341results about "Nucleotide libraries" patented technology

The invention discloses a 5 'UTR library, a recombinant expression vector and a genetically engineered bacterium for improving the yield of folamin in pathogenic bacterium Badei and application of the 5' UTR library and the genetically engineered bacterium, and belongs to the technical field of microbial genetic engineering. The method comprises the following steps: designing an SD region based on a 16S rRNA (ribosomal Ribonucleic Acid) 3'end complementary sequence of a Buddei pathogenic bacterium XBD101 serving as an original strain, regulating and controlling the number of bases between the SD sequence and an initiation codon AUG and optimizing an UTR secondary structure to construct a library containing 14 UTR sequences, and replacing three sequences N4A, N7A and N18A with the strongest translation ability in the library to the UTR region of a folamin synthesis key gene fclC, so as to obtain the folamin peptide. And finally, the capacity upgrading of the folamin chassis strain is realized, and an important support is provided for the industrial production of agricultural antibiotics.

The present disclosure provides methods and systems for screening or detecting a colorectal cancer or following colorectal disease progression that may be applied to cell-free nucleic acids such as cell-free DNA. The method may use detection of methylation signals within a single sequencing read in identified genomic regions as input features to train a machine learning model and generate a classifier useful for stratifying populations of individuals. The method may comprise extracting DNA from a cell-free sample obtained from a subject, converting the DNA for methylation sequencing, generating sequencing reads, and detecting colon proliferative cell disorder-associated signals in the sequencing information and training a machine learning model to provide a discriminator capable of distinguishing groups in a subject population such as healthy, cancer or distinguishing disease subtype or stage. The method may be used for, e.g., predicting, prognosticating, and / or monitoring response to treatment, tumor load, relapse, or colorectal cancer development.

The present application provides detection and prognosis of infectious diseases. In particular, the present application provides fragment length profiles of nucleic acid libraries, methods of generating fragment length profiles of nucleic acid libraries, and methods of using the fragment length profiles for diagnosis and / or prognosis. The present application further provides methods, compositions, and kits for determining the stage or site of infection in a subject.

The invention discloses a preparation method of a space chip, the space chip and application of the space chip, the preparation method comprises the following steps: hybridizing: connecting a single-stranded nucleic acid molecule to the surface of a solid-phase substrate, the single-stranded nucleic acid molecule comprises a first fixed sequence, a space bar code sequence, a sequencing primer binding sequence and a second fixed sequence, the surface of the solid-phase substrate of the chip substrate is connected with a first probe, and the first probe comprises a first fixed sequence complementary sequence and a second fixed sequence complementary sequence; carrying out ring closing to enable the single-stranded nucleic acid molecules to form annular nucleic acid molecules; carrying out rolling circle amplification; sequencing to obtain sequence information of the space bar code sequence; synthesizing single-stranded nucleic acid molecules by taking the rolling circle amplification product as a template to obtain a single-stranded nucleic acid molecule library; fixing and clustering: fixing the single-stranded nucleic acid molecule library on the surface of a solid-phase substrate to form a single-stranded nucleic acid molecule cluster. According to the invention, the chip with the nucleic acid probe carrying spatial position coordinate information can be prepared.

Provided herein are compositions and methods of modulating myeloid cell-mediated killing of cancer cells and modulating the activity of myeloid cell immune checkpoint inhibitors. Also provided herein are methods of screening for modulators of myeloid cell-mediated killing of cancer cells and modulators of myeloid cell immune checkpoint inhibitors.

The present disclosure belongs to the field of molecular biology, particularly to the technical field of gene analysis and detection, and specifically relates to a method for preparing a DNA library and a method for detecting a retroviral integration site. Specifically, the method for preparing the DNA library comprises the following steps: 1) fragmenting a genomic DNA from a retrovirus-infected cell to obtain DNA fragments; 2) subjecting the DNA fragments to end-repair, A-tailing, and ligation with an adapter to obtain a ligation product, wherein the adapter is an asymmetric double-strand adapter comprising a long-strand sequence and a short-strand sequence, wherein the long-strand sequence sequentially comprises, from a 5' end to a 3' end, a fixed sequence, a random UMI sequence, and an amplification primer binding sequence, and the short-strand sequence comprises a sequence complementary to the fixed sequence; and other steps. The detection method of the present disclosure has extremely high sensitivity, thus having good application potential.

