61 results about "Pseudogene" patented technology

This invention relates to compounds, compositions, and methods useful for modulating gene expression using short interfering nucleic acid (siNA) molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of genes, such as expressed pseudogenes associated with the maintenance or development of diseases, disorders, traits, and conditions in a subject or organism. The invention also provides small nucleic acid molecules with reduced or attenuated immunostimulatory properties and methods for designing and synthesizing such small nucleic acid molecules having improved toxicologic properties while retaining RNAi activity.

The invention discloses a method and a system for detection of phenotype genes and analysis of biological information. The method comprises the following steps of: performing local comparison between the sequence of target genes and nucleotide sequences of predicted genome coding regions of all allied species respectively, and obtaining a homologous sequence according to the local comparison results; screening the homologous sequence to obtain the homologous genes; extracting a DNA sequence from the homologous genes, converting the DNA sequence into a protein sequence, performing the overall comparison, and then converting the protein sequence into the DNA sequence; constructing a gene tree for the DNA sequence obtained by conversion, and working out Dn/Ds of each branch; and performing positive selection detection and detecting positive selection loci. The method and the system provided by the invention have the advantages of quickly processing a large amount of data information and discovering more accurate information, reducing misguiding of pseudogenes on analysis of biological information and helping to acquire the biological information to explain more biological problems.

Disclosed are the uses of specific genes of the mevalonate and isoprenoid biosynthetic pathways, and of inactive gene sites (the pseudogene) to (1) enhance biosynthesis of isopentenyl diphosphate, dimethylallyl diphosphate and isoprenoid pathway derived products in the plastids of transgenic plants and microalgae, (2) create novel antibiotic resistant transgenic plants and microalgae, and (3) create a novel selection system and/or targeting sites for mediating the insertion of genetic material into plant and microalgae plastids. The specific polynucleotides to be used, solely or in any combination thereof, are publicly available from GeneBank and contain open reading frames having sequences that upon expression will produce active proteins with the following enzyme activities: (a) acetoacetyl CoA thiolase (EC 2.3.1.9), (b) 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) synthase (EC 4.1.3.5), (c) HMG-CoA reductase (EC 1.1.1.34), (d) mevalonate kinase (EC 2.7.1.36), (e) phosphomevalonate kinase (EC 2.7.4.2), (f) mevalonate diphosphate decarboxylase (EC 4.1.1.33), (g) isopentenyl diphosphate (IPP) isomerase (EC 5.3.3.2), and (h) phytoene synthase (EC 2.5.1.32).

The invention provides a homologous pseudogene variation detection method. The method comprises the following steps: constructing a reference gene set according to a latest updated gene sequence; randomly obtaining normal sample original data to create a contrast set; comparing the original data of the normal sample of the reference set with the reference gene set to obtain a comparison result ofthe reference set; carrying out variation detection on each sample in the contrast set, and constructing contrast set variation site frequency data; acquiring actual measurement sample original data,comparing the actual measurement sample data with a reference gene set, and performing variation point detection on an actual measurement sample comparison result to obtain an actual measurement sample variation point detection result; and carrying out site comparison screening on the actually measured sample variation site detection result and the contrast set variation site frequency data to obtain the gene variation site of the actually measured sample. Compared with the prior art, the method can solve the problem of asynchronous updating of the reference genome sequence and the gene sequence, improve the accuracy of gene locus variation detection and shorten the detection period.

The present invention is based, at least in part, on the discovery that the pseudogene TDGF3 (Cripto-3) is expressed in cells and, in particular, that TDGF3 overexpression is associated with transformation of a cell, e.g., TDGF3 is overexpressed in cancer cell lines and cells from tumor tissue. Accordingly, the invention provides compositions, kits, and methods for detecting the presence of a TDGF3 polynucleotide or polypeptide in a sample. The invention further provides compositions, kits and methods for assessing whether a cell is transformed as well as for assessing whether a patient is a suitable candidate for an anti-Cripto antibody therapy.

