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215 results for “summary statistics”
Summary statistics from a genome-wide association study of narcolepsy
<p>Type 1 narcolepsy (T1N) is a neurological condition, in which the death of hypocretin-producing neurons in the lateral hypothalamus leads to excessive daytime sleepiness and symptoms of abnormal Rapid Eye Movement (REM) sleep. Known triggers for narcolepsy are influenza-A infection and associated immunization during the 2009 H1N1 influenza pandemic. Here, we genotyped all remaining consented narcolepsy cases worldwide and assembled this with the existing genotyped individuals. We used this multi-ethnic sample in genome wide association study (GWAS) to dissect disease mechanisms and interactions with environmental triggers (5,339 cases and 20,518 controls). Overall, we found significant associations with HLA (2 GWA significant subloci) and 11 other loci. Six of these other loci have been previously reported (<em>TRA</em>, <em>TRB</em>, <em>CTSH</em>, <em>IFNAR1</em>, <em>ZNF365</em> and <em>P2RY11</em>) and five are new (<em>PRF1</em>, <em>CD207</em>, <em>SIRPG</em>, <em>IL27</em> and <em>ZFAND2A</em>). Strikingly, in vaccination-related cases, GWA significant effects were found in <em>HLA</em>, <em>TRA</em>, and in a novel variant near <em>SIRPB1</em>. Furthermore, <em>IFNAR1</em>-associated polymorphisms regulated dendritic cell response to influenza-A infection in vitro (p-value =1.92*10<sup>-25</sup>). A partitioned heritability analysis indicated specific enrichment of functional elements active in cytotoxic and helper T cells. Furthermore, functional analysis showed the genetic variants in <em>TRA</em> and <em>TRB</em> loci act as remarkably strong chain usage QTLs for <em>TRAJ*24</em> (p-value = 0.0017), <em>TRAJ*28</em> (p-value = 1.36*10<sup>-10</sup>) and <em>TRBV*4-2</em> (p-value = 3.71*10-<sup>117</sup>). This was further validated in TCR sequencing of 60 narcolepsy cases and 60 DQB1*06:02 positive controls, where chain usage effects were further accentuated. Together these findings show that the autoimmune component in narcolepsy is defined by antigen presentation, mediated through specific T cell receptor chains, and modulated by influenza-A as a critical trigger.</p>
Additive summary statistics
<p>Provided are summary statistics for 27 traits using UK Biobank genotype and phenotype data. plink2.00 alpha is used to generate the summary statistics. </p>
Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes
<p>Data relevant to Wu et al. "Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes". </p>
NanoString autoimmune profiling panel normalized linear counts and summary of statistical analyses
<p>Occupational exposure to respirable crystalline silica (cSiO<sub>2</sub>) is linked to the development of lupus. Preclinical studies have revealed weekly repeated intranasal exposure to 1 mg cSiO<sub>2</sub> in young (8-11 wk-old) female NZBWF1 lupus-prone mice, a life-stage equivalent to 12–20-yr-old humans, triggers autoimmunity in the lungs and kidneys that is prevented by dietary supplementation with the omega-3 fatty acid docosahexaenoic acid (DHA).</p> <p><strong>Methods</strong>: Here, we characterized cSiO<sub>2</sub>'s and DHA's effects in mature adult (16–19-wk-old) female NZBWF1 mice, an age period that coincides with the onset of immunological tolerance breach and that is more representative of the age (>20-yr-old) of cSiO<sub>2</sub>-exposed workers. We fed mice either a control diet (CON) or diet amended with DHA calorically equivalent to a human daily dose of 5 g. After 2 wk, we intranasally instilled them with either saline vehicle (VEH) or 1 mg of cSiO<sub>2</sub> weekly for 4 wk. Cohorts were terminated 1 and 5 wk after the final installation. Lungs were then analyzed for inflammatory cell counts, chemokines, histopathology, B-and T-cell infiltration, autoantibody profile, and inflammatory/autoimmune gene signatures and results further related to autoimmune glomerulonephritis onset.</p> <p><strong>Results</strong>: VEH/CON mice displayed no lung or kidney pathology at either time point. In contrast, cSiO<sub>2</sub>/CON mice exhibited mild ectopic lymphoid tissue (ELT) formation in the lungs at 1 wk, which increased significantly by 5 wk. Lungs from cSiO<sub>2</sub>/CON mice also showed elevations in BALF cellularity, chemokine production, CD3 + T-cells, CD45R + B-cells, IgG + plasma cells, inflammatory/autoimmune gene expression, IgG autoantibodies. cSiO<sub>2</sub>/CON mice had visible glomerular hypertrophy and IgG deposition. Dietary DHA supplementation suppressed all these endpoints.</p> <p><strong>Discussion</strong>: Consistent with young mice, intranasal cSiO<sub>2</sub> exposure in mature adult NZBWF1 lupusprone mice elicited early pulmonary inflammation that served as a nexus for autoimmunity, suggesting these life-stage differences are not critical for cSiO2-triggered autoimmune response in this preclinical model. DHA supplementation at a translationally relevant human dosage effectively mitigated cSiO<sub>2</sub>-induced inflammation/autoimmunity in mature adult mice, resembling the protective effects observed in young mice. Together these findings further highlight the therapeutic potential of omega-3 fatty acids in mitigating toxicant-triggered autoimmune responses.</p>
Multivariate GWAS of Alzheimer's disease CSF biomarker profiles implies GRIN2D in synaptic functioning: Summary statistics
