Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
606
datasets available to search
ShareScore release 0.9.0
Dataset results
606 results for “association genetics”
Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia
<p class="MsoNormal"><span>These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of pre-eclampsia(PE). This study conducted a case-control study involving 327 PE patients and 591 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of PE.This study collected clinical samples and data, and used logistic regression, false positive report rate, multi factor dimension reduction, functional analysis and other analysis methods to process the research data. </span>Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of PE were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs).<span> Finally,it showed that the rs2106809 A>Gis significantly associated with the risk of PE via individual locus effects and/or complex gene-gene and gene-environment interactions.</span><span> </span></p>
Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure
<p>Genome-wide association study summary statistics.</p>
Data from: Genetic variation in growth and leaf traits associated with local adaptation to climate in yellow birch (Betula alleghaniensis Britton)
<p>Understanding patterns of variation in functional traits of hardwood trees is crucial for conserving and managing North American temperate forests under climate change. This study examined provenance variation of yellow birch (<em>Betula alleghaniensis</em> Britton) in growth, biomass allocation, leaf morphology, and stable carbon isotope composition. Trees were grown from ten seed sources originating from across Canada and the northern USA. Height and diameter were not significantly related to climate at seed origin, suggesting that variation may be better explained by site factors, such as soil pH and soil moisture. In contrast, carbon isotope composition and leaf morphological traits were significantly correlated to climate variables including temperature, precipitation, and solar radiation. Provenances from warmer, drier localities tended to have higher stable carbon isotope ratio (δ<sup>13</sup>C), greater specific leaf area, and narrower leaf width than their counterparts from cooler, wetter climates. Thus, variation in leaf morphological traits appears to be involved in adaptation of yellow birch to variation in temperature and moisture availability across the species' range. Our results suggest that there may exist potential for selection and breeding of drought resistant yellow birch genotypes to aid in reforestation under climate change. </p>
Comprehensive clinical and genetic analyses of circulating bile acids and their associations with diabetes and its indices
<p>Files containing source data for "Comprehensive clinical and genetic analyses of circulating bile acids and their associations with diabetes and its indices," by Choucair et al., published in <em>Diabetes</em>.</p>
Identification of genetic variants associated with clinical features of sickle cell disease
Open the record for dataset details and reuse information.
Identifying genetic variants associated with chromatin looping and genome function
<p><span>Here<span> we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of HiChIP contacts defining loops between active regulatory regions (iQTLs). We observe a substantial overlap between iQTLs and previously defined eQTLs and histone QTLs, and an enrichment for fine-mapped QTLs and GWAS variants. Furthermore, we describe a distinct subset of nCD4 iQTLs, for which the significant variation of chromatin contacts in nCD4 are translated into significant eQTL trends in CD4 T cell memory subsets. Finally, we define connectivity-QTLs as iQTLs that are significantly associated with concordant genotype-dependent changes in chromatin contacts over a broad genomic region (e.g., GWAS SNP in the <em>RNASET2</em> locus). Our results demonstrate the importance of chromatin contacts as a complementary modality for QTL mapping and their power in identifying novel classes of QTLs linked to cell-specific gene expression and connectivity.</span></span></p> <p> </p> <p><span><span>This repository contains the source code, supplementary datasets for the manuscript (Nature Communications 2024).</span></span></p>
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (GWAS)
<p>GWAS summary statistics accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals".</p>
A 4,302-patient cohort study of association of rare genetic alterations with endocrine disorders
<p><span>Endocrine pathologies including disorders such as diabetes and dysfunctions of endocrine glands, are frequently associated with genetic predisposition. This study investigated the association of endocrine diseases with genetic variants, copy number variations (CNVs), and mutational load of molecular pathways in 4302 patients with 409 ICD-10 diagnoses who underwent DNA testing using next-generation sequencing at the National Medical Research Center for Endocrinology (Moscow) from November 2017 </span><span>till</span><span> January 2024. We analyzed rare protein-altering genetic variants using three control cohorts (gnomAD3, RUSeq healthy, experimental).<span> </span>We identified 143 associated variants for diabetes mellitus and 188 genetic variants across other 18 different ICD-10 groups of diagnoses, including 25% and 30% of previously undescribed variants, respectively. In addition, we investigated the aggregation of genetic variants across individual genes and their functional ensembles (molecular pathways) and identified 105 and 101 associations with ICD-10 diagnoses, respectively. In addition, we identified 35 pathogenic and 91 likely pathogenic CNVs in 925 patients with whole exome sequencing profiles. Among them, 9 and 44 CNVs, respectively, were not previously described. Totally, we found statistically significant associations between CNVs and endocrine pathologies for 168 genes. These results expand our understanding of endocrine disease mechanisms and may indicate new potential therapeutic targets.</span></p>
Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.
