66 results about "Allele specific" patented technology

To improve allele discrimination, the inventors adapted the system combining Cas13a detection sensitivity with allele-specific PCR amplification to propose CASPER (Cas13a Allele-Specific PCR Enzyme Recognition) as a new versatile, easy-to-implement, and highly sensitive method to detect low-frequency of sequence variant. CASPER enabled specific and sensitive detection of KRASG12D with low DNA input such as DNA extracted from patient's pancreatic ultrasound-guided fine-needle aspiration fluids. CASPER is easy to implement and a versatile reliable method virtually adaptable to any point mutation.

Provided herein are methods for determining allele-specific telomere length (ATL) and telomere variant repeat (TVR) sequences from long read sequencing data. In some embodiments, the methods include clustering telomere reads together into individual alleles using their adjacent TVR regions from which allele-specific TL can then be determined.

The invention provides a KASP molecular marker related to mesosulfuron resistance of wheat and application of the KASP molecular marker, and belongs to the technical field of crop molecular genetic breeding. Through correlation analysis, it is found that the KASP molecular marker is remarkably correlated with mesosulfuron-methyl resistance, T / C polymorphism exists, and the mesosulfuron-methyl resistance of CC homozygous wheat is remarkably higher than that of TT homozygous wheat. On the basis, a KASP labeling reagent or kit containing a specific primer group is developed, the primer group comprises two allele specific upstream primers and a universal downstream primer, and the 5'ends of the upstream primers are connected with FAM and HEX fluorescent labels respectively. By optimizing a PCR reaction system and a landing procedure, high-throughput genotyping can be realized. The mesosulfuron-methyl-resistant wheat variety can be rapidly screened by applying the KASP molecular marker, a technical support is provided for herbicide resistance molecular breeding, the breeding efficiency of the resistant variety is remarkably improved, and the KASP molecular marker has important significance for guaranteeing safe production of wheat.

Among other tilings, the present disclosure provides various technologies including chirally controlled oligonucleotide compositions and technologies for manufacturing and using such oligonucleotide compositions. In some embodiments, the present disclosure provides technologies useful for allele-specific knockdown of mutant Huntingtin transcripts. In some embodiments, the present disclosure provides technologies usefill for reducing the expression, level, amount, and / or activity of mutant Huntingtin transcripts or products thereof. In some embodiments, the present disclosure provides methods for treating Huntington's disease.

The invention discloses a method for accurately identifying benign and malignant cells based on multi-dimensional characteristics of a single cell transcriptome, and belongs to the technical fields of bioinformatics, tumor molecular biology and cell identification. On the basis of single cell transcriptome sequencing data of tumor tissues and para-carcinoma tissues, three types of information including copy number variation, allele specific copy number variation and tumor-related transcriptional characteristics are synthesized, and final benign and malignant identification is performed on each EpCAM positive epithelial cell through a multi-evidence voting strategy. The method disclosed by the invention has relatively high stability and accuracy in a multi-patient, multi-sample and early tumor scene, particularly improves the recognition capability of early lesion and malignant cells in benign and malignant boundary transition state cells, and provides a reliable technical means for precise diagnosis and individualized treatment of tumors.

This invention relates to the field of plant molecular breeding technology, specifically to a KASP molecular marker PH5-KASP based on the SNP site of the maize Zm00001eb259660 gene and its application. It provides a KASP molecular marker targeting the SNP site at 226029364 bp on maize chromosome 5, which is a functional missense mutation c.485C>T in the coding region of the Zm00001eb259660 gene. The marker consists of two allele-specific forward primers carrying different fluorescent tags and one universal reverse primer, stably distinguishing between C:C and T:T homozygous genotypes, where C:C corresponds to higher plant height and T:T corresponds to lower plant height. This invention offers high marker genotyping accuracy, simple and low-cost detection, and is suitable for large-scale breeding sample detection. It can be used for early identification of maize plant height traits, germplasm screening, and assisted breeding, significantly improving the efficiency of ideal maize plant architecture improvement.

