61 results about "Genome-wide association study" patented technology

The present invention relates to the selection of a set of SNP markers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual's longevity, their protection against age-related diseases and/or their response to a particular drug or drugs.

The present invention relates to the selection of a set of polymorphism markers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual's susceptibility to Crohn's disease and/or their response to a particular drug or drugs.

The present invention is in the field of nucleic acid-based genetic analysis. More particularly, it discloses novel insights into the overall structure of genetic variation in all living species. The structure can be revealed with the use of any data set of genetic variants from a particular locus. The invention is useful to define the subset of variations that are most suited as genetic markers to search for correlations with certain phenotypic traits. Additionally, the insights are useful for the development of algorithms and computer programs that convert genotype data into the constituent haplotypes that are laborious and costly to derive in an experimental way. The invention is useful in areas such as (i) genome-wide association studies, (ii) clinical in vitro diagnosis, (iii) plant and animal breeding, (iv) the identification of micro-organisms.

Computationally-efficient techniques facilitate secure crowdsourcing of genomic and phenotypic data, e.g., for large-scale association studies. In one embodiment, a method begins by receiving, via a secret sharing protocol, genomic and phenotypic data of individual study participants. Another data set, comprising results of pre-computation over random number data, e.g., mutually independent and uniformly-distributed random numbers and results of calculations over those random numbers, is also received via secret sharing. A secure computation then is executed against the secretly-shared genomic and phenotypic data, using the secretly-shared results of the pre-computation over random number data, to generate a set of genome-wide association study (GWAS) statistics. For increased computational efficiency, at least a part of the computation is executed over dimensionality-reduced genomic data. The resulting GWAS statistics are then used to identify genetic variants that are statistically-correlated with a phenotype of interest.

Compositions and methods for the identification of agents useful for the treatment of neurological disorders, including schizophrenia, are provided.

The present invention relates to the selection of a set of polymorphism makers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual's susceptibility to IBD (ex: Chrohn's disease) and/or their response to a particular drug or drugs.

The invention provides an SNP (Single Nucleotide Polymorphism) marker related to the bitter character of cucumber and application of the SNP marker. The SNP marker is located at the NO.1178bp of the gene sequence for coding the Csa6G088690 protein of cucumber; cucumber with basic groups G at the NO.1178bp is bitter; and cucumber with basic groups A at the NO.1178bp is not bitter. According to the invention, a genome wide association study (GWAS) method is adopted to screen out the SNP marker related to the bitter taste character of cucumber, a derived cleaved amplified polymorphic sequences (dCAPS) method is adopted to detect the gene types of cucumber to be detected, and bitter or non-bitter cucumber variety breeding is carried out according to the gene types, so as to speed up the breeding process of non-bitter cucumber. The SNP marker is more accurate and reliable in result than the traditional method of subjectively judging whether cucumber is bitter or not, is simpler and more convenient than HPLC (High Performance Liquid Chromatography) for identifying bitter substances, and can be used for large-scale screening of breeding materials. Besides, the invention discovers the committed step for the Csa6G088690 protein of cucumber to control the synthesis pathway of bitter of cucumber for the first time.

The invention discloses a restrictive two-stage genome-wide association study (GWAS) method based on an SNPLDB mark, and aims at solving the problems that a traditional method cannot be used for estimating multiple allele information, and is high in false positive rate and low in efficiency of detection on inbreeding crops. By combination of the SNPLDB mark constructed on the basis of a haplotype block, correction of deviation of an inbreeding population relation analysis model and a two-stage relation analysis strategy under a multi-site model, the GWAS method suitable for conventional breeding of inbreeding crops is built; the SNPLDB mark is applied to GWAS, so that a method is provided for multiple allele estimation; candidate sites are screened on the basis of a single-site model in the first stage, and are further screened on the basis of a progressive regression analysis method in the multi-site model in the second stage, so as to balance the problems of missing of heritability and over-high heritability estimation. Therefore, the interpretation ratio of a final genetic model is controlled at trait heritability. The positioning accuracy and efficiency are improved by a feature vector and an appropriate significant level of a similarity coefficient matrix estimated by the SNPLDB mark by GWAS.