The application relates to the technical field of molecular biology, and discloses a cold-tolerance identification method of Pennisetum based on a 65-core molecular marker set, a primer group and a gene chip and application thereof. The application collects core germplasm resources of the Pennisetum through a system, and constructs a GWAS population by using multi-environment (different altitudes) conditions, so that a wide genetic background and phenotype variation are fully covered, and a material foundation for genetic analysis of cold tolerance is laid. In the aspect of cold-tolerance phenotype identification, the application innovatively takes the chlorophyll content of leaves and the percentage of green leaves after natural low-temperature stress in autumn and winter fields as the cold-tolerance evaluation indexes, judges individuals with more than 40 excellent allelic variations as high-cold-tolerance varieties, and establishes a rapid and non-destructive phenotype screening method which can be implemented at the seedling stage.

The present disclosure provides methods and kits for classifying biological samples into clinically relevant categories, the methods comprising the steps of: (i) determining, in a sample containing a plurality of cell-free DNA (cfDNA) fragments, sequence coordinates of the start and / or stop of at least 100,000 cfDNA fragments by alignment to a reference sequence; (ii) determining in the reference sequence all nucleic acid motifs composed of trinucleotides, tetranucleotides, and pentanucleotides within a) a range of 1-5 base pairs inside but adjacent to each start and / or stop sequence coordinate determined in (i) and / or b) a range of 1-5 base pairs outside but adjacent to each start and / or stop sequence coordinate determined in (i); and (iii) determining in a) a range of 1-5 base pairs inside but adjacent to each start and / or stop sequence coordinate determined in (i) for the plurality of cfDNA fragments in the sample, all nucleic acid motifs composed of trinucleotides, tetranucleotides, and pentanucleotides. (iv) calculating a ratio of each of the frequencies determined in (iii) a) and b) to a corresponding reference frequency; (v) calculating a diagnostic score separately for each ratio determined in step (iv), said score being a respective weighted sum of all respective frequency ratios of step (iv); (vi) calculating a combined diagnostic score from at least two or more of the diagnostic scores determined in (v), said score being a weighted sum of the two or more diagnostic scores determined in (v); and (vii) determining a classification of the sample by comparing the combined diagnostic score with the reference score, GENETICS PUBLIC COMPANY LIMITED CH Kilger Anwaltspartnerschaft mbBCyprus Fasanenstrase 29Our Ref.:B281-0029WO1 10719 Berlin, a sample is classified as containing tumor cfDNA if the combined diagnostic score value is higher than the mean of the reference scores by at least one standard deviation of the reference score, the reference score being calculated from one or more reference values.

The present invention provides a method for simultaneously amplifying multiple target nucleic acid regions in a single reaction volume, and a method for selecting a primer library to be used in such amplification. Furthermore, the present invention provides a primer library having desired properties, such as minimal formation of amplification primer dimers or other non-target amplification products. [Solution] For example, a method for amplifying a target gene locus in a nucleic acid sample is provided, comprising the steps of (a) contacting the nucleic acid sample with a test primer library that simultaneously hybridizes to at least 1,000 different target gene loci to generate a reaction mixture, and (b) subjecting the reaction mixture to primer extension reaction conditions to generate an amplification product containing a target amplification product.

The invention provides a cold-region low-temperature-resistant germination rice gene chip and application thereof, the cold-region low-temperature-resistant germination rice gene chip comprises 1016 SNP sites distributed in 12 chromosomes, is derived from large-scale GWAS analysis of 216 cold-region germplasms, and has the characteristics of high polymorphism, low deletion rate and low heterozygosis rate. The preparation method comprises the following steps: extracting DNA (Deoxyribonucleic Acid), sequencing, comparing and screening associated sites, and designing a specific probe based on the associated sites to prepare a liquid phase chip. The chip shows high precision (genotype consistency is greater than or equal to 98%) and high efficiency in application, and is mainly used for rapid screening, whole genome selective breeding and character correlation analysis of germplasm resources of the low-temperature-resistant rice in the cold region. By means of the chip, the breeding cycle can be shortened from traditional 6-8 generations to 3-4 generations, the screening efficiency is improved by 4-5 times compared with traditional phenotype identification, and a powerful molecular tool and a complete solution are provided for accurate breeding of low-temperature-resistant varieties of the cold-region rice.

This application belongs to the field of molecular biology technology, specifically relating to nucleic acid combo products, kits for mycobacterial identification, and their applications. This application provides a nucleic acid combo product for mycobacterial detection, comprising one or more primer pairs with nucleotide sequences as shown in SEQ ID NO.1 to SEQ ID NO.244. This specific primer combination can simultaneously detect multiple mycobacteria and distinguish them down to the subspecies level. Through highly specific primer design, this nucleic acid combo product can achieve accurate identification of common clinical mycobacteria (including complex groups, species, and subspecies levels), with a detection sensitivity of 50-100 CFU / mL, significantly superior to the detection performance of existing technologies. Furthermore, the nucleic acid combo product of this application can not only identify the species of mycobacteria but also simultaneously detect drug resistance gene mutations, providing important evidence for the selection of clinical treatment regimens.

