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94 results for “Mendelian”
Supplemental material for "Statins, type 2 diabetes and body mass index: a univariable and multivariable Mendelian randomization study"
<p>Supplemental material for "Statins, type 2 diabetes and body mass index: a univariable and multivariable Mendelian randomization study" by Guoyi Yang and C Mary Schooling.</p>
Genetically predicted lipid traits, diabetes mellitus liability and carotid intima-media thickness in African ancestry individuals: a Mendelian randomization study
<p>Genetic variants used for the analysis of 'Genetically predicted lipid traits, diabetes mellitus liability and carotid intima-media thickness in African ancestry individuals: a Mendelian randomization study'.</p>
Potential drug targets for benign prostatic hyperplasia: A proteome-wide Mendelian randomization study
<p>Additional file 3</p>
The simulation dataset of GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
<p>The simulation dataset of GRIPT: a novel case-control analysis method for Mendelian disease gene discovery</p> <p>To uncompress the data:</p> <p>tar -xvf Simulation_data.tar.gz</p> <p>The meaning of the datasets:</p> <p>sim_X_Y.tar.gz means the simulation is generated with the maximum population frequency cutoff of X and the sample size of Y.</p> <p>sim_X_Y.tar.gz is generated based on the average allele frequency in population.</p> <p>sim_X_Y_AMR.tar.gz is generated based on the allele frequency in Latino population.</p> <p>sim_X_Y_500_Z.tar.gz is mixed of Latino population with a proportion of (500-Z)/500, and African population with a proportion of Z/500.</p> <p>The allele frequency is based on the ExAC database (Lek et al Nature 2016)</p> <p>Within each folder, there are case or control folders. The case folder contains the simulation spiked in the HGMD mutation of the given gene (i.e. RPE65 or TINF2) in the given percentage of individuals (e.g. 0.5%, 1%, 2%, 3%). The control folder contains the simulation without HGMD mutation spiked in.</p>
Investigating the Casual Associations among the Gut Microbiota, Metabolites, and Bladder Cancer: A Mediation Mendelian Randomization Study
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Data for: Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs
<p><span>Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and at minimum plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.</span></p>
Online Mendelian Inheritance in Man (OMIM): Comprehensive genetic disorder database for inherited phenotypes and genes
<p><strong>ABSTRACT: </strong></p> <p>Online Mendelian Inheritance in Man (OMIM) is a comprehensive and authoritative research resource that provides curated descriptions of human genes and phenotypes, along with their intricate relationships. I have compiled a dataset that specifically focuses on genes from the Online Mendelian Inheritance in Man database. The dataset includes the unique identifiers (MIM IDs) and names of these OMIM genes.</p> <p><strong>Instructions:</strong></p> <p>Dataset was downloaded and uploaded to excel to have unnecessary columns removed. Then dataset was imported to Jupyter Notebook and further cleaned of the nullified values and unrelated gene types such as phenotypes and etc. A new column with the respective links was added to make a total of 4 columns with one type: genes. Dataset was uploaded to the drg-depot cheaha.</p> <p><strong>Inspiration:</strong></p> <p>This dataset uploaded to U-BRITE for "DRG_DEPOT" summer 2023 team project.</p> <p><strong>Acknowledgements:</strong></p> <p>Joanna S. Amberger, Carol A. Bocchini, François Schiettecatte, Alan F. Scott, Ada Hamosh</p> <p><em>Nucleic Acids Research</em>, Volume 43, Issue D1, 28 January 2015, Pages D789–D798, DOI: <a href="https://doi.org/10.1093/nar/gku1205">https://doi.org/10.1093/nar/gku1205</a></p> <p><strong>OMIM Access to Gene Information:</strong> https://omim.org/search/advanced/entry</p> <p>U-BRITE Last Updated: July 5, 2023</p>
Association between plasma lipids and ischemic stroke: a multivariable and drug-target Mendelian randomization study
<p>The sensitivity analysis results using the leave-one-out approach revealed that no individual SNP substantially drove the association between plasma lipids and each disease outcome (Figure S1-S4).</p> <p> </p> <p>The STROBE-MR checklist is also attached.</p>
Genetics of Mendelian Forms of Young Onset Alzheimer Disease
