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505 results for “genome-wide association”
A novel genome-wide association approach reveals wheat pathogen genes involved in host specialization
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Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green plant lineage
<p>Gene alignments and trees</p>
Code for manuscript A genome-wide association study of neonatal metabolites
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Structural equation models to interpret genome-wide association studies for morphological and productive traits in soybean [Glycine max (L.)]
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Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle
<p><b>Background</b></p> <p>White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date.</p> <p><b>Results</b></p> <p>Using imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2,973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes <i>KIT</i> and <i>MITF</i> as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the <i>PAX3</i> gene, which encodes a known transcription factor that controls <i>MITF </i>expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in <i>PAX3</i> (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of <i>MITF</i> transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving <i>KIT </i>and/or other genes in this region.</p> <p><b>Conclusions</b></p> <p>Our findings extend those of previous studies that reported <i>KIT</i> as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the <i>MITF</i> and <i>PAX3</i> genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.</p>
Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size measurements in the GIANT Consortium meta-analysis. Here we repeat the analyses in the UK Biobank, a much more homogeneously designed study. We show that polygenic adaptation signals based on large numbers of SNPs below genome-wide significance are extremely sensitive to biases due to uncorrected population structure. More generally, our results imply that typical constructions of polygenic scores are sensitive to population structure and that population-level differences should be interpreted with caution.
Association of SUMOlation pathway genes with stroke in a genome-wide association study in India
<p><strong>Objective:</strong> To undertake a genome-wide association study (GWAS) to identify genetic variants for stroke in Indians.</p> <p><strong>Methods:</strong> In a hospital-based case-control study, eight teaching hospitals in India recruited 4,088 subjects, including 1,609 stroke cases. Imputed genetic variants were tested for association with stroke subtypes using both single-marker and gene-based tests. Association with vascular risk factors was performed using logistic regression. Various databases were searched for replication, functional annotation, and association with related traits. Status of candidate genes previously reported in the Indian population was also checked.</p> <p><strong>Results:</strong> Association of vascular risk factors with stroke were similar to previous reports, and show modifiable risk factors like hypertension, smoking, and alcohol consumption having the highest effect. Single-marker based association revealed two loci for cardioembolic stroke (1p21 and 16q24), two for small vessel disease stroke (3p26 and 16p13), and four for hemorrhagic stroke (3q24, 5q33, 6q13, and 19q13) at P<5×10-8. The index SNP of 1p21 is an eQTL (Plowest=1.74×10-58) for RWDD3 involved in SUMOlation and is associated with platelet distribution width (1.15×10-9) and 18-carbon fatty acid metabolism (P=7.36×10-12). In gene-based analysis we identified three genes (SLC17A2, FAM73A & OR52L1) at P<2.7×10-6. 11 of 32 candidate gene loci studied in Indians replicated (P<0.05), and 21 of 32 loci identified through previous GWAS replicated based on directionality of effect.</p> <p><strong>Conclusions:</strong> This first GWAS of stroke in Indians identified novel loci and replicated previously known loci. For the first time, genetic variants in the SUMOlation pathway which has been implicated in brain ischemia were identified.</p>
Data from: Molecular insights into genome-wide association studies of chronic kidney disease-defining traits
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Data from: Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data
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Data from: Genome-wide association reveals the locus responsible for four-horned ruminant
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Data from: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
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Data from: Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice
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Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity
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Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition
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Data from: The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing
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Data from: Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)
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Data from: Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols
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Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies
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Data from: Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture
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Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.