106 results about "Phenocopy" patented technology

Exosomes can be used for detecting biomarkers for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, for example, the stage or progression of a disease. Cell-of-origin exosomes can be used in profiling of physiological states or determining phenotypes. Biomarkers or markers from cell-of-origin specific exosomes can be used to determine treatment regimens for diseases, conditions, disease stages, and stages of a condition, and can also be used to determine treatment efficacy. Markers from cell-of-origin specific exosomes can also be used to identify conditions of diseases of unknown origin.

The majority of PCR-based fingerprinting technologies generate dominant genetic markers; homozygote present and heterozygote genotypes cannot be distinguished using conventional detection methods. In contrast, codominant genetic markers provide an unambiguous distinction among each genotype. A genotyping method is described that includes procedures implemented in software. This method quantifies allele copy number and enables recovery of codominant genotypes from markers expressing ostensibly dominant phenotypes. These procedures are designed and implemented to (1) greatly reduce variability attributable to sample assay and detector noise, (2) accurately estimate allele size and copy number, (3) provide normalization criteria for intra- and inter-marker comparisons, and (4) scale the resulting data to determine the genotype of individual markers.

A database of genetic variations is analyzed to produce a haplotype map of the genome for strains of a single species. A computational method is used to rapidly map complex phenotypes onto the haplotype blocks within the haplotype map. The specific genetic locus regulating three different biologically important phenotypic traits in mice is identified using these systems and methods.

The present invention relates to methods for determining the genetic causes of certain phenotypes. The present invention further relates to methods for predicting the phenotype of a organism from its genotype. In particular, the methods of the invention relate to the use of compendia of biological response profiles of cells having known genetic mutations for comparisons with the biological response profiles of cells having unknown phenotypes and genotypes. The methods of the present invention are particularly useful for monitoring the success of genetic engineering and cross-breeding of crops and livestock. The present invention further relates to a computer system for comparing biological response profiles to a compendium of biological response profiles and to kits for relating the phenotype of a cell type to its genotype or for predicting the phenotype of a cell type.

Methods are provided for determining whether a subject has a graft tolerant phenotype. In practicing the subject methods, the expression level of one or more gene in a sample from the subject, e.g., a blood sample, is assayed to obtain a gene expression result, where the gene expression result includes a result for a biomarker of graft tolerance. The obtained gene expression result is then employed to determine whether the subject has a graft tolerant phenotype. Also provided are compositions, systems and kits that find use in practicing the subject methods. The methods and compositions find use in a variety of applications, including the determination of an immunosuppressive therapy regimen.

The invention provides for the production of several humanized murine antibodies specific for the antigen LK26, which is recognized by the murine antibody LK26. This antigen is expressed in all choriocarcinoma, teratocarcinoma and renal cancer cell lines whereas it is not expressed on cell lines of leukaemias, lymphomas, neuroectodermally-derived and epithelial tumour cell lines (excepting a small subset of epithelial cell lines). Furthermore, whereas renal cancer cell lines express the LK26 antigen, normal renal epithelial cells do not. Similarly, with the exception of the trophoblast, all normal adult and fetal tissues tested are negative for the LK26 phenotype. The invention also provides for numerous polynucleotide encoding humanized LK26 specific antibodies, expression vectors for producing humanized LK26 specific antibodies, and host cells for the recombinant production of the humanized antibodies. The invention also provides methods for detecting cancerous cells (in vitro and in vivo) using humanized LK26 specific antibodies. Additionally, the invention provides methods of treating cancer using LK26 specific antibodies.

This patent describes a novel method of detecting genetic interactions in yeast. This method can also be used to screen for function of biological effectors on yeast. The method encompasses crossing yeast strains with genetic alterations to acquire double mutants. The phenotypes of these double mutants are then checked to detect genetic interactions between the double mutants. This method can be used to assign function to yeast genes and their viral, prokaryotic, and eukaryotic homologs, and aptamers. It can also be used to study yeast two hybrid interactions and to find genes that regulate certain yeast promoters.

The present invention is directed to the identification of genostatic factors, methods of determining the association of a plurality of genes with polygenic disorders, and method of assessing the sensitivity and specificity of the risk of polygenic disorders. In particular, the present invention discovers that the association between a polygenic disorder phenotype and polygenes may be masked. Incorporating genostatic factor, such as maternal age, birth disorder, the androgen receptor gene, gender, and age, into the statistical analysis of the association between phenotypes and genotypes reveals statistically significant relationship between the two. Accordingly, the present invention provides novel methods in determining the association of a plurality of genes with a polygenic disease and the likelihood of having the polygenic disease.