<p>Summary statistics for a genome-wide association study (GWAS) of Alzheimer's disease CSF biomarkers principal components (PCs). This dataset accompanies the publication "Multivariate GWAS of Alzheimer’s disease CSF biomarker profiles implies GRIN2D in synaptic functioning". The article is currently in press at Genome Medicine. A link will be provided upon publication, but see the medRxiv preprint in the meantime:</p> <p>Neumann, A., Ohlei, O., Küçükali, F., Bos, I. J., Vos, S., Prokopenko, D., ... & Kristel Sleegers & Lars Bertram. (2022). Multivariate GWAS of Alzheimer’s disease CSF biomarker profiles implies GRIN2D in synaptic functioning. <em>medRxiv</em>, 2022-08. https://doi.org/10.1101/2022.08.02.22278185</p> <p>A GWAS was performed for five different PC biomarkers.</p> <p>PC1: Tau pathology/degeneration</p> <p>PC2: Aβ Pathology</p> <p>PC3: Injury/inflammation</p> <p>PC4: Non-AD inflammation</p> <p>PC5: Non-AD synaptic functioning</p> <p>Each GWAS was performed in either males and females ("all"), in females only ("female"), or in males only ("male"). In addition, we also ran an interaction model with sex as moderator ("interaction"). Each file includes output of the meta-analysis between the EMIF-AD study and ADNI.</p> <p>The files contain following columns:</p> <p>CHROM: Chromosome</p> <p>POS: Position according to Build 37</p> <p>ID: Chromosome:Position</p> <p>A1: Effect allele</p> <p>A2: Other allele</p> <p>BETA: Effect of one copy of the effect allele on biomarker PCs in SD. In case of sex interaction, the effect specific to females.</p> <p>SE: Standard Error</p> <p>P: p-value</p> <p>D: Direction in ADNI and EMIF-AD respectively</p> <p>Het: Heterogeneity statistics (I<sup>2</sup>, and corresponding χ<sup>2</sup>, degrees of freedom and p-value)</p>
Data from: tableone: An open source Python package for producing summary statistics for research papers
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NanoString autoimmune profiling panel normalized linear counts and summary of statistical analyses
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Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis
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The summary statistics of GWAS for individual deviations of total GMV
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Summary statistics from a genome-wide association study of narcolepsy
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Expository and narrative discourse summary statistics and demographic information for adolescents with and without traumatic brain injury
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Publicly available GWAS summary statistics, harmonized and imputed to GTEx v8' variant reference
<p># harmonized and imputed GWAS summary statistics</p> <p> </p> <p>* `harmonized_imputed_gwas.tar` contains 114 publicly available GWAS traits, harmonized and imputed to GTEx v8 reference</p> <p> </p> <p>* `gwas_metadata.txt` is a table with useful information about each trait, such as:</p> <p>- Tag: trait name (also in the file name)</p> <p>- PUBMED_Paper_Link: PUBMED or publication URL (if available)</p> <p>- Portal: URL to web portal from which data was downloaded</p> <p>- Consortium: GWAS Consortium authoring the data</p> <p>- Sample_Size: number of individuals covered in the study</p> <p>- Population: individuals'ancestry (EUR, EAS, etc)</p> <p>- abbreviation: short name used for figures</p> <p>- new_abbreviation: alternative name for additional figures</p> <p>- Deflation: whether imputed summary statistics exhibited deflation (i.e. association p-values are lower than expected by chance. The summary statistics imputation method is conservative, and in public GWAS with few observed variants (<2M), the distribution of p-values lags towards lower significance spectrums.</p> <p># Data usage policy</p> <p>When using this data, you must acknowledge the source by citing the publication "Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits" (https://doi.org/10.1101/814350).</p> <p># Disclaimer</p> <p>The data is provided "as is", and the authors assume no responsibility for errors or omissions. <br> The User assumes the entire risk associated with its use of these data. <br> The authors shall not be held liable for any use or misuse of the data described and/or contained herein. <br> The User bears all responsibility in determining whether these data are fit for the User's intended use. </p> <p>The information contained in these data is not better than the original sources from which they were derived,<br> and both scale and accuracy may vary across the data set. <br> These data may not have the accuracy, resolution, completeness, timeliness, or other characteristics<br> appropriate for applications that potential users of the data may contemplate. <br> <br> The user is responsible to comply with any data usage policy from the original GWAS studies;<br> refer to the list of traits described [here](https://www.biorxiv.org/content/10.1101/814350v1)<br> to identify their respective Consortia's requirements.</p> <p><br> THE DATA IS PROVIDED WITHOUT WARRANTY OF ANY KIND,<br> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,<br> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.<br> IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,<br> WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,<br> OUT OF OR IN CONNECTION WITH THE DATA OR THE USE OR OTHER DEALINGS IN THE DATA.</p>
Full summary statistics of mixQTL for GTEx v8 Minor_Salivary_Gland
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Colon_Sigmoid
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Artery_Coronary
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Brain_Anterior_cingulate_cortex_BA24
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Brain_Cortex
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Brain_Hippocampus
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Brain_Nucleus_accumbens_basal_ganglia
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Full summary statistics of mixQTL for GTEx v8 Heart_Atrial_Appendage
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
ScienceDex guides
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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.