47 results about "Pseudogene" patented technology

The invention belongs to the technical field of synthetic biology, and particularly relates to recombinant escherichia coli for efficiently producing O-acetyl-L-homoserine as well as a construction method and application of the recombinant escherichia coli. According to the invention, CRISPR-Cas9 gene editing is combined with metabolic modification, so as to precisely integrate OAH biosynthesis key nodes: introducing and overexpressing a mutant metX gene at a genome pseudogene site to enhance the expression of homoserine acetyltransferase, knocking out byproducts such as poxB and mgsA to synthesize genes, and carrying out high-yield synthesis of OAH. Corynebacterium glutamicum thrA (anti-feedback inhibition), aspB and bacillus subtilis acsA-acuA genes (construction of an acetic acid switch) are introduced, gene expression of gltA, tpiA and the like is optimized to increase supply of precursors such as acetyl CoA and the like, and finally a stable strain without plasmids, antibiotics and inducers is obtained. The production cost is effectively reduced, and the method has the advantage of high genetic stability and shows a good application prospect in OAH industrial production.

The invention belongs to the technical field of genes, and particularly relates to an amplification primer group of a renal cyst disease gene PKD1, a mutation detection method and application, the amplification primer group comprises four pairs of primers for specifically amplifying first to 34 exons of the PKD1 gene; the mutation detection method comprises the following steps: acquiring genome DNA (Deoxyribose Nucleic Acid); carrying out ultra-long fragment PCR amplification on the genome DNA through the primers, carrying out electrophoresis detection, and purifying a target fragment; mixing the purified amplification product with genome DNA in proportion, constructing a sequencing library, and performing high-throughput sequencing through target area capture; and analyzing sequencing data, and screening pathogenic PKD1 gene mutation. Compared with the prior art, the PKD1 ultra-long fragment PCR amplification primer and the renal cyst disease gene PKD1 mutation detection method have the advantages that true and false genes of PKD1 can be distinguished, the diagnosis accuracy is greatly improved, the operation process is simplified, the timeliness is improved, and the detection flux is improved.

The current disclosure provides for methods and compositions for classifying subjects having different biological states. The disclosure describes a method comprising: filtering sequence data obtained from a sample from a subject based on long non-coding RNA (lncRNA) and / or pseudogene RNA (pgRNA), and / or the reference genome; determining a biological state classification of the subject by providing the filtered sequence data to one or more machine learning classifiers as input, wherein the one or more machine learning classifiers is trained to output biological state classifications based on filtered sequence data of a training data set.

Provided are a theanine-producing strain and use thereof in tea fermentation production. A corynebacterium glutamicum is proposed, which includes an alanine decarboxylase CsAlaDC mutant. The theanine-producing strain is obtained by taking the corynebacterium glutamicum as a starting strain, knocking out in sequence an α-ketoglutarate dehydrogenase E1 subunit gene odhA, a glutamate external transporter gene Ncg11221 and a lactate dehydrogenase gene ldh; and / or expressesing a citrate synthase gene gltA, a pyruvate kinase gene pyk and a glutamate dehydrogenase gene gdh; and / or overexpressing an alanine dehydrogenase alaA and integrating a γ-glutamine synthetase GMAS into a cg1960 pseudogene locus of the corynebacterium glutamicum.

The invention is applicable to the technical field of biotechnology, and particularly relates to a primer composition for amplifying a coding sequence of a human B cell receptor heavy chain CDR3 and application of the primer composition, and two primer groups, namely a first primer group and a second primer group, are designed. The two primers are respectively used as an upstream primer and a downstream primer, and comprise at least one human IGH CDR3 upstream primer and at least one human IGH CDR3 downstream primer. The primers can be respectively combined with nucleic acid of human B cells, and a basis for researching a CDR3 region of a B cell receptor is provided. The first primer group and the second primer group are combined with the nucleic acid of the human B cell, so that the coding sequence of the heavy chain of the human B cell receptor is effectively enriched, part of pseudogenes are contained, the amplification efficiency of the heavy chain CDR3 library of the human B cell receptor can be improved, and the deep research on immune response of the human B cell is promoted.

