1158 results about "High throughput sequence" patented technology

Methods, systems and computer readable media for sequencing a biopolymer specimen and tracking a source from which the specimen was derived. Methods, systems and computer readable media for multiplex sequencing biopolymer samples. Methods, systems and computer readable media for efficiently sequencing biopolymeric specimens through a high-throughput sequencer. Methods, systems and computer readable media for performing ratio-based analysis with a high throughput sequencer.

Method for the detection the presence or absence of one or more target sequences in one or more samples based on oligonucleotide ligation assays with a variety of ligatable probes containing identifiers and the subsequent identification of the identifiers in the amplicons or ligated probes using high throughput sequencing technologies.

The present disclosure provides methods, compositions, and kits for methods that can improve techniques nucleic acid analysis, and can allow for more reliable and accurate targeted, multiplexed, high throughput sequencing. The methods, compositions, and kits can be used for sequencing target loci of nucleic acid. The methods, compositions, and kits disclosed herein can be used for assisted de novo targeted sequencing. The methods, compositions, and kits disclosed herein can also be used for library labeling for de novo sequencing and phasing.

Multiplex barcoded Paired-End Ditag (mbPED) library construction for ultra high throughput sequencing is disclosed. The mbPED library comprises multiple types of barcoded Paired-End Ditag (bPED) nucleic acid fragment constructs, each of which comprises a unique barcoded adaptor, a first tag, and a second tag linked to the first tag via the barcoded adaptor. The two tags are the 5′- and 3′-ends of a nucleic acid molecule from which they originate. The barcoded adaptor comprises a barcode, a first polynucleotide sequence comprising a first restriction enzyme (RE) recognition site, and a second polynucleotide sequence comprising a second RE recognition site and covalently linked to the first polynucleotide sequence via the barcode. The two REs lead to cleavage of a nucleic acid at a defined distance from their recognition sites. The length of the adaptor is set so that the bPED nucleic acid fragment fits one-step sequencing.

Described herein are methods useful for incorporating one or more adaptors and / or nucleotide tag(s) and / or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and / or quantifying alleles by primer extension.

A technology is described that is capable of generating high-throughput sequencing (HTS) read length DNA products to accurately and reliably provide exon connectivity information for alternatively spliced isoforms. The method is not limited by the initial size of the isoform as the technology removes the template oligonucleotide sequence and a newly formed full length ligated product provides an HTS-compatible read length sequence that comprises information that corresponds to the consecutive order of the exons in the original template oligonucleotide.

A method and system for quantifying the relative abundance of gene transcripts in a biological sample. One embodiment of the method generates high-throughput sequence-specific analysis of multiple RNAs or their corresponding cDNAs (gene transcript imaging analysis). Another embodiment of the method produces a gene transcript imaging analysis by the use of high-throughput CDNA sequence analysis. In addition, the gene transcript imaging can be used to detect or diagnose a particular biological state, disease, or condition which is correlated to the relative abundance of gene transcripts in a given cell or population of cells. The invention provides a method for comparing the gene transcript image analysis from two or more different biological samples in order to distinguish between the two samples and identify one or more genes which are differentially expressed between the two samples.

Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.

The invention is directed to methods for determining nucleic acids that encode immune receptor chains originating from the same cell, that is, paired immune receptor chains. Methods of the invention comprise high-throughput sequencing of rearranged nucleic acids encoding immune receptors from one or more samples of lymphocytes. In one aspect, from a plurality of subsets of a sample, nucleic acids encoding separate chains of a pair are separately sequenced, wherein the size of the sample and the number of subsets are selected so that the distribution of lymphocytes approximates a binomial model. Paired chains are determined by identifying pairs that appear together or that are entirely absent in the subsets.

The present invention is related to genomic nucleotide sequencing. In particular, the invention describes a single reaction method to co-amplify multiple subsequences of a nucleic acid fragment sequence (i.e., for example, at least two read pairs from a single library insert sequence). Nucleic acid fragment sequences may include, but are not limited to, localizing library insert sequences and / or unique read pair sequences in specific orientations on a single emulsion polymerase chain reaction bead. Methods may include, but are not limited to, annealing, melting, digesting, and / or reannealing high throughput sequencing primers to high throughput sequencing primer binding sites. The compositions and methods disclosed herein contemplate sequencing complex genomes, amplified genomic regions, as well as detecting chromosomal structural rearrangements that are compatible with massively parallel high throughput sequencing platforms as well as ion semiconductor matching sequencing platforms (i.e., for example, Ion Torrent platforms).

