1119 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.

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.

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 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 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 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 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.

The invention provides a method for detecting BCR and TCR immune repertoire in blood plasma cfDNA. The method includes: blood plasma cfDNA extraction, BCR H chain overall length multiple PCR amplification, TCR beta chain CDR3 multiple PCR amplification, PCR amplification after the products of the two previous amplifications are mixed in an equal-volume manner, high-throughput sequencing, and immune repertoire precise information analysis. The primers of the three amplifications are respectively shown in SEQ ID No. 1-28, SEQ ID No. 29-77 and SEQ ID No. 78-79. The invention further provides a kit, which contains the primers, for detecting the BCR and TCR in the blood plasma cfDNA. By the method and the kit which are promising in application prospect in the field of non-invasive detection, the BCR and TCR in the blood plasma cfDNA can be detected at the same time, precise information analysis and precise quantification of immune repertoire subcloning are achieved.

The invention relates to an STR (short tandem repeat) sequence high-throughput detection method with base selective controllable extension and a detection reagent thereof. The basic principle of an STR sequence detection method and a high-throughput DNA (deoxyribonucleic acid) sequencing technology are combined, and the method which runs on a high-throughput sequencing platform for detecting massive STR sequence samples and the corresponding detection reagent are provided. The method comprises the following steps of: directly or indirectly fixing STR sequences of the samples to be detected on a detection chip according to a library preparation method corresponding to a sequencing system, adding the appropriate detection reagent according to the detection flow process, controlling reaction conditions, adopting the base selective controllable extension technical scheme to detect fluorescence intensity signals emitted by all reaction sites where the samples are located, and finally getting the detection results of the massive samples by analyzing fluorescence signal photos of all the detection sites during the whole detection process. The greatest advantage of the method disclosed by the invention is that the number of the samples which can be detected every time is greatly increased, and detection cost and time consumption can be further greatly reduced.

The invention provides a primer set, a kit and a detection reaction system for detecting PKD1 gene mutation through the long fragment PCR and high-throughput sequencing technology, a non-diagnosis-purpose method for external PKD1 gene mutation detection, a non-diagnosis-purpose method for external PKD1 gene analysis and a method for detecting new mutation sites on the PKD1 gene. According to the method, the primer set is used for carrying out long fragment PCR amplification on the PKD1 gene of a sample, and detecting or analyzing is carried out through high-throughput sequencing. The autosomal dominant genetic polycystic nephrosis (adult polycystic nephrosis) can be diagnosed through the assistance of a detection result, previous unknown new mutation on a plurality of PKD1 real genes can be obtained and supplied to doctors or researchers so that the relevance between the mutation and the adult polycystic nephrosis can be studied.

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.