ClinicalTrials.gov study NCT01622894. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Supplementary data to the paper: Causal association between serum thyroid-stimulating hormone and obesity: A bidirectional Mendelian randomization study
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Supplementary data for: Maternal testosterone and offspring birth weight: A Mendelian randomization study
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Data from: First evidence of deviation from Mendelian proportions in a conservation program
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Data from: Sleep, major depressive disorder and Alzheimer’s disease: a Mendelian randomisation study
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Data for: Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs
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Appendix: Association between hemostatic profile and migraine: a Mendelian randomization analysis
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Data from: Risky behaviors and Parkinson's disease: a Mendelian randomization study
Objective: To examine causal associations between risky behavior phenotypes on Parkinson's disease using a Mendelian randomization approach. Methods: We used two-sample Mendelian randomization to generate unconfounded estimates using summary statistics from two independent, large meta-analyses of genome-wide association studies on risk taking behaviors (n=370,771-939,908) and Parkinson's disease (cases: n=9581, controls: n = 33,245). We used inverse variance weighted as the main method for judging causality. Results: Our results support a strong protective association between the tendency to smoke and Parkinson's disease (OR=0.714 per log odds of ever smoking; 95% CI=0.568-0.897; p-value=0.0041; Cochran Q test; p-value=0.238; I2 index=6.3%). Furthermore, we observed risk association trends between automobile speed propensity as well as the number of sexual partners and Parkinson's disease after removal of overlapping loci with other risky traits (OR=1.986 for each standard deviation increase in normalized automobile speed propensity; 95% CI=1.215-3.243; p-value=0.0066, OR=1.635 for each standard deviation increase in number of sexual partners; 95% CI=1.165-2.293; p-value=0.0049). Conclusion: These findings provide support for a causal relationship between general risk tolerance and Parkinson's disease and may provide new insights in the pathogenic mechanisms leading to the development of Parkinson's disease.
Parathyroid hormone and bone mineral density: a Mendelian randomization study
<p><b>Purpose:</b> Accumulating evidence implicates parathyroid hormone (PTH) in the development of osteoporosis. However, the causal effect of PTH on bone mineral density (BMD) remains unclear. Thus, this study aimed at exploring the association between the concentrations of serum PTH and BMD.</p> <p><b>Methods:</b> The<b> </b>instrumental variables for PTH were selected from a large-scale genome-wide association study (GWAS) [n = 29,155]. Outcomes included BMD of forearm (FA) [n = 8143], femoral neck (FN) [n = 33,297], lumbar spine (LS) [n = 32,735], heel (HL) [n = 394,929] and risk of fractures in these bones (n = 361,194). Furthermore, the BMD of five different age groups; 15 or less [n = 11,807], 15-30 [4180], 30-45 [10,062], 45-60 [18,805] and 60 or more [22,504] were extracted from a GWAS meta-analysis study. The analyses were performed using the two-sample Mendelian randomization (MR) method.</p> <p><b>Results: </b>MR analysis revealed that the level of serum PTH were inversely associated with BMD of FA (95% CI: -0.763 to -0.016), FN (95% CI: -0.669 to -0.304) and LS (95% CI: -0.667 to -0.243). A causal relationship between serum PTH levels and BMD was observed in individuals aged 30-45 (95% CI: -0.888 to -0.166), 45-60 (95% CI: -0.758 to -0.232) and over 60 years (95% CI: -0.649 to -0.163).</p> <p><b>Main conclusions: </b>This study demonstrated that the concentrations of serum PTH is inversely associated with BMD of several bones. Further analysis revealed a site and age-specific correlations between serum PTH levels and BMD, which implies that the levels of serum PTH contribute to the development of osteoporosis.</p>
Data from: Relative effects of LDL-C on ischaemic stroke & coronary disease: a Mendelian randomization study