The invention discloses a method for capturing a genome target sequence based on Crispr / cas9 and application thereof in high-throughput sequencing. The method for capturing a target gene sequence from a genome DNA on the basis of a Crispr / cas9 system comprises the steps that 1, a plurality of gRNAs are designed and synthesized according to the target gene sequence; 2, the multiple gRNAs and a cas9 enzyme are adopted for performing a cleavage reaction on the genome DNA, and a cleavage product containing multiple 100-300 bp fragmentation products is obtained; 3, the multiple 100-300 bp fragmentation products in the cleavage product are captured. On the basis of the CRISPR gene, the target sequence is edited and captured, and the method can be used for high-throughput sequencing and is applicable to screening of specific population with family heredity, the public physical examination market and the like.

The present disclosure generally relates to sequencing two or more genes expressed in a single cell in a high-throughput manner. More particularly, the present disclosure relates to a method for high-throughput sequencing of pairs of transcripts co expressed in single cells (e.g., antibody VH and VL coding sequence) to determine pairs of polypeptide chains that comprise immune receptors.

The present invention relates to molecular microscopy or volumetric imaging by proximal unique molecular identifiers (“UID”) reaction (“VIPUR”) microscopy methods to record the cellular co-localization and / or spatial distributions of arbitrary nucleic acid sequences, or other biomolecules tagged with nucleic sequences. The method involves one or both of two DNA sequence-components such as an α-UID, which may identify the targeted sequences-of-interest themselves and / or spatial beacons relative to which their distances are measured, and a −β-UID, which labels α-UID association events.

The invention provides unique index sequences with a length of 7bp. The index sequences can be respectively imported into a DNA(deoxyribonucleic acid) index library through adapter link and PCR (polymerase chain reaction). The invention provides a method for building the DNA index library by using the index sequences based on a solexa sequencing platform of the current illumina company, and the method is applied to solexa DNA sequencing and has the effects on improving the preparation efficiency of the DNA index library, increasing the sequencing throughput of the DNA samples and lowering thesolexa sequencing cost of a single sample.

The invention is directed to methods for increasing the sensitivity of high throughput sequencing, particularly for distinguishing true rare mutations from amplification, sequencing and other sample processing errors that occur in sequencing techniques. In one aspect, methods of the invention includes steps of (a) preparing templates from nucleic acids in a sample; (b) labeling by sampling the templates to form tag-template conjugates, wherein substantially every template of a tag-template conjugate has a unique sequence tag; (c) linearly amplifying the tag-template conjugates; (d) generating a plurality of sequence reads from the linearly amplified tag-template conjugates; and (e) determining a nucleotide sequence of each of the nucleic acids based on the frequencies, or numbers, of each type of nucleotide at each nucleotide position of each plurality of sequence reads having identical sequence tags.

The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant.

The invention provides a preparation method of a non-transgenic mutant based on a CRISPR-Cas9 technology. Specifically, the preparation method comprises a construction method and a screening method. The construction method is characterized in that CRISPR-Cas9 and sgRNA are preassembled and are located at T-DNA of agrobacterium tumefaciens; site-directed change of a target gene of a target plant can be realized by infection of the target plant by the agrobacterium tumefaciens and coculture without integrating the sequences of the CRISPR-Cas9 and the sgRNA into a genome of the target plant, so that an obtained site-directed mutant material of the target gene does not need the processes of sexual reproduction, segregation posterity, population screening and the like or does not contain any exogenous gene sequence. The obtained regeneration seedlings are screened by a high-throughput sequencing and high-resolution melting curve technology provided by the invention; mutant plants of which target genes are mutated can be obtained by identifying the regeneration seedlings efficiently and quickly at the current generation of transgene, even if low-proportion mutants of which the proportionis 1 / 100 of a mixed population can be screened. The screening method provided by the invention still can ensure excellent accuracy and sensitivity.

The invention discloses a lung cancer somatic mutation detection and analysis method based on a high-throughput sequencing technique. The method comprises the steps of (1) controlling quality; (2) comparing sequences; (3) detecting mutations; (4) annotating the mutations; (5) reporting the results. Compared with the prior art, the method of the invention has the advantages that the detection results are reliable; the detection content is diversified; the detection method is flexible; the data results are visualized.

The invention provides a construction method of a high-flux sequencing library and a reagent kit for library construction. The reagent kit comprises one or more of the following components: a high-flux sequencing Y-shaped joint, a universal primer for single-end linear PCR amplification, a biotin labeling specific primer for single-end linear multiplex PCR amplification, forward and backward library amplification primers, a UDG enzyme and the like. The invention relates to a method for constructing a targeting dimolecular identifier (UMI (unique molecular identifier) and chain unique molecularidentifier) high-flux sequencing library based on the reagent kit. According to the method, double error correcting mechanisms of a random UMI and a chain unique molecular identifier having sequencepolymorphism in a targeting sequencing system based on multiplex PCR amplification are realized, and disadvantages of most of conventional multiplex PCR amplification targeting sequencing systems areavoided, so that all false positives and false negatives in mutation detection are avoided, and high-sensitivity high-accuracy high-depth detection can be performed on low-frequency nucleic acid mutation in samples.