The invention provides a high-throughput low-cost SNP (single nucleotide polymorphism) genotyping method based on a liquid molecular hybridization principle. The method comprises the following steps: extracting biological genome DNA (deoxyribonucleic acid) and carrying out biotin labeling on the biological genome DNA; designing site-specific hybridization primers LSP1 and LSP2 and carrying out 5' phosphorylation on LSP2; hybridizing an LSP1 mixture and an LSP2 mixture with the genome DNA to obtain a hybridization adsorption product; carrying out extended linkage reaction to obtain a target DNA fragment; carrying out a round of PCR (polymerase chain reaction) amplification on a universal primer; carrying out PCR amplification on the Barcode specific primer of the recovered target fragment; carrying out high-throughput sequencing; obtaining SNP site genotyping information through analysis. The method combines the site selection flexibility of the liquid hybridization technology with the advantages of high throughput and low cost of the high-throughput sequencing technology and has great application value and wide popularization prospect in the research fields such as large-scale screening of SNP, genome-wide association study, population diversity evaluation, gene function analysis and the like.

The invention discloses a method for developing waxy1-gene internal molecule markers on the basis of association analysis and KASP. One indel and two snap markers located in waxy1 gene and remarkablyassociated with content of amylase are found out mainly through genome-wide association study and candidate gene association analysis techniques; the detected indel is marked as a major mutant type ofglutinous maize in China; glutinous maize materials can be identified through agarose gel by the markers developed on the basis of the indel, and convenience and rapidness is achieved as compared with that of original polyacrylamide gel identification; meanwhile, paired linkage disequilibrium test of 59 parts of waxy1-gene sequence regions of maize hybrid line materials is performed, close linkage of the indel marker and the two snp markers is tested, primers of the two snps are developed on the basis of the KASP technology, the glutinous maize materials can be identified rapidly, efficientlyand accurately, and molecular breeding of glutinous maize is facilitated.

The invention provides application of maize gene ZmGFT1 in increasing folic acid content in plants. 5-Formyltetrahydrofolate content in 513 selfing line materials of a maize natural variant group is measured, the influence of group structure and genetic relationship of the natural variant group is estimated in connection with genotype data mined from RNA-Seq data, gene GFT1 having significant influence on the 5-formyltetrahydrofolate content and located on maize 5th chromosome is located by means of genome-wide association study, and the gene GFT1 encodes glutamate formiminotransferase 1. The invention also provides an SNP marker associated with maize folic acid content and its application. The maize gene ZmGFT1 and discovery of the key SNP site therein having significant influence on the 5-formyltetrahydrofolate content not only provide theoretical basis for studying folic acid metabolism in maize and other crops, but also enable the hidden hunger problem of human in terms of folic acid nutrition to be solved through the increase in the folic acid content of transgenic plants.

The present invention is in the field of nucleic acid-based genetic analysis. More particularly, it discloses novel insights into the overall structure of genetic variation in all living species. The structure can be revealed with the use of any data set of genetic variants from a particular locus. The invention is useful to define the subset of variations that are most suited as genetic markers to search for correlations with certain phenotypic traits. Additionally, the insights are useful for the development of algorithms and computer programs that convert genotype data into the constituent haplotypes that are laborious and costly to derive in an experimental way. The invention is useful in areas such as (i) genome-wide association studies, (ii) clinical in vitro diagnosis, (iii) plant and animal breeding, (iv) the identification of micro-organisms.

The present invention relates to a method of discovering pharmacogenomic biomarkers that are correlated with varied individual responses (efficacy, adverse effect, and other end points) to therapeutic agents. The present invention provides a mean to utilize archived clinical samples to perform genome-wide association study in order to identify novel pharmacogenomic biomarkers. The newly discovered biomarkers can then be developed into companion diagnostic tests which can help to predict drug responses and apply drugs only to those who will be benefited, or exclude those who might have adverse effects, by the treatment.

The invention relates to a type 2 diabetes susceptibility genetic locus as well as a detection method and a kit of the type 2 diabetes susceptibility genetic locus. Particularly, the invention discloses the type 2 diabetes susceptibility genetic locus found on the basis of genome-wide association study. The invention also provides the method for detecting the type 2 diabetes susceptibility. The method comprises steps of detecting individual GRK5 gene and RASGRP1 gene, and determining whether the transcript and/or protein has variation compared with normal transcript and/or protein, if yes, the individual is more likely to be attacked by the type 2 diabetes than normal people. The invention also discloses the corresponding kit for detection.

