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186
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ShareScore release 0.9.0
Dataset results
186 results for “genome wide association study”
Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]
GEO Series GSE107294. Mus musculus. 7 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-Wide Association Study Towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats
GEO Series GSE145419. Capra hircus. 276 samples. Type: Genome variation profiling by SNP array.
A novel nonsense mutation in DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep
GEO Series GSE26310. Ovis aries. 20 samples. Type: SNP genotyping by SNP array.
Genome-wide association study on craniofacial microsomia
GEO Series GSE69664. Homo sapiens. 939 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genome-wide association studies reveal susceptibility loci for noninfectious claw lesions in Holstein dairy cattle
GEO Series GSE165945. Bos taurus. 326 samples. Type: Genome variation profiling by SNP array.
Genome-wide association studies for sheep growth and meat production traits using Illumina OvineSNP50 BeadChip
GEO Series GSE46231. Ovis aries. 329 samples. Type: SNP genotyping by SNP array.
Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer [Metadata_SJLIFE_controls_282]
GEO Series GSE197676. Homo sapiens. 282 samples. Type: Methylation profiling by genome tiling array.
Genome-Wide Association Study of Hospitalized COVID-19 Patients in the United Arab Emirates
GEO Series GSE184150. Homo sapiens. 646 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Associations between gene expression variations and ovarian cancer risk alleles identified from genome wide association studies
GEO Series GSE37582. Homo sapiens. 121 samples. Type: Expression profiling by array.
Identification of loci and signaling pathways associated with ITP using pooling genome-wide association study in Han Chinese
GEO Series GSE76744. Homo sapiens. 4 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Deciphering the genetic regulation of peripheral blood transcriptome in pigs through allele-specific expression analysis and expression genome-wide association study
GEO Series GSE97374. Sus scrofa. 243 samples. Type: Expression profiling by array.
Genome-wide association study of abnormal Paneth cell phenotype in Japanese patients with Crohn's disease
GEO Series GSE90102. Homo sapiens. 98 samples. Type: Genome variation profiling by SNP array.
Genome-wide association study of body weights in Hu sheep
GEO Series GSE152717. Ovis aries. 240 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genome wide association study between segregate wild-type and homozygous mutant
GEO Series GSE197891. Arabidopsis thaliana. 2 samples. Type: Other.
Multi-omics co-localization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus [RNA-Seq]
GEO Series GSE172367. Homo sapiens. 190 samples. Type: Expression profiling by high throughput sequencing.
A Human Induced Pluripotent Stem Cell Array-Based Genome Wide Association Study Identifies Virus Susceptibility Locus and Variants
GEO Series GSE182376. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
Data from: The identification of loci for immune traitsin chickens using a genome-wide association study
The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.
Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate
Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted p= 2.2 x 10-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.
Data from: Genome-wide association study for tobiano spotting coat color in Korean Jeju × Thoroughbred horse population
Korean Jeju horse features a small to medium frame size and stature having varieties of coat colors including grey, milky, spotted and bay1. Crossbreeding with Thoroughbred has been a long tradition in Korea to have intermediate frame size horse suitable for racing, leisure activities and meat production2. Tobiano white-spotting pattern is preferred by many horse breeders and owners which is inherited as an autosomal dominant trait1,3. Polymorphisms in proto-oncogene receptor tyrosine kinase (KIT) gene were strongly associated with tobiano and sabino coat color pattern in American and European horse breeds3,5. In addition, ECA3 inversion locus near KIT gene also significantly associated with tobiano spotting pattern in horses4,5. Here, we report SNPs and harbored genes associated with tobiano coat color in a crossbred horse population through genome-wide SNP association analysis. In this study, coat color patterns of 142 crossbred horses (Jeju indigenous horse × Thoroughbred) were verified according to previously described methods3,5 and coded as "0" or "1" (Figure S1). Genomic DNA was extracted from blood samples using DNeasy 96 blood DNA extraction Kit (QIAGEN, USA). Genotyping was performed using Equine SNP 50K BeadChip (Illumina, San Diego, USA) at AGBD, NIAS, Korea. A total of 45,204 SNPs passed the set quality control criteria as minor allele frequency (MAF<0.01), missing genotype (GENO>0.10) and Hardy-Weinberg equilibrium (HWE<0.0001) in 142 individuals. Finally, a set of 16,223 independent SNPs were generated through –indep –pairwise 25 5 0.25 pruning6. Genome wide association study revealed 18 Bonferroni adjusted SNPs located on chromosome 3 (ECA3) significantly associated with tobiano coat color in the studied population (Figure 1, Table S1). These SNPs broadly plotted on 40 Mbp region (from 39 to 79 Mbp) of ECA3 which might be due to high LD among the significant SNPs. The most significant association was found between ECA3 inversion locus (77657979 bp) and tobiano pattern (P< 5.56×10-17) while the second highest association was detected with SNP rs68555258 (48853535 bp; P< 4.04×10-12, Table S1). Apart from this, genotypes of ECA3 inversion locus by pyrosequencing matched perfectly in our study (Table S2). All tobiano horses (n = 37) were heterozygous for inversion locus (+/To) while solid-colored horses (n = 103) were homozygous (+/+). ECA3 inversion is located 70 kbp downstream from KIT gene which possessed causal variants for tobiano pattern in horse5,6. The Biomart and Variant Effect Predictor tools in Ensembl Genome Browser (http://www.ensembl.org/index.html) identified several significant SNPs harboring genes of which GPRIN3, ARHGAP24, SCFD2, RASSL11B and WDFY3 are noticeable (Table S3). Based on our genome wide association and inversion locus genotyping results, it is suggested that ECA3 inversion locus variant is either causative or completely linked with causative variants for tobiano coat color in this crossbred horse population. Moreover, a set of putative mutations in other genes might be in high LD with causative variants that could be explored for functional annotations associated with tobiano coat color pattern in horse population.
Data from: pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies
Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise. Markers on one chromosome were included simultaneously in a multilocus model and least angle regression was used to select the most potentially associated single-nucleotide polymorphisms (SNPs), whereas the markers on the other chromosomes were used to calculate kinship matrix as polygenic background control. The selected SNPs in multilocus model were further detected for their association with the trait by empirical Bayes and likelihood ratio test. We herein refer to this method as the pLARmEB (polygenic-background-control-based least angle regression plus empirical Bayes). Results from simulation studies showed that pLARmEB was more powerful in QTN detection and more accurate in QTN effect estimation, had less false positive rate and required less computing time than Bayesian hierarchical generalized linear model, efficient mixed model association (EMMA) and least angle regression plus empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model and fast multilocus random-SNP-effect EMMA methods had almost equal power of QTN detection in simulation experiments. However, only pLARmEB identified 48 previously reported genes for 7 flowering time-related traits in Arabidopsis thaliana.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.