The invention relates to a method of determining somatic allele-specific copy number alterations (CNAs) in the genomes of cells in a test-sample from a subject, the method comprising: i) providing an indexed-DNA library of DNA fragments resulting from whole-genome amplification of genomic DNA from cells of the test-sample, ii) providing whole genome sequencing data of reference non-cancer cells from a reference-sample from the subject; and iii) determining somatic allele-specific copy number alterations in the genome(s) of the cells of the test-sample; and associated methods and uses in cancer therapy.

Phospholamban (PLN) is a critical regulator of calcium cyclin and contractility in the heart. The deletion of Arginine 14 of the phospholamban gene (R14del) is associated with the pathogenesis of an inherited form of cardiomyopathy with prominent arrhythmias. Although the genetic etiology is well defined, there are currently no therapies for this rare disease. This disclosure provides an allele-specific silencing approach by interfering RNA (RNAi) to reduce the expression levels of the R14del allele of the PLN gene.

The invention provides a primer probe, a kit and a method for identifying A1 / A2-beta casein in milk and dairy products. The primer probe comprises an allele specific primer A1A2-F, an allele specific primer A1A2-R, a probe A2-P and a probe A1-P. The invention further discloses a kit for detecting the allele specific primer A1A2-F, the allele specific primer A1A2-R and the probe A1-P. According to the present invention, based on the 67th single nucleotide polymorphism (SNP) of the ruminant A1 / A2-beta casein gene (CSN2), the gene typing method with characteristics of high specificity and high sensitivity is constructed; according to the method, an ARMS-PCR technology, a locked nucleic acid (LNA) modification strategy and an MGB probe signal detection system are integrated, so that the A1 / A2 allele is accurately distinguished.

The invention belongs to the technical field of biology, and provides a method for detecting low-frequency gene mutation based on PNA-PCR combined with a Cas13a system and application of the method. According to the method, a target mutation sequence is enriched through PNA-mediated allele specific amplification, a Cas13a / crRNA system is used for carrying out high-specificity recognition and fluorescence signal amplification on an amplification product, and the high-frequency gene mutation is detected through the Cas13a / crRNA system. High-sensitivity detection of low-frequency gene mutation in plasma circulating tumor DNA (ctDNA) is achieved, and the lower detection limit can reach 0.1%-0.01% VAF. The invention solves the problems of insufficient sensitivity, complex operation, high cost or strong equipment dependence and the like in the prior art such as next-generation sequencing, digital PCR and the like during low-frequency mutation detection, and is suitable for noninvasive rapid screening and precise diagnosis and treatment of clinical tumor gene mutation.

Compositions include CRISPR RNAs, guide RNAs, and nucleic acid molecules encoding the same. Vectors and host cells comprising the nucleic acid molecules are also provided. Further provided are RNA-guided nuclease (RGN) systems for cleaving a mutHTT allele, wherein the RGN system comprises an RNA-guided nuclease and a guide RNA. The compositions find use in cleaving or modifying a mutHTT allele, and / or modifying the expression of a mutHTT allele. The compositions are additionally useful for treating Huntington's disease (HD), particularly in an allele-specific manner.

The present disclosure provides, among other things, a variety of techniques, including chirally controlled oligonucleotide compositions, and techniques for making and using such oligonucleotide compositions. In some embodiments, the present disclosure provides techniques useful for allele-specific knock-down of a mutant Huntingtin transcript. In some embodiments, the present disclosure provides techniques useful for reducing the expression, level, amount, and / or activity of a mutant Huntingtin transcript or product thereof. In some embodiments, the present disclosure provides methods for treating Huntington's disease.