The invention discloses a detection method and a detection kit for PKD1 gene and PKD2 gene mutation. Amplification is performed by creatively designing multiple pairs of specific long fragment PCR primers, and when amplification is performed by adopting the human genome DNA as a template, amplification of pseudogenes with high homology can be avoided, and therefore the appearance of the false positive and false negative result brought by the pseudogenes can be avoided, and the detection accuracy of mutation of the PKD1 gene and PKD2 gene can be greatly improved. A high-throughput sequencing technique is combined, and the method and the kit when compared with a traditional medical exon trapping technique, can simplify a technical process, reduce the detection cost and shorten the detectionperiod.

The invention discloses a CYP21A2 gene NGS data analysis method and device and application. The method comprises the steps: setting a window and a sliding window for a chip capture area, performing the depth correction according to the depth of each window and GC content, and calculating the copy number of each window according to a hidden horse model for the corrected depth; counting CYP21A2 gene region sequences, selecting paired sequences, judging bases of a target site and an auxiliary site according to the positions of the target site and the auxiliary site in a paired sequence interval, and judging whether the paired sequences support true gene mutation or not by contrasting bases at true and false genes of the target site of a reference sequence; setting a threshold value by comparing with each site according to a copy number correction value of the sample to be detected, and determining the sample smaller than the threshold value as a mutation candidate sample; synthesizing the results, adding mutation site numbers of all samples to prompt CNV, and obtaining CNV and point mutation results of the CYP21A2 gene. According to the method disclosed by the invention, the copy number variation and point mutation information of the CYP21A2 gene can be accurately and effectively obtained by utilizing high-throughput sequencing data.

The invention discloses a detection kit for early diagnosis of colorectal cancer. The detection kit comprises three pairs of specific amplification primers which are respectively used for detecting rRNA-pseudogene, HECTD1 and ZNF843 gene promoter and endogene region methylation and a methylation-specific sequencing primer, wherein the three pairs of specific amplification primers which are respectively used for detecting rRNA-pseudogene, HECTD1 and ZNF843 gene promoter and endogene region methylation comprise methylation-specific forward primers and methylation-specific reverse primers. According to the detection kit, auxiliary diagnosis of the colorectal cancer is realized by detecting the methylation degree of the rRNA-pseudogene, HECTD1 and ZNF843 gene promoter region and endogene region associated with the colorectal cancer; the detection kit is simple, convenient, high in detection efficiency and high in targeting property, has the advantages of accuracy, reliability, flexibility, rapidness and economy and contributes to early discovery and timely treatment of the colorectal cancer.

The invention belongs to the field of molecular biology, and particularly relates to a method for detecting CAH related true and false genes. Specifically, the invention discloses the detection methodfor determining the mutation condition of the CAH related genes. The CAH related genes comprise a CYP21A2 gene and a CYP11B1 gene. The method comprises the following steps of S1, extracting DNA in asample and carrying out PCR amplification by using a primer group; S2, detecting an amplification product by using a third-generation sequencing platform; and S3, analyzing the sequencing result to obtain the mutation condition of the CAH related genes. According to the method, the true and false genes are expanded together by designing the primer group, a mutation type can be detected by long-fragment library building sequencing, known CYP21A2 and CYP11B1 gene pathogenic mutations can be detected at the same time, the sensitivity is high, only 1-50ng of DNA is required to be contained in thesample, the operation is convenient, the deletion of long fragments can be detected, the true and false genes can be distinguished, and meanwhile, the unknown chromosome structural variation can be detected.

Provided herein are methods and associated compositions, kits, systems, devices and instruments useful for genetic analysis where there i s/a re a sequence(s) similar to the gene of interest in a sample, e.g. for determining the spinal muscular atrophy (SMA) carrier status. In the methods, a combined copy number for related genes (e.g., a gene of interest and its pseudogene, e.g. SMN1 and SMN2) 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 relates to the field of genetic disease gene detection, in particular to a PCR primer group for amplifying a PKD1 gene. The PCR primer group comprises one or more pairs in a first primerpair, a second primer pair, a third primer pair and a fourth primer pair. According to the primer group disclosed by the invention, the length of an amplicon covering an exon No.1 is increased, stable amplification of an exon No.1 region is successfully realized, and an amplification product covers all exon regions and most of intron regions of PKD1; a PKD1 gene sequence is specifically obtained,and a pseudogene sequence of PKD1 cannot be completely amplified; and under the condition that pseudogene interference is completely eliminated, the variation of the PKD1 gene, including known variation and unknown variation, can be detected more accurately.