The present invention relates to an in vitro method for detecting somatic mutations in humans, comprising the following steps: (i) providing a human sample, preferably a blood sample from a subject, more preferably a plasma sample, or a serum sample, or a buffy coat sample; (ii) preparing a first nucleic acid sequencing library from nucleic acids present in the sample; (iii) hybridizing one or more TAC oligonucleotides from a first TAC oligonucleotide pool (TAC oligonucleotide-1) into the first nucleic acid library, thereby isolating a first subset of library nucleic acid molecules; (iv) sequencing the first subset of library nucleic acid molecules, comparing the determined sequence with a human reference sequence, thereby creating a first group of putatively useful sequence variants (PISV1); and (v) preparing The process includes (i) to (iv) hybridizing one or more TAC oligonucleotides from a second, smaller TAC oligonucleotide pool containing TAC oligonucleotides (TAC oligonucleotide-2) specific to the first group of nucleic acid molecules of the above beneficial sequence variants into a first library of nucleic acid molecules, thereby isolating a second subset of library nucleic acid molecules; (vi) sequencing the second subset of library nucleic acid molecules and comparing the determined sequences with human reference sequences to create a second group of putative beneficial sequence variants (PISV2); and (vii) analyzing the putative beneficial sequence variants (PISV2) to detect somatic mutations in a sample from the subject. Steps (i) to (iv) are collectively referred to as Step A. Steps (v) to (vii) are collectively referred to as Step B.

The invention relates to generally to the field of oncology. Provided herein is a method for detecting for detecting and classifying nasopharyngeal cancer.

The invention relates to a method for evaluating and positioning nucleic acid pollution of a nucleic acid extraction kit, which comprises the following steps: 1) taking nucleic acid-free water as a negative sample, and performing nucleic acid extraction on the nucleic acid-free water by using the nucleic acid extraction kit according to nucleic acid extraction steps in the kit, the obtained nucleic acid is presumed as the polluted nucleic acid in the nucleic acid extraction kit; 2) amplifying polluted nucleic acid, purifying a PCR product, enriching double-chain cDNA, and determining the concentration of the double-chain cDNA so as to perform quantification, sample mixing and quality control treatment before library construction; (3) carrying out high-throughput deep sequencing by adopting a platform of the Illumina company, and then carrying out bioinformatics analysis to obtain classification information and gene sequences of polluted nucleic acid; and 4) designing a specific primer based on the gene sequence of the polluted nucleic acid, and carrying out pollution evaluation and positioning verification on each component of the nucleic acid extraction kit through qPCR (Quantitative Polymerase Chain Reaction).

The present invention relates to a method for obtaining a nucleic acid library of a sample containing polynucleotides, a. providing a plurality of modified primers to the polynucleotide, wherein the modified primer serves as a starting point for nucleic acid amplification for a polymerase, b. amplifying the polynucleotide using a polymerase, c. obtaining a mixture of fragmented polynucleotides containing the modified primer and non-fragmented polynucleotides by fragmenting the amplified polynucleotide, d. obtaining a mixture of polynucleotides containing the adapter oligonucleotide by ligating a plurality of adapter oligonucleotides to the mixture obtained in step c), wherein the adapter oligonucleotide contains a binding site for an amplification primer, e. providing an amplification primer to the mixture obtained in step d), wherein the amplification primer serves as a starting point for nucleic acid amplification for a polymerase, f. initiating nucleic acid amplification by providing a polymerase comprising a method, wherein the modified primer provided in step a) contains a functional group, wherein · the functional group is a blocking group at the 5'-end of the modified primer that prevents ligation of the adapter oligonucleotide, or · the functional group is at least one nucleotide analog, in which case the nucleotide analog is excised by an endonuclease after step d) to remove the primer binding site provided by the adapter oligonucleotide, thereby preventing binding of the amplification primer provided in step f) and nucleic acid amplification of the fragmented polynucleotide containing the modified primer, characterized in that it is directed to a method.

