40 results about "Genome scale" patented technology

The present invention provides methods of designing PCR primers that allow the efficient and simultaneous amplification of a large number of different desired DNA fragments in a single multiplex PCR and minimize the formation of nonspecific extensions of undesired DNA fragments. The present invention allows a multiplex PCR to use at least 50 pairs of primers and produce at least 50 DNA fragments of interest. The present invention significantly broadens the application of multiplex PCR in the identification of multiple genes related to multifactorial diseases, the genome-scale detection of genetic alterations, the studies in large-scale pharmacogenetic reactions, the genotyping genetic polymorphism in a large population, the gene expression profiling in various samples, and high throughput genotyping technologies.

The present invention generally relates to libraries, kits, methods, applications and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof. The present invention also relates to rules for making potent single guide RNAs (sgRNAs) for use in CRISPR-Cas systems. Provided are genomic libraries and genome wide libraries, kits, methods of knocking out in parallel every gene in the genome, methods of selecting individual cell knock outs that survive under a selective pressure, methods of identifying the genetic basis of one or more medical symptoms exhibited by a patient, and methods for designing a genome-scale sgRNA library.

Particular aspects provide methods and compositions (e.g., gene marker panels) having substantial utility for at least one of diagnosis, identification and classification of colorectal cancer (CRC) (e.g., tumors) relating to distinctive DNA methylation-based subgroups of CRC including CpG island methylator phenotype (CIMP) groups (e.g., CIMP-H and CIMP-L) and non-CIMP groups. Exemplary marker panels include: B3GAT2, FOXL2, KCNK13, RAB31 and SLIT1 (CIMP marker panel); and FAM78A, FSTL1, KCNC1, MYOCD, and SLC6A4 (CIMP-H marker panel). Further aspects relate to genetic mutations, and other epigenetic markers relating to said CRC subgroups that can be used in combination with the gene marker panels for at least one of diagnosis, identification and classification of colorectal cancer (CRC) (e.g., tumors) relating to distinctive CIMP and non-CIMP groups.

The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions useful for assessing prostate cancer. In a specific embodiment, present inventors have developed and applied a new technology and associated computation methods enabling simultaneous genome-scale analysis of genetic (copy number) and epigenetic (total methylation (TM) and allele-specific methylation (ASM) alternation, This method, called MBD-SNP, features affinity enrichment or methylated genomic DNA fragments using a methyl-binding domain polypeptide.

Methods for identifying and/or distinguishing a homogeneous population of cells based on their replication domain timing profile using high resolution genomic arrays or sequencing procedures are provided. These methods may be used to compare the replication timing profile for a population of cells to another replication timing profile(s), a replication timing fingerprint, and/or one or more informative segments of a replication timing fingerprint, which may be simultaneously or previously determined and/or contained in a database, to determine whether there is a match between them. Based on such information, the identity of the population of cells may be determined, or the identity of the population of cells may be distinguished from other populations of cells or cell types. Methods for determining a replication timing fingerprint for particular cell types are also provided.

The invention discloses a library versus library yeast two-hybrid massive interaction protein screening method. The method takes a genome-grade cDNA as the bait to screen the genome-grade cDNA library. In the application process of the method, the cDNA library is subjected to a homogenization treatment so as to reduce the masking effect of the high-abundance interaction proteins to the low-abundance interaction proteins, and thus the screening efficiency is improved; and moreover the characteristic of yeast URA3 gene is utilized so as to automatically remove the sequences, which have the self-activating function, in bait cDNA. The invention establish a library versus library yeast two-hybrid massive interaction protein screening method, which has the advantages of high feasibility, low cost, low requirements on experiment conditions, and low workload; and successfully applies the method to a screening of pathogen-host plant interaction proteins.

A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was created using a new semi-automated reverse engineering algorithm. This invention includes algorithms and software that can reconstruct genome-scale metabolic networks for cell-types available through the Kyoto Encyclopedia of Genes and Genomes. This method can also be used to complete partial metabolic networks and cell signaling networks where adequate starting information base is available. The software may use a semi-automated approach which uses a priori knowledge of the cell-type from the user. Upon completion, the program output is a genome-scale stoichiometric matrix capable of cell growth in silico. The invention also includes methods for developing flux constraints and reducing the number of possible solutions to an under-determined system by applying specific proton flux states and identifying numerically-determined sub-systems. Although the model-building and analysis tools described in this invention were initially applied to C. acetobutylicum, the novel algorithms and software can be applied universally.

The present application relates to novel composite primers which make it possible to amplify in multiplex at a quantitative level of precision, and to the application of these composite primers for detecting gnomic rearrangements in general and cryptic chromosomal rearrangements in particular. These composite primers contain a tag the sequence of which is absent from or poorly represented in the genome analyzed, and which exhibits a very low propensity to form stable pairings. The composite primers, which contain them, make it possible to carry out multiplex amplifications with quantitative precision on the scale of a genome such as the human genome.