The present application provides a method and system for accurately distinguishing between micro-partitions configured with a target gene and micro-partitions configured with a pseudo gene, and counting the target gene with high precision in digital PCR using melting curve analysis. The method includes: a step of configuring DNA solution in multiple partitions; a step of performing nucleic acid amplification reaction; a step of changing the temperature of each partition and measuring the fluorescence intensity; a step of calculating the melting temperature of the double-stranded DNA for each partition; a step of counting the number of partitions for each type of DNA; a step of outputting the number of counted partitions for each type of DNA; and a step of distinguishing the first gene and the pseudo gene based on the melting temperature and the number of counted partitions.

The invention relates to a gene mutation identification method and system under coexistence of genes and pseudogenes. The gene mutation recognition method under the coexistence of the gene and the pseudogene in the embodiment of the invention comprises the following steps: acquiring sequencing data of a to-be-detected sample, and acquiring a specific nucleotide site of the pseudogene under the condition that the pseudogene exists in a target gene; variation information obtained based on sequencing data recognition is obtained; according to the mutation information and the specific nucleotide sites, identifying error comparison to identify mutation information of the target gene in the to-be-detected sample. According to the embodiment of the invention, a specific primer does not need to be designed and an amplification reaction does not need to be carried out, so that the gene mutation detection efficiency is improved, interference of pseudogenes can be eliminated, and the stability and accuracy of a detection result are improved.

The invention discloses a nucleic acid product, a kit and a device for detecting gene variation and application. The nucleic acid product comprises one or more primer groups, and related information of the primer groups is shown in the application. The nucleic acid product, the kit and the device provided by the invention at least can effectively solve the interference of pseudogenes (high homologous sequences) on a target detection result, so that the detection becomes easier; the different primer groups can share one reaction system and amplification conditions without additionally adding a PCR (Polymerase Chain Reaction) enhancer, so that the experimental operation is simple and convenient; the target amplification product can be used for first-generation sequencing, second-generation sequencing and third-generation sequencing; the method can be simultaneously applied to multiple scenes according to requirements, and target amplicon three-generation sequencing realizes distinguishing between cis-mutation and trans-mutation and whether the mutation has a linkage effect or not.

Provided herein is a transgenic chicken comprising a genome having an endogenous immunoglobulin heavy chain gene in which the IgY CH1 coding sequence is functionally deleted. In certain embodiments, in B cells of the chicken the endogenous immunoglobulin heavy chain gene comprises: (a) a functional immunoglobulin heavy chain gene comprising, in operable linkage, a nucleic acid encoding an antibody heavy chain variable domain and a constant region coding sequence in which the IgY CH1 coding sequence is functionally deleted; and (b) a plurality of pseudogenes that are operably linked to said functional immunoglobulin heavy chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding the variable domain of (a), wherein the pseudogenes are upstream of the nucleic acid encoding an antibody heavy chain variable domain of (a).

This disclosure provides, among other things, a transgenic animal that uses gene conversion for antibody diversification, comprising B cells in which the endogenous immunoglobulin heavy chain locus comprises: (a) a functional immunoglobulin heavy chain gene comprising a nucleic acid encoding an autonomous heavy chain (AHC) variable domain; and (b) a plurality of pseudogenes that are operably linked to said functional immunoglobulin heavy chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding the AHC variable domain of (a), wherein the pseudogenes are upstream or downstream of the functional immunoglobulin heavy chain gene.

This disclosure provides, among other things, a transgenic chicken. In some embodiments, the transgenic chicken comprises B cells in which the endogenous immunoglobulin heavy chain locus comprises: (a) a functional immunoglobulin heavy chain gene comprising a nucleic acid encoding a heavy chain variable domain in which the CDR3 is in the range of 30-60 amino acids in length and comprises at least 2 cysteine residues; and (b) a plurality of pseudogenes that are operably linked to said functional immunoglobulin heavy chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding the heavy chain variable domain of (a), wherein the pseudogenes are upstream or downstream of the functional immunoglobulin heavy chain gene.