<p>The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.</p>
Data from: The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighboring nests
<p>The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behavior. Conversely, genetic structure can determine where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (<i>Polyergus mexicanus</i>), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighboring parasitic ant nests at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between nests. However, 35% of nests had a closely related neighboring nest, indicating that kinship could potentially affect the nature of some interactions between nests of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.</p>
Genetic disruption of synthesis pathways of Arabidopsis secondary metabolites dramatically affects root-associated nematode populations directly and via modulation of microbial communities
<p>Dataset of nematode, fungal and bacterial sequence reads of Arabidopsis roots. Dataset of fungal and bacterial sequence reads of Arabidopsis microbial suspension. DNA concentration of Arabidopsis root microbial suspension. Meloidogyne incognita J2 invasion into tomato roots. qPCR dataset of Meloidogyne hapla infection pressure into Arabidopsis roots. </p>
Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish
<p>Sociality is often seen as a single phenotypic trait, but it relies on motivational and cognitive components implemented by specific causal mechanisms. Hence, these components may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general domain across social and non-social contexts. Here we have characterized the phenotypic architecture of sociality in zebrafish, which has been increasingly used as a model organism in social neuroscience. For this purpose, we have behaviorally phenotyped zebrafish from different wild type lines in four tests: social tendency, social and non-social recognition, and open-field test. Our results indicate that: (1) sociality has two main components that are independent from each other (social tendency and social recognition), hence not supporting the occurrence of a sociality syndrome; (2) both social traits are phenotypically linked to non-social traits (non-social exploration and non-social memory, respectively), forming two general behavioral modules, general inspection and general recognition, and suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between genetic polymorphisms (i.e. single nucleotide polymorphisms, SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the general inspection (motivational), but not with a general recognition (cognitive), behavioral module. The SNPs associated with general inspection are widespread across different chromosomes and include neurotransmitters, neuromodulators, and synaptic plasticity genes, suggesting that this behavioral module is regulated by multiple genes, each of them with small effects. Together, these results support the occurrence of general domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.</p>
Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
<p>A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiont <em>Sinorhizobium meliloti</em> paired with two genotypes of the host <em>Medicago truncatula</em> in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype – partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments.</p> <p><span>IMPORTANCE:</span><strong> </strong>Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.</p>
Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat
<p>The study material in the GWAS panel with 193 bread wheat genotypes from Indian and exotic collections was selected to map the genomic regions responsible for grain iron and Zinc content under drought and heat stress treatments.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR), Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on Grain Iron and Grain zinc content along with thousand-grain weight. Around 20 g of grain sample from each of 282 genotypes from the GWAS panel under all three conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >10%, and heterozygote frequency >50% were removed from the analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS analysis.</p>
Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
<p><span>Mungbean (<em>Vigna radiata</em> (L) Wizcek) is an important pulse crop, increasingly used as a source of protein, fiber, low fat, carbohydrates, minerals, and bioactive compounds in human diets. Mungbean is a dicot plant with trifoliate leaves. Leaves are central to various plant processes like photosynthesis, light interception, and overall canopy structure. The objectives were to study leaf morphological traits, use image analysis to extract leaf traits from images from the Iowa Mungbean Diversity (IMD) panel, develop a regression model for the prediction of leaflet area, and conduct association mapping for leaf morphological traits. We collected more than 5000 leaf images of the IMD panel consisting of 484 accessions over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet's area (adjusted R<sup>2</sup> = 0.97; residual standard errors of <= 1.10). The candidate genes <em>Vradi01g07560</em>, <em>Vradi05g01240</em>, <em>Vradi02g05730</em>, and <em>Vradi03g00440</em>, are associated with multiple traits (length, width, perimeter, and area) across the leaflets (left, terminal, and right). These are suitable candidate genes for further investigation in their role in leaf development, growth, and function. Future studies will be needed to correlate the observed traits discussed here with yield or important agronomic traits for use as phenotypic or genotypic markers in marker-aided selection methods for mungbean crop improvement.</span></p>
Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies
<p>Resource specialization and host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the general rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary time scales. We applied genome-wide SNP data obtained through low-coverage genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies collected from seven shared willow (<em>Salix</em>) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their <em>Salix</em> hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species than are most bud gallers. In contrast to bud gallers, leaf gallers also exhibit statistically significant cophylogenetic signal with their <em>Salix</em> hosts. The observed discordant patterns of resource specialization and long-term host use in two related galler groups that have radiated in parallel across a shared resource base indicate a general lack of evolutionary repeatability and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.</p>
Genetic variation in sexual size dimorphism is associated with variation in sex-specific plasticity in Drosophila
<p><span>The difference in body size between females and males, or sexual size dimorphism (SSD), is ubiquitous, and yet we have a poor understanding of the developmental-genetic mechanisms that generate it, and how these mechanisms may vary within and among species. Such an understanding of the genetic architecture of SSD is important if we are to evaluate alternative models of SSD evolution, but is difficult to describe because SSD is a characteristic of populations, not individuals. Here, we overcome this challenge by using isogenic lineages of <em>Drosophila</em> to measure SSD for 196 genotypes. We demonstrate extensive genetic variation for SSD, primarily driven by higher levels of genetic variation for body size among females than males. While we observe a general increase in SSD with sex-averaged body size (pooling for sex) among lineages, the vast majority of variation in SSD is independent of sex-averaged body size, and shows a strong genetic correlation with sex-specific plasticity, such that increased female-biased SSD is associated with increased body-size plasticity in females. Our data are consistent with the condition-dependence hypothesis of sexual dimorphism, and suggest that SSD in <em>Drosophila</em> is a consequence of selection on the developmental-genetic mechanisms that regulate the plasticity of body size. </span></p>
Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations
<p>Individual heterozygosity may influence the expression of fitness-related traits, via genome-wide or local genetic effects. Earlier studies have shown negative relationships between heterozygosity and sperm variation, predominantly in captive, highly inbred populations. Little is known about the possible influence of variation in heterozygosity on sperm traits in wild, outbred populations. We studied two populations of the bluethroat, one from the widely distributed northern subspecies (<em>Luscinia</em>. <em>s</em>. <em>svecica</em>) and the other from the smaller, more patchily distributed subspecies breeding along the French coast of Brittany (<em>L. s. namnetum</em>). The two subspecies differed significantly in body size, plumage colour, sperm traits and the degree of genetic diversity. However, there was no evidence that sperm traits (total length and motility) were influenced by the degree of heterozygosity at the individual level. In contrast, we found that male body size was positively related to heterozygosity across both populations, indicating a possible relationship between overall genetic diversity and general vigour or ability to obtain food. We conclude that sperm traits are unrelated to levels of heterozygosity in the studied outbred and weakly genetically depauperate bluethroat populations.</p>
Data from: Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund
<p class="MsoNormal"><span>A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of <em>Streptococcus bovis/Streptococcus equinus </em>complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living on a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.</span></p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
ScienceDex guides
Understand access before you commit
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.