The present application provides a SNP molecular marker related to wet damage tolerance of Brassica napus and application thereof, wherein the sequence of the SNP molecular marker is shown as SEQ ID No. 1, and an A / G base mutation exists at 11872958 of the sequence shown as SEQ ID No. 1. The SNP molecular marker provided by the present application is based on a competitive allele-specific PCR marker detection method, and is used for detection and identification of the wet damage tolerance trait of Brassica napus. The detection method is simple in operation, low in cost, accurate in detection result, good in repeatability and stability, and different detection laboratories and different data results can be compared and verified with each other, and the data has universal comparability.

The present disclosure provides methods and compositions for reducing the level of an RNA transcript produced from a mutant Huntingtin (mHtt) allele in a neuron in an individual with Huntington's disease. The present disclosure provides methods for reducing the level of an RNA transcript produced from an mHTT allele in an allele-specific manner. The present disclosure provides systems and compositions for carrying out the methods.

The present invention provides compositions and methods for cleaving a mutant Huntington (mutHTT) allele. The composition comprises CRISPR RNA, guide RNA and nucleic acid molecules for coding the CRISPR RNA and the guide RNA. Vectors and host cells comprising the nucleic acid molecules are also provided. Further provided is an RNA-guided nuclease (RGN) system for cleaving mutHTT alleles, wherein the RGN system comprises an RNA-guided nuclease and a guide RNA. The compositions may be used to cleave or modify the mutHTT allele, and / or to modify the expression of the mutHTT allele. The compositions are further useful for the treatment of Huntington's Disease (HD), especially in an allele-specific manner.

The application discloses a method for detecting thyroid cancer driving gene mutations based on multiplex fluorescence PCR, and belongs to the technical field of molecular biology detection. The method simultaneously detects nine mutation sites, namely BRAF V600E, NRAS Q61R, NRAS Q61K, HRAS Q61R, HRAS Q61K, KRAS G12V, KRAS G12D, TERT C228T and TERT C250T in a single tube reaction. The method enhances the distinguishing ability of wild type and mutant types by using a locked nucleic acid modified allele-specific primer, suppresses wild type amplification by using a peptide nucleic acid clamp, introduces a competitive internal reference probe to correct amplification efficiency difference, and reduces the sample usage to one fifth of that of a traditional multi-tube scheme. The mutation detection lower limit reaches 0.5% allele frequency, and the total time consumption is not more than 2.5 h.

The invention discloses a method for identifying the purity of a cauliflower 'Youpon 65' hybrid as well as a molecular marker and application. According to the method, on the basis of double-parent re-sequencing data of the Youshon 65 variety, SNP loci with stable genetic difference between parents are obtained through screening, and two pairs of competitive allele specific PCR primers based on the KASP technology are developed respectively according to the SNP loci. By utilizing the two SNP markers and combining a fluorescence detection technology, the male parent, the female parent and the hybrid variety of the variety can be quickly and accurately distinguished in a single reaction. The method provided by the invention can be directly applied to purity identification and authenticity identification of the Youpon 65 commodity species, and provides a reliable technical basis for variety right protection and market supervision. Through early rapid identification of seed purity, production loss and market disputes caused by false hybrids can be effectively reduced, and identification efficiency and accuracy are significantly improved.

The present invention relates to the treatment of myopathy. We report the identification of effective AS-siRNAs against two nucleotide versions of two non-pathogenic DNM2 SNPs that can be used to silence any mutations carried by the same mRNA. In addition, the first AS-siRNA was developed targeting a DNM2 mutation associated with a severe neonatal phenotype, namely the p.S619L mutation. They then developed other AS-siRNAs targeting the p.S619L and p.R465W mutations. They also report the functional benefits of this new set of siRNAs for several defects identified in patient-derived cell lines. The development of these new AS-siRNAs, in addition to the previous one targeting the p.R465W mutation, provides a large number of allele-specific molecules that can target the majority of AD-CNM patients. Interestingly, siRNAs against DNM2 SNPs are versatile molecules with greater potential applications in silencing DNM2 mutations in CMT and HSP, as well as in reducing DNM2 expression in a controlled manner in diseases associated with deleterious overexpression. Thus, the present invention relates to allele-specific siRNAs (AS-siRNAs) that can silence the expression of only one allele of a heterozygous DNM2 gene, where the target allele comprises a non-pathological polymorphism selected from the group consisting of rs2229920 (C or T) or rs12461992 (A or T), and / or a disease-causing mutation selected from the group consisting of c.1393C>T or c.1856C>T.