At least one genotype-phenotype relationship is extracted based on genotype data of a group of genes for different organisms of a group of organisms. A first database stores genotype data of each organism of the group of organisms. For each organism a genotype vector is stored having a vector component for each gene of the group of genes. A second database stores phenotype data of each organism of the group of organisms. For each organism a phenotype vector is stored having a vector component for each phenotype feature of a group of phenotype features of the organism. A calculation unit uses a machine learning process to classify organisms with different phenotypes depending on the genotype vectors stored in the first database and the phenotype vectors stored in the second database to extract the genotype-phenotype relationship.

The present application relates to somatic hypermutation (SHM) systems and synthetic genes. Synthetic genes can be designed using computer-based approaches to increase or decrease susceptibility of a polynucleotide to somatic hypermutation. Genes of interest are inserted into the vectors and subjected to activation-induced cytidine deaminase to induce somatic hypermutation. Proteins or portions thereof encoded by the modified genes can be introduced into a SHM system for somatic hypermutation and proteins or portions thereof exhibiting a desired phenotype or function can be isolated for in vitro or in vivo diagnostic or therapeutic uses.

A method for detecting aberrant phenotypes expressed by neoplastic cells includes the steps of: 1) staining one or more normal / reactive samples and one neoplastic sample with multiple combinations of monoclonal antibodies, 2) measuring fluorescence emissions associated to the stained cells, 3) storing two independent list mode data files of information on light scatter and fluorescence characteristics of each cell, 4) creating new data files by mixing list mode data from the data file containing information the neoplastic sample into the data file containing information on the normal samples, 5) defining corresponding to normal cells and areas corresponding to empty spaces in normal / reactive samples that may be occupied by tumor cells in neoplastic samples, 6) identifying events corresponding to neoplastic cells and events corresponding to normal cells coexisting in a multidimensional space, and 7) establishing the most relevant phenotypic aberrations displayed by the neoplastic cells as compared to their normal counterpart.

The disclosure provides evidence that the abundance of this particular “oncogenic HSP90” species, which is not dictated by HSP90 expression alone, predicts for sensitivity to HSP90 inhibition therapy, and thus is a biomarker for HSP90 therapy. The disclosure also provides evidence that identifying and measuring the abundance of this oncogenic HSP90 species in tumors predicts of response to HSP90 therapy. “Oncogenic HSP90” is defined herein as the HSP90 fraction that represents a cell stress specific form of chaperone complex, that is expanded and constitutively maintained in the tumor cell context, and that may execute functions necessary to maintain the malignant phenotype. Such roles are not only to regulate the folding of overexpressed (i.e. HER2), mutated (i.e. mB-Raf) or chimeric proteins (i.e. Bcr-Abl), but also to facilitate scaffolding and complex formation of molecules involved in aberrantly activated signaling complexes (i.e. STATS, BCL6).

Gamete donor selection includes receiving a specification including a phenotype of interest, receiving a genotype of a recipient and a plurality of genotypes of a respective plurality of donors, determining statistical information pertaining to the phenotype of interest based at least in part on different pairings of the genotype of the recipient and a genotype of a donor in the plurality of donors, and identifying a preferred donor among the plurality of donors, based at least in part on the statistical information determined.

The invention provides an SNP (single nucleotide polymorphism) marker (comprising SNP1 and SNP4) for evaluating growth performance of ctenopharyngodonidella and a primer pair for amplifying a gene segment where an SNP locus is positioned by virtue of methods of molecular genetics and molecular biology. SNP1 is positioned at the 940th locus in a promoter of a complete sequence of a MyoD (myogenic determining factor) gene of the ctenopharyngodonidella, and a base T is inserted or deficient at the position; SNP4 is positioned in a 107th locus in a first intron of the complete sequence of the MyoD gene of the ctenopharyngodonidella, and a base at the position is A or T. The growth performance of the ctenopharyngodonidella is determined by detecting haplotypes of the two SNP loci. The adopted haplotypes are mutated according to bases generated in the MyoD gene, so that genetic exchange and further phenotype verification are avoided. By virtue of the haplotypes of the SNP marker, rapidly growing ctenopharyngodonidella can be simply and rapidly identified, and rapidly growing ctenopharyngodonidella of a new line can also be guided to be bred.

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, and also for predicting likely phenotypic outcomes using mathematical models and given genetic, phenotypic and / or clinical data of an individual, and also relevant aggregated medical data consisting of genotypic, phenotypic, and / or clinical data from germane patient subpopulations. 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.