Provided is an analysis method promptly applicable to a greater number of cancers. This library is composed of multiple probes and / or primers for detecting cancer-related mutation in a gene selected from the group consisting of ARID1A, BRAF, EGFR, FGFR2, FGFR3, HRAS, KRAS, and PIK3CA, or a promotor region thereof, wherein the multiple probes and / or primers include: those for detecting c.5965C>T, c.5548dup, c.3826C>T for ARID1A; those for detecting c.1799T>A for BRAF; those for detecting c.2573T>G, c.2235_2249del, c.2236_2250del for EGFR; those for detecting c.755C>G, c.1650T>A, c.1147T>C for FGFR2; those for detecting c.746C>G, c.1124A>G, c.742C>T for FGFR3; those for detecting c.37G>C, c.182A>G, c.35G>T, c.182A>T, c.181C>A, c.34G>A, c.35G>A for HRAS; those for detecting c.35G>A, c.35G>T, c.38G>A, c34G>T for KRAS; and those for detecting c.3140A>G, c.1633G>A, c.1624G>A for PIK3CA.

The invention relates to the technical field of DNA library establishment and sequencing, and particularly discloses a method for performing full-coverage amplification on a DNA sample, a rapid DNA library establishment method, a sequencing method and application thereof. The amplification method comprises the following steps: carrying out low-temperature denaturation PCR (Polymerase Chain Reaction): contacting a DNA (Deoxyribonucleic Acid) sample with a plurality of groups of pre-amplification primer pairs, carrying out PCR amplification, and overlapping an amplification product of any one group of pre-amplification primer pairs in the plurality of groups of pre-amplification primer pairs and an amplification product of any adjacent group of pre-amplification primer pairs with at least 20 basic groups; the library building method comprises the amplification method. The sequencing method comprises the library building method. According to the sequencing method disclosed by the invention, the sequencing result can be quickly and efficiently obtained with high precision and high sequencing depth.

[Problem] To provide: an adapter for binding to polynucleotide fragments that is used for preparing a genome-wide gRNA library for genome editing systems; a gRNA library that is obtained by using the adapter; and uses of the gRNA library. [Solution] An adapter having a structure described in A). A) A structure having i) to iii). i) A polynucleotide chain having sequences i)-1 to i)-3. i)-1: Sequence corresponding to the forward primer. i)-2: Sequence of the recognition site of a restriction enzyme capable of excising a gRNA spacer sequence from the 5' end of a polynucleotide fragment bound to the adapter. i)-3: Sequence of the recognition site of a restriction enzyme capable of cleaving an adapter having the structure of A) from the polynucleotide fragment. ii) A polynucleotide chain having the sequence complementary to i). iii) A single-stranded polynucleotide chain for formation of a loop connecting the 5' end of i) and the 3' end of ii) of the double strand resulting from the binding of i) and ii).

This invention provides a method and system for detecting the cellular state in biological samples. [Solution] A method for determining cell type or cell state is provided. The method includes: providing, or already providing, a sample containing DNA or RNA, and creating, or providing, or already providing, a methylation profile of the DNA or RNA in the sample.

The invention discloses a broccoli 6K liquid phase breeding chip as well as a special single nucleotide polymorphism variation site and application thereof. The 6K liquid phase breeding chip provided by the invention comprises a probe combination for detecting 5971 single nucleotide polymorphism variation sites in a broccoli genome, and the position information of a probe corresponding to each single nucleotide polymorphism variation site in a broccoli reference genome is shown in a table 3 in the specification. Single nucleotide polymorphism variation sites involved in the liquid phase breeding chip provided by the invention have the advantages of high polymorphism, good repeatability, stable and reliable marking, convenience in statistics and the like, and a DNA fingerprint database for identifying the authenticity of broccoli varieties can be established on the basis of the liquid phase breeding chip. The method can be used for the authenticity of broccoli varieties, the early breeding and identification of the broccoli varieties and the identification of broccoli seed resources, provides technical support for the enrichment of broccoli germplasm resources, the breeding of new varieties and the protection of the new varieties, and has a wide application prospect.

We provide a system for screening compounds. [Solution] This application provides beads with covalently attached compounds and covalently attached DNA barcodes, as well as methods for using such beads. The beads have many substantially identical copies of compounds and many substantially identical copies of DNA barcodes. The compounds consist of one or more chemical monomers, and the DNA barcodes take the form of barcode modules, each module enabling the identification of corresponding and corresponding chemical monomers. The nucleic acid barcodes may have a chain-like or orthogonal structure. Methods for sequencing bead-bound nucleic acid barcodes, methods for cleaving compounds from beads, and methods for evaluating the biological activity of released compounds are provided.

Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.

The invention provides a marker for evaluating biological age, a probe composition and application thereof. The marker is an SCGN gene and / or a TRIM59 gene. According to the present invention, with the application of the marker, the methylation state of the genes can be sensitively and specifically detected, and the marker is used for constructing the age prediction model based on DNA methylation so as to detect the biological age.

