306 results about "Genotyping by sequencing" patented technology

The invention relates to methods for isolating and amplifying small fragments of genomic DNA for genotyping polymorphisms in human populations.

This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.

Methods and systems of performing multiple reactions in a high throughput format by utilizing interfacial mixing of adjacently positioned reagent slugs in a fluid conduit. Preferred applications of the methods and systems are in performing biochemical analyses, including genotyping experiments for multiple different loci on multiple different patient samples. Microfluidic systems are provided that increase throughput, automation and integration of the overall reactions to be carried out.

The present invention relates to the identification of a particular nucleotide polymorphism in a nucleic acid sample in a single reaction utilizing oligonucleotide primers with different melting temperature characteristics.

The invention provides nucleic acid sequences that are complementary, in one embodiment, to a wide variety of human polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relatesd to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

A system and method for genotyping tandem repeats in sequencing data. The invention uses Bayesian model selection guided by an empirically-derived error model that incorporates properties of sequence reads and reference sequences to which they map.

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 computer controlled method for detecting and diagnosing a rare cell type in a tissue sample is provided, said method comprising treating the tissue sample such that it generates a first signal indicative of the presence at a location of a rare cell, detecting the first signal, treating the location at which the first signal is detected to generate a second signal indicative of a diagnostically useful cellular characteristic and detecting the second signal. The first signal can be morphological or a color present in a sought cell either before or after staining. The second signal can be generated by in situ PCR or PCR in situ hybridization. In one preferred embodiment, the rare cell type is a fetal cell in a maternal blood tissue sample, said sample consisting of a smear of unenriched maternal blood. In another embodiment, the method is used to diagnose or genotype cancer cells in a blood or tissue biopsy sample.

Reagents and method for genotyping mice and other animals by in situ Polymerase Chain Reaction amplification of a target polynucleotide in the tissue biopsy. The reagent is comprised of non-ionic detergents, a protease, a buffering agent, a metal ion cofactor, a chelating agent and a salt. The method is comprised of taking a tissue biopsy; admixing it with the reagent; a Lysing Cycle, an inactivation cycle, an amplification step and a detection step.

The present invention relates to methods for identifying substances that modulate the immune response in a genotype specific manner. In general, methods of the invention involve genotyping subjects to identify those having a genotype associated with one or more inflammatory disorder. These subjects, or cells derived therefrom, are monitored for a biomarker for activation of the inflammatory system. The subjects or cells are then contacted with a test substance and the biomarker is re-measured. If the biomarker changes to indicate a decreased activation of the inflammatory system, the test substance may have an anti-inflammatory effect on subjects with that genotype.

The invention provides a set of highly orthogonal six-code universal sequences for use in bDNA singleplex and multiplex nucleic acid hybridization assays. The six-code orthogonal sequences do not cross-hybridize and thus, minimize or eliminate the 3-mer cross-hybridization inherent in the second and third generation bDNA assays. The highly orthogonal universal sequences may be used in singleplex or multiplex bDNA assays quantitatively and qualitatively to determine mRNA levels in a sample; to screen for and genotype targets, such as viruses, that are present in low volumes in a sample; to screen for and genotype SNPs; and to measure changes in the amount of a gene in a sample such as when gene amplifications or deletions occur. The highly orthogonal universal sequences may also be used as universal capture probes to selectively bind assay components in a way that facilitates their further analysis.

The present invention provides a set of oligonucleotide probe for detecting CYP450 enzyme gene hot mutant site and its uses, belonging to clinical molecular diagnosis field. The probe is designed at whole gene sequence of each subtype enzyme of CYP450 and has relative high sensitivity and specifity. The present invention also provides a gene chip for detecting cytochrome P450 enzyme series mutant sites and can detect gene typing of DNA specimen. The inventive probe can be used in P450 genetype diagnosi, clinical medicament and preventing drug adverse reaction.

The invention discloses a composite STR determination method with improved resolution capability in Chinese people, in particular a method for carrying out genotyping to the Chinese people. The method comprises synchronous amplification and the analysis of the locus group consisting of the following loca: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, AMEL, FGA, D5S818, and at least one of D6S1043 and D12S391. The invention also discloses a kit and a primer applied to the method.

A method of predicting whether a subject is predisposed to developing early-onset menopause is provided. The method involves genotyping a patient at the IL-1 gene loci.