This disclosure provides, among other things, strategies for minimizing antibody diversification in a transgenic animal that uses gene conversion for antibody diversification. In some embodiments, the animal may comprise a genome comprising an endogenous immunoglobulin light chain locus comprising: (a) a functional immunoglobulin light chain gene comprising a nucleic acid encoding a light chain variable region; and (b) a plurality of pseudogenes that are operably linked to the functional immunoglobulin light chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding a light chain variable region, wherein the pseudogenes are upstream or downstream of the functional immunoglobulin light chain gene and encode the same amino acid sequence as the light chain variable region of the functional immunoglobulin light chain gene of (a). In other embodiments, the locus may have a tandem array of coding sequences for the light chain.

The current disclosure provides for methods and compositions for classifying subjects having different biological states. The disclosure describes a method comprising: filtering sequence data obtained from a sample from a subject based on long non-coding RNA (lncRNA) and / or pseudogene RNA (pgRNA), and / or the reference genome; determining a biological state classification of the subject by providing the filtered sequence data to one or more machine learning classifiers as input, wherein the one or more machine learning classifiers is trained to output biological state classifications based on filtered sequence data of a training data set.

Described herein is a method for detecting pseudogenes, including processed pseudogenes, further including detection for measuring retrotrasposon element activity. Such measurements are useful in screening and detecting cancer in subjects, including predicting the likelihood or cancer, recurrence, treatment responsiveness and selection.

This disclosure provides, among other things, a transgenic chicken. In some embodiments, the transgenic chicken comprises B cells in which the endogenous immunoglobulin heavy chain locus comprises: (a) a functional immunoglobulin heavy chain gene comprising a nucleic acid encoding a heavy chain variable domain in which the CDR3 is in the range of 30-60 amino acids in length and comprises at least 2 cysteine residues; and (b) a plurality of pseudogenes that are operably linked to said functional immunoglobulin heavy chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding the heavy chain variable domain of (a), wherein the pseudogenes are upstream or downstream of the functional immunoglobulin heavy chain gene.

The invention relates to a method for producing deoxyuridine triphosphate from a recombinant strain, which comprises the following steps: step 1, carrying out directional modification on an escherichia coli genome by utilizing a CRISPR / Cas9 mediated gene editing method, and the directional modification comprises the following contents: a, knocking out a nucleotidase gene (yfbR / yfdR / ushA / umpH / umpG / yjjG), and blocking a path for degrading dUMP into dU; b, integrating an endogenous uridine kinase gene tdk of escherichia coli at the pseudogene locus mbhA, and strengthening a phosphorylation path of dU; c, an endogenous dUMP kinase gene tmk of escherichia coli is integrated at the pseudogene locus yeeP, and a phosphorylation path of dUMP is strengthened. The invention provides a method for producing deoxyuridine triphosphate from a recombinant strain, the conversion rate of the method reaches 80-90%, and the purity of deoxyuridine triphosphate can reach more than 99% after purification by ion exchange chromatography.

The present invention relates to a modified live attenuated Salmonella strain comprising at least one chromosomal integrated synthetic polynucleotide sequence inserted in a predetermined pseudogenomic position, said sequence comprising at least one defined recombination site for introducing a heterologous polynucleotide sequence encoding a polypeptide, wherein the chromosome integration synthetic polynucleotide sequence is located within at least one genomic site, the genomic site being defined by any one of SEQ ID NO: 1-30 or a sequence having at least 70% identity with any one of SEQ ID NO: 1-30. The invention also relates to vaccine compositions comprising the modified strains and various uses and methods thereof.

The present invention provides, among other things, a transgenic chicken. In some embodiments, the transgenic chicken comprises a B cell having an endogenous immunoglobulin heavy chain locus comprising: (a) a functional immunoglobulin heavy chain gene comprising a nucleic acid encoding a heavy chain variable domain having a length of CDR3 in the range of 30 to 60 amino acids and containing at least two cysteine ​​residues; and (b) a plurality of pseudogenes operably linked to the functional immunoglobulin heavy chain gene and, by gene conversion, providing a nucleotide sequence to the nucleic acid encoding the heavy chain variable domain of (a), wherein the pseudogenes are located upstream or downstream of the functional immunoglobulin heavy chain gene.

Provided herein are methods and associated compositions, kits, systems, devices and instruments useful for genetic analysis where there is / are a sequence(s) similar to the gene of interest in a sample. In the methods, a combined copy number for related genes (e.g., a gene of interest and its pseudogene) can be determined via an assay. In addition, relative amounts of the related genes, i.e., a ratio of the related genes can be determined via the assay. Using the data of the combined copy number and the ratio of the related genes, the genotype of the gene of interest (as well as its pseudogene(s), if desired) can be determined with high accuracy.