A method comprising receiving a transaction request to print a genetic sequence, the transaction request including an account and a key, a state of the account managed by a blockchain where a plurality of copies of the blockchain include a state of the account; retrieving a stored key associated with the account; authenticating the transaction request based on the stored key and the transaction request key; determining a state of the account in a first copy of the blockchain is the same as in at least a second copy of the blockchain; validating the transaction request based on the determining a state of the account in a first copy of the plurality of copies of the blockchain is the same as in at least a second copy of the plurality of copies of the blockchain; and authorizing the transaction request based on the authentication and validation of the transaction request.

The invention relates to new methods for synthesising polynucleotide molecules according to a predefined nucleotide sequence. The invention also relates to methods for the assembly of synthetic polynucleotides following synthesis. The invention further relates to supports and systems for synthesising a double-stranded polynucleotide having a predefined sequence.

A method and composition for preparing a DNA library for replicating a target nucleic acid sequence are provided. A target DNA template containing the target sequence is circularized via a terminal adapter to form a circular construct, which is extended bidirectionally by polymerase-mediated elongation initiated at a nick site on the terminal adapter. Following polymerase-mediated elongation, a diploid DNA template is formed containing two copies of the target DNA template (and thus two copies of the target sequence). Each strand of the diploid DNA template contains a parent polynucleotide chain ligated to a newly synthesized daughter strand copy of the parent polynucleotide chain. Predetermined sequences, such as primer sequences, unique molecular identifiers, and sequence indices, can be included in the diploid DNA template. Sequencing of the diploid DNA template can reveal genetic / epigenetic information related to the target sequence. A method for constructing asymmetric and multiploid DNA template constructs is also provided.

The invention discloses a pig whole genome breeding functional site gene chip and application thereof. The chip contains a probe for detecting 42476 SNP (Single Nucleotide Polymorphism) sites, and the 42476 SNP sites are functional sites related to growth, reproduction and slaughter traits of pigs; the 42KSNP sequencing chip designed by the invention contains a large number of functional sites related to the growth, reproduction and slaughter traits of pigs, so that the breeding accuracy of the growth, reproduction and slaughter traits can be effectively improved in the breeding process, the genetic progress is remarkably improved, and the breeding cycle is shortened.

A double-stranded template nucleic acid molecule may include an adaptor that includes a mismatched moiety. The mismatch moiety may include a first mismatch sequence in a first chain and a second mismatch sequence in a second chain that is not complementary to the first mismatch sequence. When the double-stranded template nucleic acid molecule is amplified to produce a cluster of amplified strands and the cluster is sequenced to produce a sequenced read, the double-stranded template nucleic acid molecule is amplified to produce the sequenced read. A portion of the sequencing read corresponding to the mismatch portion can be analyzed to determine whether the cluster of amplified strands originates only from one strand or both strands of the double-stranded template nucleic acid molecule. A sequencing signal between two chain derivatives in the cluster, a base recognition, or an inconsistency at one or more loci in a sequencing read can be used to correct for sequencing errors and improve sequencing accuracy.

The present application provides an anti-cTnI antibody, which comprises a heavy chain variable region and / or a light chain variable region; the aforementioned heavy chain variable region comprises an amino acid sequence as shown in SEQ ID NO: 1 or a variant thereof, the variant of the aforementioned SEQ ID NO: 1 comprises a mutation in at least one of positions 28, 54 and 60, compared with the amino acid sequence shown in SEQ ID NO: 1; the aforementioned light chain variable region comprises an amino acid sequence as shown in SEQ ID NO: 2 or a variant thereof, the variant of the aforementioned SEQ ID NO: 2 comprises a mutation in at least one of positions 27 and 89, compared with the amino acid sequence shown in SEQ ID NO: 2. The antibody of the present application can effectively bind to cTnI and can be used for qualitative or quantitative detection of cTnI.

The present disclosure provides methods and systems for screening or detecting colorectal cancer or subsequent colorectal disease progression, which can be applied to cell-free nucleic acids, such as cell-free DNA. The methods can train a machine learning model using detection of methylation signals within single sequencing reads in identified genomic regions as input features, and generate a classifier suitable for stratifying a population of individuals. The methods can include extracting DNA from a cell-free sample obtained from a subject, transforming the DNA for methylation sequencing, generating sequencing reads, and detecting colon proliferative cell disorder related signals in the sequencing information, and training a machine learning model to provide a discriminator capable of distinguishing between groups such as healthy, cancer, etc. in a population of subjects, or distinguishing between disease subtypes or stages. The methods can be used, for example, to predict, prognosticate, and / or monitor response to treatment, tumor burden, recurrence, or progression of colorectal cancer.