The present invention relates to set of inter-simple sequence repeats (ISSR)-PCR primers of SEQ ID Nos. 1 to 37 for genotyping eukaryotes and a method of genotyping diverse genomes of plant and animal systems using FISSR-PCR primers and SSR markers; more particularly, a FISSR and SSR method of distinguishing Basmati rice varieties from Non-Basmati (NB) rice varieties, and Traditional Basmati (TB) rice varieties from Evolved Basmati (NB) rice varieties, and also, a method for determining adulteration of Basmati rice with other rice varieties and a kit thereof.

Disclosed herein are embodiments for genotyping an animal for the presence of polymorphic alleles in the IGF-1R gene that are associated with reproductive longevity and/or ability to better sustain stress, and preferably selecting those animals for future breeding purposes.

The invention relates to a comprehensive genetic analysis method of susceptibility of complex diseases, which comprises the following steps: 1) establishing related genetic databases of complex diseases and determining related detection sites; 2) carrying out genotyping for SNPs sites within individual whole genome by using the Affymetrix6.0 chip technology to obtain the corresponding genotype of each SNP site; 3) exporting determined disease-related SNP site typing results from 900,000 SNP site detection results of a 6.0 chip, and calculating a CGR value according to the genotyping results; and 4) carrying out particular and deep genetic analysis for increased-risk diseases and high-risk diseases according to the calculated disease-related CGR value. The invention can improve the certainty of the susceptibility predication of complex diseases of Chinese Han population, shortens genetic analysis time and prevents calculation errors caused by manual calculation.

The invention relates to methods for enzymatic, genotyping of polymorphisms on solid supports. In some aspects the methods include ligation of allele or base specific interrogation probes to an array probe. The array probe is labeled by ligation of the interrogation probe. Ligation is dependent on the identity of the base immediately adjacent to the end of the array probe. In other aspects array bound probes are labeled by template dependent extension.

The invention provides a kit for genotyping folate metabolism gene. The kit includes a PCR reaction liquid and a DNA hybrid membrane strip, the DNA hybrid film strip comprises a matrix vector and probes, four probes for MTHFR genes, two probes for MTRR genes and two probes designed for human genome are sequentially fixed on the matrix vector, each of the probes is an oligonucleotide sequence hybridized with the SNP locus of each of the corresponding gene, and the nucleotide sequences of the probes are represented by SEQ ID NO:1-8. The kit provided by the invention has the advantages of high sensitivity, rapid detection, good stability, realization of high or low flux detection, high flexibility, strong maneuverability for small clinical samples in some hospitals, less equipment investment and low cost.

The invention provides nucleic acid sequences that are complementary, in one embodiment, to a collection of human single nucleotide polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel by, for example, allele specific hybridization. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

The present invention discloses a gene detection kit using the multiplex PCR technology combined with the SNP sensitive molecular switch technology for genotyping of cytochrome 4502C19 gene, an amplification method and a detection method. Three common polymorphic sites on the CYP2C19 gene significantly changing the product activity are genotyped by the kit, wherein the three common polymorphic sites include: rs4244285SNP site, rs4986893 site and rs12248560 site. The kit includes a wild-type 2*PCR buffer, a 2*mutant amplification buffer, and a polymerase. The two buffers respectively includes a sequence-specific primer and an internal reference primer corresponding to SNP wild and mutant phenotype, and can complete genotyping for the three SNP sites in two multiplex PCR reactions, and thus the CYP2C19 gene is genotyped, and molecular biological evidence is provided for the gene-expressed enzyme activity prediction.

The invention belongs to the gene field of biological technologies, and relates to a single nucleotide polymorphic site (SNP) related to liver cancer susceptibility and application thereof. The invention firstly provides a partial sequence (shown as SEQ. ID. NO.1) of an STAT4 gene and an SNP site rs7574865 of the gene (the sequence is shown as SEQ. ID. NO.2). The invention also provides a method for detecting the SNP site, specificity nucleic acid primers and a UEP (ultra high molecular weight polyethylene) primer, wherein the sequences of the specificity nucleic acid primers are shown as SEQ.ID.NO.3 and SEQ.ID.NO.4, the sequence of the UEP primer is shown as SEQ.ID.NO.5. The invention also relates to a detection kit for the SNP site rs7574865 and application thereof. The method for genotyping of the rs7574865 site is simple and convenient and rapid, and is accurate and clear in result, and the single nucleotide polymorphic site rs7574865 provides a new way for identifying the liver cancer susceptibility and preventing and treating the liver cancer.