Objective: To examine the causal relevance of lifelong differences in LDL-C for ischaemic stroke (IS) relative to that for coronary heart disease (CHD) using a Mendelian randomization approach. Methods: We undertook a two-sample Mendelian randomization, based on summary data, to estimate the causal relevance of LDL-C for risk of IS and CHD. Information from 62 independent genetic variants with genome-wide significant effects on LDL-C levels was used to estimate the causal effects of LDL-C for IS and IS subtypes (based on 12,389 IS cases from METASTROKE) and for CHD (based on 60,801 cases from CARDIoGRAMplusC4D). We then assessed the effects of LDL-C on IS and CHD for heterogeneity. Results: A 1 mmol/L higher genetically-determined LDL-C was associated with a 50% higher risk of CHD (OR: 1.49, 95%CI: 1.32-1.68, p=1.1x10-8). By contrast, the causal effect of LDL-C was much weaker for IS (OR: 1.12, 95%CI: 0.96-1.30, p=0.14; p for heterogeneity=2.6x10-3) and, in particular, for cardioembolic stroke (OR: 1.06, 95%CI: 0.84-1.33, p=0.64; p for heterogeneity=8.6x10-3) when compared with that for CHD. Conclusions: In contrast with the consistent effects of LDL-C lowering therapies on IS and CHD, genetic variants that confer lifelong LDL-C differences show a weaker effect on IS than on CHD. The relevance of aetiologically distinct IS subtypes may contribute to the differences observed.
Data from: Resistance to a bacterial parasite in the Crustacean Daphnia magna shows Mendelian segregation with dominance
The influence of host and parasite genetic background on infection outcome is a topic of great interest because of its pertinence to theoretical issues in evolutionary biology. In the present study we use a classical genetics approach to examine the mode of inheritance of infection outcome in the crustacean Daphnia magna when exposed to the bacterial parasite Pasteuria ramosa. In contrast to previous studies in this system we use a clone of P. ramosa, not field isolates, which allows for a more definitive interpretation of results. We test parental, F1, F2, backcross and selfed parental clones (total 284 genotypes) for susceptibility against a clone of P. ramosa using 2 different methods, infection trials and the recently developed attachment-test. We find that D. magna clones reliably exhibit either complete resistance or complete susceptibility to P. ramosa clone C1 and that resistance is dominant and inherited in a pattern consistent with Mendelian segregation of a single-locus with two alleles. The finding of a single host locus controlling susceptibility to P. ramosa suggests that the previously observed genotype-genotype interactions in this system have a simple genetic basis. This has important implications for the outcome of host-parasite coevolution. Our results add to the growing body of evidence that resistance to parasites in invertebrates is mostly coded by one or few loci with dominance.
Data from: Antagonistic coevolution between quantitative and Mendelian traits
Coevolution is relentlessly creating and maintaining biodiversity, and therefore has been a central topic in evolutionary biology. Previous theoretical studies have mostly considered coevolution between genetically symmetric traits (i.e., coevolution between two continuous quantitative traits or two discrete Mendelian traits). However, recent empirical evidence indicates that coevolution can occur between genetically asymmetric traits (e.g., between quantitative and Mendelian traits). We examine consequences of antagonistic coevolution mediated by a quantitative predator trait and a Mendelian prey trait, such that predation is more intense with decreased phenotypic distance between their traits (phenotype matching). This antagonistic coevolution produces a complex pattern of bifurcations with bistability (initial state dependence) in a two-dimensional model for trait coevolution. Further, with eco-evolutionary dynamics (so that the trait evolution affects predator-prey population dynamics), we find that coevolution can cause rich dynamics including anti-phase cycles, in-phase cycles, chaotic dynamics, and deterministic predator extinction. Predator extinction is more likely to occur when the prey trait exhibits complete dominance rather than semidominance and when the predator trait evolves very rapidly. Our study illustrates how recognizing the genetic architectures of interacting ecological traits can be essential for understanding the population and evolutionary dynamics of coevolving species.
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Allen Brain Atlas
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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.