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opencc-by-4.0Apr 2024View details →

GWAS summary stats in "Genome-wide association meta-analysis identifies two novel loci associated with dental caries."

Summary stats of the genome-wide meta-analysis for dental caries and periodontal diseases in our study (population A and B). Article "Genome-wide association meta-analysis identifies two novel loci associated with dental caries." https://doi.org/10.1186/s12903-024-04799-1

opencc-by-4.0Nov 2024View details →

GWAS Summary Statistics for Publication: Identifying novel genetic and phenotypic associations to genomic features by leveraging off-target reads in exome sequencing data

This dataset contains summary statistics for genome-wide association studies (GWAS) conducted on genomic features derived from off-target reads in whole-exome sequencing (WES) data. The study utilized tools like Seeing Beyond the Target (SBT) and ImReP to construct novel phenotypic features from unmapped reads in ~50,000 participants in the UK Biobank. Features include mitochondrial DNA (mtDNA) copy number, ribosomal DNA (rDNA) copy number (5S, 18S, 28S), immune repertoire metrics (e.g., T-cell receptor alpha diversity), and microvial genome load (viral and fungal). Summary statistics can be used for replication studies, meta-analyses, or further exploration of these phenotypes.

opencc-by-4.0Dec 2021View details →

Genome-wide association analyses identify novel Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility

The Brugada syndrome GWAS summary statistics Brugada syndrome is a cardiac arrhythmia disorder associated with sudden death in young adults. With the exception of SCN5A, encoding the cardiac sodium channel NaV1.5, susceptibility genes remain largely unknown. We performed a genome-wide association meta-analysis comprising 2,820 unrelated cases with Brugada syndrome and 10,001 controls.

opencc-by-4.0Mar 2022View details →

Deciphering the Neurosensory Olfactory Pathway and Associated Neo-Immunometabolic Vulnerabilities Implicated in COVID-Associated Mucormycosis (CAM) and COVID-19 in a Diabetes Backdrop—A Novel Perspective

Raw data files of transcriptomic profiling experiments, which form the basis for our publication (https://www.mdpi.com/2673-4540/3/1/13).

opencc-by-4.0Dec 2018View details →

Data for: Bivariate Genome-Wide Association Scan Identifies 6 Novel Loci Associated With Lipid Levels and Coronary Artery Disease.

Summary of Bivariate GWAS scan results reported in: <a href="https://pubmed.ncbi.nlm.nih.gov/30525989/">Bivariate Genome-Wide Association Scan Identifies 6 Novel Loci Associated With Lipid Levels and Coronary Artery Disease. </a>Siewert KM, Voight BF. Circ Genom Precis Med. 2018 Dec;11(12):e002239. doi: 10.1161/CIRCGEN.118.002239. PMID: 30525989

opencc-by-4.0Sep 2018View details →

Genome-wide association meta-analysis of 30,000 samples identifies seven novel loci for quantitative ECG traits

Introduction These are the Summary Level-data as presented in: "Genome-wide association meta-analysis of 30,000 samples identifies seven novel loci for quantitative ECG traits". Eur J Hum Genet. 2019 Jan 24. doi: 10.1038/s41431-018-0295-z. [Epub ahead of print] If you use these data please cite the corresponding manuscript, which can be downloaded here: <a href="http://em.rdcu.be/wf/click?upn=lMZy1lernSJ7apc5DgYM8eFz0euOx0-2B13Abimi4Sb0A-3D_2NNavOiAD9A7CPFnsa04dGla3sU002fLfkDtL-2FhGlad0GuoM-2B3OlDb0C5GiEhwIvtH7ba4KKF45ipTOFodx6CqvVvoP2GQ992sPGoV9ZPWIe04tUd8-2BGWey0In0TXPII5zK-2Bfp8Wk9TpEqEcSd-2BEmywqZc8o5TW4xGPXZqmchfUH8chy3P4SEtpzHXMG1LwsIYrKfwegqTXG85RAJPr-2B21Tk9SobtpvFs0frMkJ4ekKsl33ryoZfFPk1byjQunJYn4-2BB0iqMgGs6cXv0AOgAxg-3D-3D">https://rdcu.be/bh8mu</a>. When you have any questions or comments regarding this study or these files, please contact me via: Jessica van Setten, PhD | Department of Cardiology, University Medical Center Utrecht, Utrecht University | j.vansetten [at] umcutrecht [dot] nl   Files and description There are four files available: <ol> <li>RR_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for RR interval</li> <li>PR_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for PR interval</li> <li>QT_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for QT interval</li> <li>QRS_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for QRS duration</li> </ol> All these files have the same lay-out and are gzipped. The reference used for meta-analysis of GWAS was Genome of the Netherlands v4.  <ul> <li>SNP - variantID (rsID), please note that few hundred variants do not have an rsID, but are NA instead. These can still be identified by chromosome and position.</li> <li>CHR - chromosome numbers [1-22 and X].</li> <li>POS - base pair position, hg19 / build37.</li> <li>CODED_ALLELE - coded allele, i.e. the effect allele, as represented (and harmonized) across cohorts. Note that this is not necessarily the minor allele.</li> <li>NON_CODED_ALLELE - the other allele, i.e. the non-effect allele.</li> <li>CODED_ALLELE_FREQ - coded allele frequency, i.e. the effect allele frequency. Note that this is not necessarily the minor allele frequency.</li> <li>BETA - beta from the fixed-effects model.</li> <li>SE - standard error from the fixed-effects model.</li> <li>P - P-value from the fixed-effects model.</li> <li>NEAREST_GENE - the gene closest to the respective variant.</li> </ul>