The invention discloses a PKD1 and PKD2 amplification primer group, a kit and a gene mutation type detection method, by optimizing primer design sites, interference of pseudogenes in an amplification process can be avoided, a PKD1 gene and a PKD2 gene can be specifically amplified in a single tube, a long fragment is combined with a nanopore sequencing technology, the defect of structural variation detection by NGS sequencing can be overcome, and the detection accuracy is improved. The detection time and cost can be greatly reduced, and polycystic kidney disease detection can be effectively assisted.

The application provides a STRC gene copy number variation detection method based on whole genome sequencing. The STRC gene and the STRCP1 gene are subjected to sequence alignment to find each difference site of the STRC gene and the STRCP1 gene. For each difference site, the sequence of the corresponding STRC position and STRCP1 position in the genome is read from a variation detection file. The total copy number of the true gene and the false gene is calculated by taking the reference site in the genome as a reference. The STRC gene copy proportion on each difference site is calculated. The STRC gene copy number on each difference site is calculated according to the total copy number and the STRC gene copy proportion. The STRC gene copy number on each exon is determined according to the STRC gene copy number on each difference site. The method can realize the detection of the STRC copy number, simplifies the detection process, improves the detection throughput and reduces the cost.

To provide a method for detecting genetic variation in homologous regions of the genome.SOLUTION: The method combines experimental and analytical approaches to resolve the structure of a genomic region in the genome of a subject whose sequence is highly homologous to one or more other regions of the genome. For example, the genomic region may be a gene, and the highly homologous other region may be a pseudogene. The method involves independent alignment, pairing and analysis of sequence reads from the genomic region and the highly homologous other region to identify genetic variation. Also described herein is a computer-assisted method for such methods.SELECTED DRAWING: Figure 1A

The invention provides a primer group and a kit for detecting various mutations of a Gaucher disease GBA1 gene and a pseudogene GBAP1 of the Gaucher disease GBA1 gene, and application of the primer group and the kit. Specifically, the invention provides a primer group which is used for simultaneously amplifying or detecting various mutations of a GBA1 gene and a pseudogene GBAP1 thereof, and the primer group comprises a GBA-F primer, a GBA-R primer and a GBAP-R primer and further comprises a Gap-F primer. The invention also provides a kit which comprises the primer group. Based on a specific combination of homologous region multiple long fragment GAP PCR amplification and single molecule length high-throughput sequencing, the kit can be used for simultaneously detecting multiple mutations of GD-related GBA1 pathogenic genes and pseudogenes GBAP1 thereof in multiple samples in a high-specificity, accurate and rapid manner.

This disclosure provides, among other things, strategies for minimizing antibody diversification in a transgenic animal that uses gene conversion for antibody diversification. In some embodiments, the animal may comprise a genome comprising an endogenous immunoglobulin light chain locus comprising: (a) a functional immunoglobulin light chain gene comprising a nucleic acid encoding a light chain variable region; and (b) a plurality of pseudogenes that are operably linked to the functional immunoglobulin light chain gene and that donate, by gene conversion, nucleotide sequence to the nucleic acid encoding a light chain variable region, wherein the pseudogenes are upstream or downstream of the functional immunoglobulin light chain gene and encode the same amino acid sequence as the light chain variable region of the functional immunoglobulin light chain gene of (a). In other embodiments, the locus may have a tandem array of coding sequences for the light chain.

The present invention relates to the field of mucins and mRNA isoforms thereof, more in particular the use of mucins and mRNA isoforms in subjects suspected having an intestinal disorder. Provided herein is an in vitro method for determining the presence of barrier damage to the intestinal tract and / or prediction of therapy response and recovery thereto by determining the expression of at least 3 mRNA isoforms originating from genes selected from the list comprising: MUC1, MUC2, MUC3A, MUC4, MUC5AC, MUC5B, MUC6, MUC12, MUC12-AS1, MUC13, MUC16, MUC17, MUC19, MUC20 or an overlapping transcript or a pseudogene thereof.