The invention discloses a construction method of a single cell transcriptome sequencing library and application of the construction method. The construction method includes the following steps of preparing a cDNA sample from a single cell and conducting fragmentized library construction on the cDNA sample to obtain the transcriptome sequencing library of the single cell, wherein fragmentation is conducted on the cDNA sample with a physical breaking method in the step of constructing the fragmentized library, and the step for purifying the fragmentized cDNA sample is not needed. According to the method, fragmentation is conducted on the sample of the single cell with the physical breaking method, and therefore fragments obtained through breaking are small and relatively uniform, and the peak width of the constructed single cell transcriptome sequencing library is concentrated; the purification step is not needed for the fragmentized sample, sample loss is reduced, construction of the single cell transcriptome sequencing library of the micro-sample can be achieved, stability of output of data volume can be improved, and therefore the reliability of large-scale and high-throughput sequencing of the single cell transcriptome sequencing library is improved.

The invention provides a primer set for simultaneously detecting mutation of a plurality of regions of two or more exons of one or more cancer drive genes in a sample on the basis of multiplex PCR (polymerase chain reaction) and high-flux sequencing techniques, a kit comprising the primer set, and a method for amplifying the cancer drive gene or detecting the cancer drive gene by using the primer set and / or kit. The mutation detection result can be used for instructing cancer clinic medication, auxiliary diagnosis or prognosis judgment on certain cancers.

The embodiment of the invention discloses a universal primer mixture for animal mitochondria genome amplification as well as a design and amplification method thereof, and a kit comprising the universal primer mixture. By utilizing the primer mixture or the kit and the animal mitochondria genome amplified method and combining the novel high throughput sequencing technique, the animal mitochondria genome information can be efficiently obtained in low cost.

The invention provides a method for analyzing copy number variation in a genome of a testee. According to the method, mathematical manipulation is creatively performed on variables extracted from sequencing data, new two-dimensional variables, namely a sequencing depth ratio (SDR) and alternate allele frequency (AAF) or alternate allelic haploid frequency (AHF) are derived, the signal / noise ratio is further increased, detection sensitivity and precision are improved, and information contained in the high-throughput DNA sequencing data is utilized more fully. Besides, the method is used for processing free DNA in a body fluid sample of the testee, wherein when a CNV feature signal of a certain locus of the genome is extracted from the sequencing data, the information close to the locus is introduced, so that signal strength is greatly improved, and the copy number variation in the free DNA in urine or serum can be effectively detected. The invention furthermore provides a system for implementing the method.

The invention discloses the application of LncRNA-GAS5 in preparing a glaucoma diagnosis reagent and a glaucoma lesion diagnosis reagent kit. Through high-throughput sequencing and quantitative PCR validation, it is found that the LncRNA-GAS5 has a significant correlation with the occurrence of glaucoma. The LncRNA-GAS5 can be used for screening clinical glaucoma patients and providing a theoretical basis for early intervention in glaucoma.

The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids anchor copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extension. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.

The invention discloses an establishing method of a circular RNA high-throughput sequencing library and a kit thereof. The establishing method sequentially comprises the following steps: (S1) extracting total RNA from a sample; (S2) removing DNA in the sample; (S3) detecting and evaluating the quality of the total RNA in the sample, and determining that the RNA quality meets a requirement; (S4) removing rRNA; (S5) removing linear RNA; (S6) constructing the circular RNA library for high-throughput sequencing. The establishing method of the circular RNA high-throughput sequencing library, provided by the invention, is high in efficiency, stable, low in residual ratio of the rRNA, high in circular RNA detection efficiency, good in data reproducibility, and high in sequencing result verifying success rate, and is especially applicable to an FFPE tissue and other samples with poor RNA quality.

Methods and compositions are provided related to the amplification of target polynucleotide sequences as well as total RNA and total DNA amplification. In some embodiments, the methods and compositions also allow for the immobilization and capture of target polynucleotides with defined 3′ and or 5′ sequences to solid surfaces. The polynucleotides attached to the solid surfaces can be amplified or eluted for downstream processing. In some cases, nucleotides attached to solid surfaces can be used for high throughput sequencing of nucleotide sequences related to target DNA or target RNA.

The invention provides a method for carrying out large-scale gene typing based on an n SLAF-seq (Specific-Locus Amplified Fragment Sequencing) technology. Complexity of the genome is reduced by utilizing the SLAF-seq technology, and genetic typing is carried out on large-scale products. High-throughput sequencing is carried out on the genome, marker-developing, genetic map drawing and whole genome association analyzing are carried out on the samples by utilizing the technology. Compared with the conventional method, the large-scale genetic typing method disclosed by the invention has the advantages that the throughput is greatly improved, and the cost is greatly reduced. The method is mainly applied to marker-developing, genetic map drawing and whole genome association analyzing.