The invention discloses a genome breeding value estimation method for integrating dominant effect, which relates to the technical field of livestock and poultry genetic selection. The method comprisessteps identifying a reference group and a candidate group, the phenotype of the target traits of the reference population was determined, Genome-wide marker typing of reference population, quality control of gene marker of reference population, statistics of heterozygous marker deviation of reference population, formulation of genome marker re-coding rules, genome-wide marker typing of candidatepopulation, quality control of gene marker of candidate population, re-coding of genome marker and estimation of genome breeding value, etc. Based on the deviation degree between the phenotype of theheterozygous genotype and the phenotype of the homozygous genotype, the invention formulates coding rules, starts from the genomic marker end, re-codes the heterozygous genotype, causes the gene marker coding to include dominant effect, and then estimates the genomic breeding value. The invention is adapted to the needs of livestock and poultry genetic breeding, and can greatly improve the accuracy of genome estimation breeding value without increasing the complexity of the model.

A genetic algorithm architecture implements a two-stage completion genetic algorithm with respect to an evolving current population data set. The two-stage completion genetic algorithm that includes genotype and phenotype completion loops. The genotype completion loop operates to compete the current population data set based on genotype field fitness scores. The genotype completion loop also implements a phenogenesis operator used to generate a current phenotype set. The phenotype completion loop operates, concurrently with the genotype completion loop, to evaluate the current phenotype set, constrained relative to the current population data set, against a fitness function to produce phenotype fitness scores. The phenotype completion loop implements a genotype reduction operator that then determines corresponding genotype fitness scores for use as the basis for competition in the genotype completion loop.

Formation of nitrogen fixing root nodules in legumes is induced by perception of lipochitin-oligosaccharide signal molecules secreted by compatible Rhizobium bacteria, which triggers a common symbiotic pathway. The present invention provides a spontaneous nodule formation (snf2) mutant, in which the formation of symbiotic nodules is spontaneous, leading to nodule development in the absence as well as in the presence of Rhizobium bacteria and / or exogenous rhizobial signals. The invention further provides an isolated DNA sequence encoding a mutant cytokinin-independent histidine kinase whose activity results in this ‘gain of function’ dominant phenotype of spontaneous nodule formation. Furthermore the snf2 gene is shown to confer a phenotype, characterised by regulated organogenesis of spontaneous nodules, to plants having a nodulation deficient genetic background. A gene of the invention, that confers this spontaneous nodulation phenotype, has 15 utility for the transfer and establishment of nitrogen fixing capability in non-nodulating plants, and thereby reducing the nitrogen fertiliser dependence of non-nodulating crop plants.

The presently disclosed subject matter provides methods for improving the efficacy of a plant breeding program aimed at altering phenotypic traits for which associations with genetic markers can be established. Genome-wide genetic values of individuals are computed based on the individuals' marker genotypes and the associations established between genetic markers and phenotypic traits. Individuals and breeding schemes are then selected based both on the individuals' genome-wide genetic value and on the distributions of these genetic values for the potential progenies derived through the breeding schemes under evaluation. The presently disclosed subject matter also provides systems and computer program products for performing the disclosed methods as well as plants selected, provided, or produced by any of the methods herein and transgenic plants created by any of the methods herein.

The present invention relates to a method for gene mapping from chromosome and phenotype data, which utilizes linkage disequilibrium between genetic markers mi, which are polymorphic nucleic acid or protein sequences or strings of single-nucleotide polymorphisms deriving from a chromosomal region. All marker patterns P that satisfy a certain pattern evaluation function e(P) are searched from the data, each marker mi of the data is scored by a marker score and the location of the gene is predicted as a function of the scores s(mi) of all the markers mi in the data.

The invention discloses a method of detecting phenotypic character genes related in a nuclear genome. The method includes: S1) measuring a target phenotypic character of an F1-generation hybrid population and selecting an extreme target phenotypic character; S2) extracting RNA of the individuals with the extreme target phenotypic character, grouping by a BSA method, and constructing an expression gene chip; and S3) finding differentially expressed genes according to information of the expression gene chip, wherein the genes are the phenotypic character related genes in the nuclear genome. By application of the technical scheme, the target phenotypic character of the F1-generation hybrid population is screened by a plurality of times of measurement, the individuals with the stable extreme target phenotypic character are selected, mixing and grouping are performed by adoption of the BSA method and gene pools are constructed, thus highlighting differences of the target phenotypic character. A large number of genes are hybridized at the same time by combination of a gene chip technology. The differentially expressed genes related to the target phenotypic character are screened through analyzing chip results.

The invention discloses a high-throughput method for segregating a quantitative character regulatory gene, which comprises the following steps of: 1) construction of a target character segregation population, in which the population is a population in two parent hybridization progenies (F2 and F3), a DH system and a RIL; 2) mixing of extreme samples and segregation of total RNA in the population, in which a progeny segregation population is divided into three categories according to character phenotype; 3) gene expression analysis, in which the difference and sameness of gene expressions between two extreme mixed samples are compared by utilizing a gene expression analysis method, namely one of chip, EST sequencing, subtraction, cDNA-AFLP, and the like; and 4) acquisition and verification of a candidate gene, in which a differential expression gene between the two extreme mixed samples is found and is a candidate regulatory gene related to target character, and the function of the gene is verified through transgene, gene expression, molecular marker correlation and a contribution rate analysis method to obtain a target gene with regulatory character phenotype. The method is suitable for the segregation of a certain quantitative character regulatory gene controlled by multigene of all organisms, and is a simple, quick, high-throughput and economical gene segregation method.