The invention provides 16 common genes for detecting a human natural killer cell immunoglobulin-like receptor KIR, wherein the 16 common genes comprise 14 KIR functional genes (2DL1, 2DL2, 2DL3, 2DL4,2DL5A/B, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3 and 3DS1) and 2 pseudo genes (2DP1 and 3DP1), and a combination of a PCR amplification primer group and a Taqman probe of the common variant ofthe 2DS4; and the combination comprises six primer groups. The invention also provides a kit containing the combination of the PCR amplification primer group and the Taqman probe. The invention has the following technical effects that: an ARMS analysis method is combined with a Taqman multiplex fluorescence PCR technology to carry out qualitative typing detection on the KIR gene; furthermore, improvement is carried out on the basis of a traditional ARMS; various defects of an existing detection method are overcome; and the method disclosed by the invention has wide application prospects and clinical reference value.

The invention discloses a method for determining an optimal sequence alignment threshold for a gene database. The method comprises the following steps: 1) acquiring a protein sequence; 2) removing sequences included in the gene database from the protein sequences, and creating a pseudogene data set; 3) dividing protein sequences in the gene database into subclasses to serve as a true gene data set; 4) combining the pseudogene data set and the true gene data set, and simulating a DNA sequence with a specific length generated by high-throughput sequencing for any protein sequence to obtain a simulated data set; 5) performing sequence comparison, and comparing a comparison threshold value to obtain a value; 6) judging a sequence comparison result, and calculating the numbers of true positive,mismatch, false positive, false negative and true negative; 7) calculating sensitivity, accuracy and a Mathesian correlation coefficient; 8) drawing a three-dimensional curved surface graph by takingthe similarity as an X axis, the E value as a Y axis and the sensitivity, the accuracy or the Malaysian correlation coefficient as a Z axis; and 9) determining an optimal sequence alignment thresholdof the gene database in the three-dimensional curved surface graph.

The invention provides primers and reagent kits for detecting CYP21 gene mutation and an application of the primer and reagent kit. The primers comprise a specific primer for an overall length sequence of a CYP21A2 gene, a specific primer with 30kb deletion and mutation of a CYP21 authenticity gene and a specific primer of recombination/fusion mutation of the CYP21 authenticity gene. The constructed reagent kits and primers are small in quantity, detection of various mutation types of the CYP21 gene can be completed once, the process is simple, the results are high in precision, and the primers and the reagent kits have broad application prospects in the field of diagnosis of congenital adrenal hyperplasia.

The present disclosure provides methods and compositions for diagnosis and for providing a prognosis of a cancer patient by assessing CK2 alpha 1 pseudogene (CSNK2A1P) status. The present disclosure also provides polypeptide, polynucleotide, host cell, and transgenic animal compositions associated with CSNK2A1P.

The invention discloses a gene detection kit used for [beta] receptor antagonist medication, and a detection method and application of the gene detection kit. The detection kit designs specific amplification primers and sequencing primers by aiming at the polymorphism and the CYP2D6 effective copy number of two genes, including CYP2D6C100T and ADRB1G1165C. The kit comprises the following ingredients: amplification reaction liquid, a CYP2D6C100T sequencing primer, an ADRB1G1165C sequencing primer, a CYP2D6 effective copy number sequencing primer and a positive control. The gene detection kit adopts asymmetric multiplex PCR one-tube amplification on CYP2D6(C100T), ADRB1(G1165C and the CYP2D6 effective copy number, a great quantity of biotin-labeled single-strand DNA is generated, in a single-strand amplification process, a CYP2D7-PNA blocking probe blocks binding of a biotin-labeled probe and a pseudogene CYP2D7 so as to prevent the pseudogene from disturbing a sequencing result, the biotin-labeled single-strand DNA carries out binding with streptavidin, after washing is carried out, the sequencing primers and a sequencing raw material are added, pyrophosphoric acid sequencing is carried out, injuries to an amplified fragment by a strong basicity reagent are reduced, sequencing procedures are simplified, and sequencing time is shortened.