The invention relates to the technical field of gene detection, in particular to an IKBKG gene mutation detection probe group and a kit for liquid phase hybridization capture of a Pacbio sequencing platform. The probe group comprises sequences as shown in SEQ ID NO. 1 to SEQ ID NO. 329; by designing an IKBKG gene specific probe and combining the advantages of long reading length and high accuracy of Pacbio sequencing, synchronous detection of IKBKG gene point mutation, insertion and deletion and large-fragment structure variation is realized. The invention overcomes the interference of pseudogene IKBKGp1, is suitable for clinical diagnosis of pigment disorder and other related diseases, and has important clinical transformation value.

The invention relates to the technical field of molecular diagnosis of hereditary nephropathy, and particularly discloses a capture probe group, an amplification primer group and a detection method of related genes of renal cystic diseases. The probe group is used for capturing 42 gene regions closely related to renal cyst, such as ALG8, PKD1, PKD2, GANAB, TSC2 and the like, each probe is 120 bp and is flatly designed along a sense strand, and the density of the probes in a low GC region is increased; the primer group comprises four pairs of long-fragment primers for amplifying first to 34 exon segments of the PKD1 gene, has high specificity, and can effectively distinguish PKD1 from a pseudo gene. An amplification product and original genome DNA are mixed according to a specific ratio to build a library and are subjected to high-throughput sequencing, so that the sequencing coverage and mutation detection rate of the PKD1 are remarkably improved. In 59 clinical samples, the positive detection rate reaches 93.2%, and the method is suitable for screening, diagnosis and genetic typing of renal cystic diseases.

The invention relates to the technical field of gene detection, in particular to a system and a method for detecting congenital adrenal hyperplasia. The system comprises a sample processing module used for extraction, interruption and fragment screening of high molecular weight gDNA; the Y-shaped pre-library preparation module is used for terminal repair and 3 'A-tailing reaction, and carrying out Y-shaped linker connection, fragment screening and long fragment PCR amplification to obtain a Y-shaped pre-library, the targeted enrichment module is used for library hybridization, targeted enrichment and long fragment PCR amplification to obtain a capture library, and the PacBio three-generation library construction module is used for DNA damage repair, terminal repair, purification, sequencing linker connection and digestion. A PacBio three-generation library is obtained, and a sequencing analysis module is used for analyzing and obtaining the variation type of CYP21A2; according to the present invention, the detection result is accurate, and the mutation of the CYP21A2 and the pseudogene CY21A1P thereof can be distinguished.

Provided herein are methods, as well as associated compositions, kits, systems, devices, and instruments, useful for genetic analysis in which one or more sequences similar to a gene of interest in a sample are present, e.g., for determining the state of a spinal muscular atrophy (SMA) vector. In the methods, the combined copy number of related genes (e.g., genes of interest as well as their pseudogenes, such as SMN1 and SMN2) can be determined by analytical assays. In addition, the relative amount of the related genes, i.e. The ratio of the related genes, can be determined by the analytical assay. Using the data of the combined copy number and the ratio of the related genes, the genotype of the gene of interest (and one or more pseudogenes thereof, if desired) can be determined highly accurately.

The invention discloses a II-III stage colorectal cancer molecular typing method, system, device and medium, and relates to the technical field of biology, transcriptome expression analysis is performed on an RNA-seq sample of a II-III stage colorectal cancer patient, transcriptome expression profile data is generated according to a coding gene, a non-coding gene and a pseudogene, and the transcriptome expression profile data is analyzed according to the coding gene, the non-coding gene and the pseudogene. Carrying out hypervariant gene screening and survival analysis on the basis of the transcriptome expression profile data to obtain characteristic genes, executing clustering analysis, synthesizing analysis results of ten clustering algorithms to recognize molecular subtypes of the colorectal cancer in the stages II-III, and providing specific gene expression characteristics and enriched biological functions of each molecular subtype; through big data analysis of gene expression profiles and clinical data of colorectal cancer patients, a II-III stage colorectal cancer molecular typing evaluation model and a detection method based on next-generation sequencing and a PCR platform are established, the II-III stage colorectal cancer patients are divided into a CS1 type, a CS2 type and a CS3 type, and help is provided for improving the clinical treatment efficiency of the colorectal cancer.