23 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 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.

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.

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 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.

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.

Methods and systems for array-based methods for genotyping multiallelic markers are disclosed. Also disclosed herein are methods for whole genome amplification and locus specific multiplex PCR for selectively biasing amplification for reducing effects of undesired pseudogenes in resulting data.

The invention belongs to the technical field of bioinformatics and gene detection, and particularly relates to a method for realizing high-accuracy and high-resolution human leukocyte antigen HLA typing based on whole exon sequencing data. By incorporating complete exon and intron sequences, different alleles sharing a G-DOMAIN sequence are effectively distinguished, HLA-AP pseudogene sequence correction is combined, typing errors caused by pseudogene interference are effectively avoided, and the anti-interference capability is high. The HLA typing method provided by the invention is adaptive to high and low coverage WES data, can still obtain an accurate typing result for NGS data of fragmented or limited DNA samples, does not need strict coverage screening, and is wide in adaptability. The HLA allele dictionary can be conveniently expanded along with updating of the IMGT / HLA database. According to the HLA typing method, high-resolution typing can be achieved, the typing accuracy of high-coverage NGS data reaches 100%, and the typing precision is high.

The application provides a CYP21A2 gene mutation detection method, system and storage medium, comprising the following steps: identifying difference sites and homologous intervals by reference genome self alignment, and constructing a paralog characteristic site fingerprint library; constructing a Masker reference genome according to the homologous intervals on the reference genome, and obtaining a candidate variation list; using the physical link information of a double-end sequencing read pair and the characteristic site fingerprint library to determine the true or false gene source of each candidate variation; quantitatively calculating the true gene copy number based on re-alignment sequencing depth, background reference library and characteristic site allele frequency; and determining whether a recombination event occurs between the true gene and the false gene based on the physical link information of the double-end sequencing read pair across multiple characteristic sites. The application effectively distinguishes different copy states such as gene deletion, single copy, normal double copy and duplication, and assists in clinically determining gene deletion or duplication events.

The invention provides a genetically engineered bacterium for high yield of D-pantothenic acid and a construction method and application thereof, the construction method comprises the following steps: in a chassis bacterium genome, integrating panD genes from bacillus subtilis to pseudogene loci in a multi-copy manner by applying a CRISPR-Cas9 mediated gene editing technology; a pyc gene and an aspB gene derived from corynebacterium glutamicum and a ppc gene and an aspA gene derived from escherichia coli are over-expressed; the lacI gene in the genome is knocked out, and the high-yield D-pantothenic acid genetically engineered bacterium which is free of plasmid dependence, free of beta-alanine and free of inductive agent IPTG is prepared. A CRISPR / Cas9 gene editing technology is applied, ten to fifteen panD genes are overlaid and copied on the basis of an existing engineering bacterium, meanwhile, the expression level of key genes in a beta-alanine synthesis route of the engineering bacterium is further finely up-regulated, and then a lacI gene is knocked out, so that the beta-alanine is obtained. The plasmid-dependence-free high-yield D-pantothenic acid gene engineering bacterium without adding the beta-alanine is obtained.

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 expressing 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.

Provided herein are compositions and method for the treatment of cancer by inhibiting expression of the breast cancer gene 1 pseudogene 1 (BRCA1P1). In particular, provided herein are nucleic acid inhibitors of BRCA1P1 and methods of use thereof for the treatment and prevention of non-breast cancers.

The application relates to a gene mutation recognition method and system under coexistence of genes and pseudogenes. The gene mutation recognition method under coexistence of genes and pseudogenes in the embodiment of the application comprises the following steps: obtaining sequencing data of a sample to be detected, and obtaining specific nucleotide sites of a pseudogene in the case that a target gene exists; obtaining variation information recognized based on the sequencing data; and according to the variation information and the specific nucleotide sites, recognizing wrong alignment to identify mutation information of the target gene in the sample to be detected. The application does not need to design specific primers and perform amplification reaction, improves the efficiency of gene mutation detection, can exclude the interference of the pseudogene, and improves the stability and accuracy of the detection result.

The application provides a primer probe and kit for detecting SMN1 gene mutation. The kit comprises primers for detecting deletion mutation of SMN1 gene exons 7 and 8 respectively, and corresponding mutation detection probes and blocking probes. The application is more accurate and reliable by reducing the interference of SMN2 pseudogene. The triple amplification of SMN1 gene exons 7 and 8 and the reference Actin gene is completed in a single reaction tube by using the principle of multiplex PCR amplification, thereby improving the efficiency. Through reaction system optimization, the micro blood sample can be used for PCR amplification without purification of genomic DNA, the pretreatment is completed in 15 minutes, the whole detection is completed in about 2.5 hours, time and purification cost are saved, and the kit is suitable for high-throughput screening and detection of neonatal dried blood spots.

The invention discloses a method for producing L-aromatic amino acid by improving the utilization efficiency of carbon atoms. In order to break through the carbon efficiency bottleneck in aromatic amino acid production, a rubisco gene (encoding 1, 5-diphosphate carboxylase / oxygenase) from rhodospirillum rubrum and a prk gene (encoding ribulose phosphate kinase) from spinach are integrated into pseudogene loci of ytfI and ygaQ of an escherichia coli genome, a Kalvin circulation path is constructed, and the carbon efficiency bottleneck in aromatic amino acid production is broken through. The method aims at recovering CO2 and regenerating 3-phosphoglyceric acid to enter central carbon metabolism, and promoter optimization is combined, so that the utilization efficiency of carbon atoms is further improved.

The invention belongs to the technical field of biological medicines, and particularly relates to an application of Oct4-pg4 and Oct4-pg5 long-chain non-coding RNA (Ribonucleic Acid) interference in liver cancer treatment and a verification mechanism. The interfering Oct4-pg4 and Oct4-pg5 long-chain non-coding RNA inhibits proliferation, migration and invasion of liver cancer cells, induces apoptosis of the liver cancer cells, and regulates and controls the cycle of the liver cancer cells and expression of immune escape related genes. Through in-vivo and in-vitro experiments, the expression of Oct4-pg4 and Oct4-pg5 is specifically interfered by using an RNAi technology, and the influence of the Oct4-pg4 and Oct4-pg5 on biological behaviors such as proliferation, migration, invasion and cell cycle of liver cancer cells is observed. Meanwhile, the regulation and control effects of Oct4-pg4 and Oct4-pg5 expression changes on the original gene Oct4 and cell cycle, apoptosis and differentiation related genes are further discussed, and it is proved that interference on Oct4 pseudogenes pg4 and pg5 regulates and controls expression of a plurality of key genes, and a new thought is provided for treatment of liver cancer.

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.