The invention provides an SNP molecular marker related to the breast muscle weight and the breast muscle percentage of a chicken and application of the SNP molecular marker. The invention finds that the SNP molecular marker remarkably related to the breast muscle weight and the breast muscle percentage exists in a GJA1 gene on the basis of GWAS (Genome Wide Association Study). The invention provides a kit for detecting the SNP molecular marker; and the kit contains a pair of primers of which the nucleotide sequences are shown in SEQ ID NO. 1-2. The invention further provides a method for selecting a high-quality chicken pure line with high breast muscle weight and breast muscle percentage by utilizing the SNP site of the GJAI gene. The method comprises the following steps: obtaining a chicken genome DNA; detecting the genetype of the SNP T1289c site of the GJAI gene by virtue of the pair of primers of which the nucleotide sequences are shown in SEQ ID NO. 1-2; and selecting chicken individuals with superior genetype CC. The kit provided by the invention is simple to operate, high in flexibility, high in accuracy and low in detection cost and has an important application value.

The invention discloses a SNP molecular marker related to daily gain of Duroc and an application thereof. Through genome-wide association study (GWAS), an SNP site (ASGA0056780) related to the daily gain of Duroc is identified at the No. 13 chromosome of a pig; the GG type individual at the site has faster daily gain. The invention also provides a method for detecting the SNP molecular marker at the same time; the Taq probe can judge the site rapidly. The method can exactly and rapidly classify the ASGA0056780 with low cost, and provide technical support to the establishment of the breeding method of the Duro type daily gain molecular marker.

The invention discloses a molecular marker influencing the feed conversion ratio character of a pig and application, and belongs to the technical field of marker-assisted selection technologies and genetic breeding. The molecular marker is obtained through the genome-wide association study (GWAS), the nucleotide sequence of the molecular marker is shown in SEQ ID NO:1, the C>A nucleotide single-base mutation (named as g.690C>A) is located at the 690bpth position of the genomic sequence of the pig, and the feed conversion ratio character of the pig is remarkably influenced through mutation. The invention discloses preparation and application of the molecular marker.

The invention discloses a method for predicting complex diseases and phenotypic related metabolites based on Mendel randomization analysis. The method comprises the following steps: (1) collecting andsorting blood metabolite whole genome association research data; (2) screening tool variables and removing multiple effects; and (3) performing double-sample Mendel randomization analysis according to the screened tool variables, and obtaining metabolites related to diseases or phenotypes by integrating judgment of effect values and sensitivity analysis of multiple analysis methods. According tothe method, the influence of 363 blood metabolites on complex diseases and phenotypes is predicted through double-sample Mendel randomization analysis in combination with screening and discriminationof multiple methods, and an important foundation is laid for subsequent searching of drug targets for the blood metabolites and nutrition intervention.

The invention discloses a molecular marker for detecting anti-scab QTL (quantitative trait loci) Qfhb.hbaas-5AS and an application method of the molecular marker. The invention further provides application of a substance for detecting the genotype of SNP IWB21456 loci of wheat chromosomes 5AS in identification or auxiliary identification of the resistance of the wheat scab resistance, and application of the substance for detecting the genotype of the SNP IWB21456 loci of the wheat chromosomes 5AS in preparation of products for identification or auxiliary identification of the wheat scab resistance. Through genome-wide association study (GWAS), the loci Qfhb.hbaas-5AS on short arms of the wheat chromosomes 5AS are discovered, and are further correlated with the SNP IWB21456 to be convertedinto common PCR markers KASP-Fhb5AS, and the concordance rate of the two for 240 materials is 96.7%. The molecular marker can be used for detecting the genotype of the anti-scab QTL Qfhb.hbaas-5AS, and for anti-scab molecular breeding.

The invention discloses a gene SbAn-1 with the function of controlling existence of sorghum awn and belongs to the field of molecular biology and sorghum breeding. The gene SbAn-1 capable of controlling existence of sorghum awn is obtained through genome-wide association study. According to the technology, a plurality of nucleotide polymorphic sites can be detected at a time, and therefore large-batch excavation and simple trait genes are facilitated. The gene is selected on the basis of the PCR technology, and the technology can be directly used for identifying the gene SbAn-1 with the function of controlling existence of sorghum awn and allelic genes thereof, so that molecular marker assisted breeding is achieved.