when expression of the mutated ras p21 protein was down-regulated by antisense RNA and cells remained viable. The growth of H460a tumors in nu/nu mice was substantially reduced by expressed K-ras antisense RNA.