The invention discloses a network construction and analysis method for oxidized bacterium gluconicum genome scale metabolism. The method comprises the steps of utilizing annotation information of oxidized bacterium gluconicum and biochemistry information of corresponding enzymes in the KEGG database to construct a reaction list sketch; modifying the sketch; adding reactions of biomass synthesis, transport and exchangeto form a metabolism network; converting the metabolism network to an SBML format, utilizing Matlab and Bobara Toolbox to debug the metabolism network, analyzing gaps and ineffective cycles and making correction according to the result of debugging; inthe light of the metabolism network, drawing a metabolism diagram by using Pagek and analyzing the network topology structure; and according to the metabolism network, analyzing one or more of the robustness, gene essentiality and flux changeability by utilizing the Matlab and Cobra Toolbox. The metabolism network can be used for analyzing the different metabolism states of oxidized bacterium gluconicum when the oxidized bacterium gluconicum produces dihydroxy acetone, vitamin C and glucose acid.

Provided are methods and models for an alternative source of disease risk, which identifies not genetic variants for a phenotype per se, but variants for variability itself. Also provided are methods and models for a genome-scale, gene-specific analysis of DNA methylation in the same individuals over time, in order to identify a personalized epigenomic signature that may correlate with common genetic disease. Also provided are methods and models for simulating stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease.

The invention relates to the technical field of biology, and aims to provide a construction method of a fringed iris gene silencing system. According to the construction method of the fringed iris gene silencing system, the TRV-VIGS system is applied to the gene function research of fringed iris for the first time. By establishing a rapid and efficient fringed iris virus-mediated gene silencing system, the optimal fringed iris infection receptor, the optimal bacterial liquid concentration and the optimal infection part are determined, fringed iris plants are infected by adopting a leaf back cross cutting injection method, so that the efficiency of agrobacterium infection and gene silencing is remarkably improved, and high-throughput and functional analysis of iris plant gene functions in monocotyledonous plants on a genome scale are realized. The fringed iris gene silencing system is simple, convenient, rapid and efficient, and can lay a foundation for analyzing a molecular mechanism of important characters of fringed iris.

The invention provides a method for acquiring specific expressed genes of peanut seeds in a whole genome scale and application thereof. According to the method provided by the invention, the specificexpressed genes of the peanut seeds can be screened in the whole genome scale, and the specific expressed genes of the peanut seeds can be arranged according to the magnitude of expression quantities;the method is capable of dividing plant tissues into seed tissues and non-seed tissues, so that the expenditure for transcriptome sequencing is greatly reduced, and the accuracy of acquiring the specific expressed genes of the peanut seeds is improved. The application of the method for acquiring the specific expressed genes of the peanut seeds in the whole genome scale in identifying specific expressed promoters of the peanut seeds is beneficial for screening and acquiring the specific expressed promoters of the peanut seeds in the genome scale. The method and the application, provided by theinvention, have important application value on cloning and identification of specific promoters of high-expression seeds of peanuts and other plants and also have important application value in acquisition of the specific expressed genes of other tissues of the peanut and the specific expressed genes of other plant tissues.

A method for designing all coverage of valid primer pairs, which satisfy various filtering constraints provided by users with respect to a given sequence database and has validated specificity to given sequences, is provided. By screening all suitable primer pairs present on a given DNA sequence database without omitting any one primer pair and also screening all primers having a coverage of 1 or more as well as primers having a coverage of 1, a user can be allowed to give rankings to the primers in order to easily select the primers having a high success rate in biological experiments from the resulting primers.

Although metabolic networks have been reconstructed on a genome-scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here such an integrated network was constructed for amino acid metabolism in Escherichia coli. Analysis of ChlP-chip and gene expression data for the transcription factors ArgR, Lrp, and TrpR showed that 19/20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis, and metabolism leads to elucidation of regulatory motifs constituting the integrated network's basic building blocks. The regulatory logic of these motifs was determined based on the relationships between transcription factor binding and changes in transcript levels in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules. This reveals the overarching regulatory principles of the amino acid stimulon.

The present invention relates to the field of functional analysis of Jatropha genes on a genomic scale. More specifically, the present invention relates to a method for high-throughtput functional analysis of Jatropha curcas genes on a genomic scale using virus-induced gene silencing. The method involves use of the tobacco rattle virus (TRV).

The present invention provides Genome-Scale T Cell Activity Arrays (GS-TCAA), as well as methods of making these arrays and methods of using them to identify immune modulators.

The invention discloses a whole-genome random mutation method based on a CRISPR-Cas system and application of the whole-genome random mutation method. The whole-genome random mutation method is based on the CRISPR-Cas system, through the guidance of a random gRNA library, the whole genome of a living body is subjected to scattered bullet type random cutting, and random mutation on the whole genome scale is triggered under the non-fidelity type DNA repair effect. The whole-genome random mutation method can be used for directed evolution and iterative evolution, saccharomyces cerevisiae is used for producing beta-carotene to serve as a verification model, seven rounds of iterative mutation screening are completed within two months, and an evolved strain with the yield increased to 10.5 times is obtained. The omics analysis shows that about 122 mutations can be introduced into each operation on average, the transcription level of about 50% of genes is remarkably changed, it shows that deep remodeling occurs in saccharomyces metabolism through mutation evolution, and experiments prove that the method is a simple and controllable new genome variation technology.