The invention belongs to the field of rape breeding, particularly relates to rape self-incompatibility complete linkage dominant SCAR labels and the application thereof. Cabbage type rape self-incompatibility S locus dominant SCAR molecular labels are produced artificially, which includes self-incompatibility S locus dominant labels and self-incompatible restorer line S locus dominant labels, wherein the self-incompatibility S locus dominant SCAR labels are named as SRKa, SEKb and SP11a, whose nucleotide sequences are displayed in sequence tables with SEQ ID NO: 1, 2, 6; the self-incompatible restorer line S locus dominant SCAR labels are named as SLGa, SLGb and SLGc, whose nucleotide sequences are displayed in sequence tables with SEQ ID NO: 3, 4, 5. The molecular labels can differentiate homozygous-compatible, hybrid-compatible and homozygous-incompatible genes. The molecular labels are used to verify the cabbage type rape self-incompatibility phenotype. The invention provides practical labels and a usage method for rape molecular breeding.

Aspects of the present invention also provide novel compositions and methods based on novel PAPD1 single nucleotide polymorphisms selected from the group consisting of AAFC02034082.1:g.9224G>A, g.9330A>C, g.9367G>C, g.9419A>C, g.9435T>G, g.9409[(G)4]+[(G)5], g.10084T>C, g.10228G>T, c.10326C>T and c.10364A>G, which may provide novel markers for intramuscular fat deposition. Additional aspects provide for novel methods which may comprise marker-assisted selection or marker-assisted management to improve intramuscular fat deposition in cattle.

Compositions and methods for producing a plant population lacking sexually derived embryos are provided. Compositions include suppression cassettes encoding polynucleotides and promoters resulting in parthenogenesis. Further provided are parthenogenesis genetic elements used to prevent sexual reproduction in self-reproducing plants.Methods include: utilizing maternal embryo defective recessive mutations which are maintained as a sterile inbred maintenance system, allowing generation of populations that are homozygous for recessive mutant alleles, but transgenically complemented. Methods include utilizing a toxin genes expressed via egg-cell specific promoters, creating a dominant, embryo-less phenotypes, non-transmittable through female gametes. Resultant hemizygous plants are transformed with egg-cell promoters driving the antidote, a pollen ablation PTU and a seed color marker for identification of transgenic seed. The generation of a plants 50% female fertile, having seed which when grown in the next generation will yield plants with 50% viable transgenic seed, and 50% non-viable embryo-less seed.

The expression map and the chromosome distribution characteristic of a DS (down syndrome) fetal genome-wide miRNAs are studied by an Illumina deep sequencing technology so as to obtain a down syndrome 21 chromosome-related miRNA differential expression map model, which consists of an up-regulated miRNA, four down-regulated miRNAs and 9 zero-expression miRNAs. miRNA molecules with significant difference and specific expression help to understand a molecular regulation mechanism for occurrence and development of a clinical phenotype of a DS disease and lay the foundation for further studying gene expression disorder of a DS patient genome-wide and a relationship between the gene expression disorder and relevant clinical symptoms.

Fertility problems affect (1 in 10) couples in Western society, making it one of the most common serious health issues. Despite this, little is known about the causes of infertility, and thus patient counseling and treatment are suboptimal. With infertility being such a common problem, identification of any cause would impact on a large number of patients, allowing better counseling, clearer diagnoses and the possibility of making more informed choices (e.g. adoption vs. IVF treatment). The present invention provides methods to identify a cause of infertility in a subject based on the genotype of the subject, in particular, by evaluating the status of the gene encoding FK506 binding protein-like (FKBPL). In particular, the present invention relates to use of the status of the gene encoding FK506 binding protein-like for identification of a cause of an infertile phenotype in a subject. Also provided, are methods method for identifying an infertile phenotype in a subject, and identifying a cause of an infertile phenotype in a subject. This diagnostic tool finds wide clinical utility in the identification of a cause of infertility, resultantly impacting on a large number of patients. Further aspects of the present invention relate to the targeting of FKBPL in order to temporarily and reversibly induce infertility in a subject. Such aspects of the present invention find utility in the development of a male contraceptive pill. Moreover, due to the high degree of homology between the human and mouse FKBPL gene, FKBPL can be targeted in order to induce infertility in mice (or other species) as a form of pest control or animal husbandry.