This invention provides a KASP molecular marker associated with wheat resistance to mesosulfuron-methyl and its application, belonging to the field of crop molecular genetics and breeding technology. Association analysis revealed a significant association between this KASP molecular marker and the mesosulfuron-methyl resistance trait, exhibiting T / C polymorphism. Specifically, CC homozygous wheat showed significantly higher resistance to mesosulfuron-methyl than TT homozygous wheat. Based on this, a KASP marker reagent or kit containing a specific primer set was developed. The primer set includes two allele-specific upstream primers and one universal downstream primer, with FAM and HEX fluorescent tags attached to the 5' ends of the upstream primers, respectively. High-throughput genotyping can be achieved by optimizing the PCR reaction system and landing procedure. The application of this KASP molecular marker can rapidly screen wheat varieties resistant to mesosulfuron-methyl, providing technical support for herbicide-resistant molecular breeding, significantly improving the efficiency of resistant variety selection, and playing a vital role in ensuring safe wheat production.

Novel compositions and methods are provided that are useful for treating, preventing and potentially curing genetic diseases, such as familial Alzheimer's disease, by disrupting a genomic sequence comprising one or more SNPs that are highly epidemic in a population but independent of a particular disease, in some embodiments, their genomic positions are within the same gene exon as the disease-related alleles, and upstream of such disease-related alleles present in the genome of a treatment recipient.

A method of generating a homologous recombination deficiency score includes generating single nucleotide polymorphism (SNP) panel data describing allele abundance at each SNP locus of a plurality of SNP loci, generating double strand break (DSB) feature panel data describing nucleotide sequences at a plurality of DSB feature loci from the nucleic acid sample, generating allele specific copy number data for the plurality of SNP loci based on the SNP panel data, determining an entropy of the allele specific copy number data, comparing the DSB feature panel data to a known genomic sequence to identify a set of DSB mutations, determining a portion of the set of DSB mutations that are repaired by non-homologous end joining, and generating the homologous recombination deficiency score from the entropy of the allele specific copy number data and the portion of DSB mutations repaired by non-homologous end joining.

The invention discloses a KASP mark closely linked with the fruit shape of a bottle gourd and application of the KASP mark. According to the invention, a method of combining QTL positioning with fine positioning is utilized to obtain an SNP marker closely linked with the shape of the bottle gourd fruit, the SNP marker is converted into a KASP marker of a competitive allele specific PCR technology, then typing is carried out based on specific matching of basic groups at the tail ends of primers, two site specific probes and two fluorescent probes are used for detecting marker sites, and the detection result is accurate. And judging whether the to-be-detected material contains the fruit shape related gene or not according to the genotype.

The invention relates to an allele specific expression analysis method and device oriented to individual genetics, and a computer program product. The method comprises the following steps: estimating an expression change trend of an allele based on to-be-analyzed data to obtain an expression trajectory curve; constructing a quasi-dynamic ordinary differential equation model based on the expression trajectory curve, converting the quasi-dynamic ordinary differential equation model into a linear regression model, and performing parameter estimation based on the linear regression model to obtain a parameter estimation result; according to the parameter estimation result and the quasi-dynamic ordinary differential equation model, carrying out regulation and control relationship analysis on alleles to obtain an analysis result; and determining the functional attribute of the corresponding allele pair according to the effect values of the two alleles in each allele pair. According to the invention, interaction of alleles on internal regulation and cross-loci can be effectively captured, and analysis of a dynamic regulation relationship is focused.

