1501 results about "Allelic gene" patented technology

This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Improved methods of genetic haplotyping and DNA sequencing and mapping, including methods for making amplified ssDNA, methods for allele determination, and a DNA barcoding strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs or polymorphic sites on a single DNA molecule.

Method includes receiving sequencing data including a plurality of sample reads that have corresponding sequences of nucleotides and assigning the sample reads to designated loci. The method also includes analyzing the assigned reads for each designated locus to identify corresponding regions-of-interest (ROIs) within the assigned reads. Each of the ROIs has one or more series of repeat motifs. The method also includes sorting the assigned reads based on the sequences of the ROIs such that the ROIs with different sequences are assigned as different potential alleles. The method also includes analyzing, for designated loci having multiple potential alleles, the sequences of the potential alleles to determine whether a first allele of the potential alleles is suspected stutter product of a second allele of the potential alleles.

A method is provided for assessing allelic losses on specific chromosomal regions in melanoma patents. The method relies on the evidence that free DNA may be released in the plasma/serum of cancer patients allowing the detection of DNA with LOH in the plasma/serum of cancer patients by analysis for microsatellite markers. The amount of and specific allelic loss allows a prognosis to be made regarding tumor diagnosis and progression, tumor metastasis, tumor recurrence, and mortality.

The invention provides an exogenous gene knocking-in and integrating system on the basis of CRISPR/Cas9, a method for establishing the exogenous gene knocking-in and integrating system and application thereof. The exogenous gene knocking-in and integrating system comprises vectors with report/donor functions and Cas9 expression vectors. Each report/donor vector comprises two target gent homologous arms and an exogenous sequence fragment positioned between the two target gene homologous arms; homologous sequences, which are positioned on a target gene, of the two target gene homologous arms of each report/donor vector are respectively positioned on two sides of a target sequence of the target gene and are connected with the target sequence of the target gene; the exogenous sequence fragments comprise promoters, resistant genes, shorn peptide sequences, report genes and polyA tails which are sequentially arrayed, two SSA repair homologous sequences of each resistant gene are inserted into the resistant gene, and the target sequence of each target gene is inserted in a space between the two corresponding SSA repair homologous sequences. The exogenous gene knocking-in and integrating system, the method and the application have the advantages that exogenous genes can be integrated with endogenous gene sequences in an efficient site-directed and accurately targeted manner, and double-chromosome allelic gene double-knocking-in can be efficiently carried out.

Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

The invention provides a breeding method capable of changing the glume color of rice varieties with yellow glume to brownness. The breeding method comprises the following steps: selecting a target fragment in an extron region of a glume color determining gene OsCAD2, constructing a plant CRISPR/Cas9 targeting recombinant vector, guiding the recombination vector into a rice cell, regenerating the rice cell into seedlings, and sequencing genome target fragments of regenerated strains so as to obtain the strains, two allelic genes OsCAD2 of which simultaneously suffer function deletion mutation. Through phenotype identification, the change of the glume color is realized. Experiments prove that the breeding method can quickly change the glume color of the rice varieties.

In various aspects, the invention provides Brassica juncea plants, seeds, cells, nucleic acid sequences and oils. Edible oil derived from plants of the invention may have significantly higher oleic acid content than other B. juncea plants. In one embodiment, the B. juncea line MJ02-086-3 contains a mutant allele MJ02-086-3/BjFAD2-a at the BjFAD2-a gene locus, having a premature stop codon, so that there are no functional copies of the FAD2 gene in MJ02-086-3 plants. Seeds from MJ02-086-3 plants may for example yield an oil having oleic acid content of greater than about 70% by weight.

The invention provides a method of karyotyping (for example for the detection of trisomy) a target cell to detect chromosomal imbalance therein, the method comprising: (a) interrogating closely adjacent biallelic SNPs across the chromosome of the target cell (b) comparing the result at (a) with the SNP haplotype of paternal and maternal chromosomes to assemble a notional haplotype of target cell chromosomes of paternal origin and of maternal origin (c) assessing the notional SNP haplotype of target cell chromosomes of paternal origin and of maternal origin to detect aneuploidy of the chromosome in the target cell. Also provided are related computer-implemented embodiments and systems.

Provided is an isolated human naive pluripotent stem cell (PSC), wherein: (i) when the naive PSC is a female PSC, then said naive female PSC has two unmethylated alleles of an X-inactive specific transcript (XIST) gene; and (ii) when said naive PSC is a male PSC, then said naive male PSC has an unmethylated allele of said XIST gene. Also provided is a culture medium which comprises an ERK1/2 inhibitor, a GSK3beta inhibitor, a p38 inhibitor, a JNK inhibitor, a STAT3 activator and at least one agent selected from the group consisting of: bFGF, TGFbeta 1, a PKC inhibitor, a ROCK inhibitor and a NOTCH inhibitor; or at least agent selected from the group consisting of: a TGFR inhibitor, a FGFR inhibitor, a PKC inhibitor, a ROCK inhibitor and a NOTCH inhibitor.

Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.

The invention provides a method for analyzing copy number variation in a genome of a testee. According to the method, mathematical manipulation is creatively performed on variables extracted from sequencing data, new two-dimensional variables, namely a sequencing depth ratio (SDR) and alternate allele frequency (AAF) or alternate allelic haploid frequency (AHF) are derived, the signal/noise ratio is further increased, detection sensitivity and precision are improved, and information contained in the high-throughput DNA sequencing data is utilized more fully. Besides, the method is used for processing free DNA in a body fluid sample of the testee, wherein when a CNV feature signal of a certain locus of the genome is extracted from the sequencing data, the information close to the locus is introduced, so that signal strength is greatly improved, and the copy number variation in the free DNA in urine or serum can be effectively detected. The invention furthermore provides a system for implementing the method.