Methods and compositions for analyzing Tandem Repeats and single nucleotide polymorphisms use unlabeled, allele-specific PCR primers, a quenched fluorescent probe, and blocking nucleic acids which prevent amplification of specific numbers of tandem repeat units.

The invention belongs to the technical field of biological detection, and particularly relates to a probe-free multiple SNP (Single Nucleotide Polymorphism) typing method, a kit and application thereof. The invention provides a method for realizing multiple SNP (Single Nucleotide Polymorphism) typing without using a probe, and the method takes a melting temperature (Tm) as a discrimination index to distinguish different allele specific PCR (Polymerase Chain Reaction) products for adjusting the Tm through differential tailing so as to identify allele types of each SNP. Compared with an existing method, the reagent cost, the experiment time and the workload are greatly reduced, and meanwhile high accuracy and stability are kept. The method has the characteristics of high efficiency, expandability and economical efficiency, and is expected to play an important role in the fields of large-scale gene screening, crop breeding, clinical typing analysis and the like, so that the method has a good practical application value.

The invention discloses a molecular marker for identifying or assisting in identifying the size of a peanut seed kernel and application of the molecular marker. The Indel molecular marker is located at the 106411958 nucleotide to the 106411977 nucleotide on the fifth chromosome of a peanut genome, and the sequence of the Indel molecular marker is TGCATAATTCCTCATCT. According to the invention, a site which obviously influences the size of a peanut seed kernel is localized by virtue of a segregation population grouping analysis method, a linked competitive allele specific PCR (KASP) functional molecular marker is developed, a candidate gene Arahy.L1PMVE is determined by combining a haplotype of the candidate gene in a natural population, and the gene is named as Ahsseed. The size of the peanut seed kernel can be regulated and controlled through the Indel. The Indel molecular marker disclosed by the invention can identify the size of the peanut seed kernel, is beneficial to promoting the breeding of a peanut variety with a large seed kernel, and improves the breeding efficiency.

Methods and oligonucleotide reagents for genotyping Epstein-Barr virus are disclosed. In particular, genetic profiling is used to detect BALF2 variants in the genome of Epstein-Barr virus in an infected individual to predict the risk of an individual developing nasopharyngeal carcinoma. Primers and allele-specific probes are provided for performing nucleic acid-based diagnostic assays to determine which alleles are present at single nucleotide polymorphisms (SNPs) in the BALF2 gene of Epstein-Barr virus in biological samples from potentially infected subjects. These primers and allele-specific probes can be used for amplifying target sequences to allow rapid detection of a single mutation or multiple mutations in the BALF2 gene simultaneously in a single assay. In addition, methods are provided for identifying individuals at high risk of developing nasopharyngeal carcinoma who are in need of further screening and treatment.

Provided herein are systems and methods for allele-specific copy number (ASCN) calling using sequencing data. The presently described systems and methods can support various configurations based on different sequencing assays and disease contexts. The techniques include segmentation of target regions of interest based on similarity of coverage ratio and B-allele frequency (BAF) values for adjacent target regions, and estimation of an allele-specific copy number for each segment based at least one the observed coverage ratio, an expected coverage ratio, an observer BAF value, and an expected BAF value for each segment, wherein the expected coverage ratio and / or the expected BAF are calculated based on tumor purity, tumor ploidy, and total copy number for each segment.

The invention discloses a method for rapidly mining quantitative trait genes of peanuts. The method comprises the following steps: constructing a nested correlation mapping group based on a breeding incomplete group, positioning to a site which obviously influences the size of a peanut seed kernel by combining a segregation group grouping analysis method, developing a linked competitive allele specific PCR (KASP) functional molecular marker, further reducing the interval, and analyzing and screening candidate genes through gene sequence difference and expression mode, so as to obtain the molecular marker. And finally determining the candidate gene Arahy.L1PMVE in combination with the haplotype of the candidate gene in a natural population. The method can be used for rapidly and accurately assisting in selection of breeding target characters of the sizes of the peanut seed kernels.