opencc-by-4.0Nov 2018View details →

Association mapping identified novel candidate loci affecting wood formation in Norway spruce

Data sets associated with the study for the Association mapping and identification of novel candidate loci affecting wood formation in Norway spruce

opencc-by-4.0Sep 2019View details →

Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

130 Lotus japonicus accessions were used. The names and accession numbers are listed in S6 Table. Seeds were scarified with sandpaper and then sterilized 14 minutes in 0.05% sodium hypochlorite. Subsequently, seeds were rinsed and washed 5 times in sterile distilled water. For the germination, seeds were positioned in imbibed filter paper, in sterile Petri dishes, and wrapped in aluminium foil. After 3 days at 21°C, young seedling were transferred to square plates (12 x 12 cm) containing growth medium. Both media used in this study were based on Long-Ashton solution (with two levels of phosphate concentration -20 or 750 μM, LP or HP, respectively) with 0.8% MES buffer (Duchefa Biochemie, Haarlem, The Netherlands), 0.8% agarose (to minimize phosphate contamination), and adjusted to pH 5.7 with 1M KOH. After adding the medium, plates were dried, closed, overnight in a sterile laminar flow hood. Two accessions, with four replicates per each accession, were placed on each plate. Each plate was replicated, with mirrored position of each accession to minimize any positional growth effects. Plates were placed vertically, and plants grown under long-day conditions (21°C, 16 h light/8 h dark cycle) with white light bulbs emitting 50 μmol/m 2 /s and roots were exposed to light. Every day at the same time, the racks were transported to the image acquisition room where images of each plate were acquired with eight Epson V600 CCD flatbed color image scanners (Seiko Epson) and then immediately returned to the growth chamber.

opencc-by-4.0Feb 2023View details →

datset related to article "THE NOVEL I213S MUTATION IN PSEN1 GENE IS LOCATED IN A HOTSPOT CODON ASSOCIATED WITH FAMILIAL EARLY-ONSET ALZHEIMER'S DISEASE"

Electropherogram of the proband psen1 exon 7 ngs analysis of causal and risk genes associated to dementia

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Data from: Non-additive association analysis using proxy phenotypes identifies novel cattle sydromes

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publicMar 2021View details →

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Novel major loci shape habitat-associated flowering time variation in Yellowstone monkeyflowers

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publicDec 2025View details →

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Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism

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publicOct 2020View details →

opencc-zeroJul 2020View details →

Experimental infection of bumble bees with honey bee associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts

Pathogen spill-over represents an important cause of biodiversity decline. For wild bee species such as bumble bees, many of which are in decline, correlational data point toward viral spill-over from naged honey bees as a potential cause. Yet impacts of honey bee viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well characterised viral inocula, we show that three viral types isolated from honey bees (Deformed wing virus genotype A, Deformed wing virus genotype B and Black queen cell virus) readily replicate within hosts of the bumble bee Bombus terrestris. Impacts of these honey bee-derived viruses – either injected or fed – on the mortality of B. terrestris workers were, however, negligible and likely dependent on host condition. Our results highlight the potential threat of viral spill-over from honey bees to novel wild bee species, though they also underscore the importance of additional studies on this and other non- bee species under field-realistic conditions to evaluate whether pathogen spill-over has a negative impact on wild bee individuals and population fitness.

opencc-zeroAug 2020View details →

Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function

Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3.

opencc-zeroNov 2020View details →

Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology

Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in TMEM106B (p-value < 5´10-8, rs1990620G) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together, our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.

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Data associated with: Recording animal-view videos of the natural world using a novel camera system and software package

Data associated with Vasas V, Lowell MC*, Villa J*, Jamison QD*, Siegle AG*, Katta PVR*, Bhagavathula P*, Kevan PG, Fulton D, Losin N, Kepplinger D, Salehian S, Forkner RE, Hanley D (2023) Recording animal-view videos of the natural world using a novel camera system and software package. PLoS Biology. DOI: 10.1371/journal.pbio.3002444

opencc-by-4.0Nov 2023View details →

opencc-zeroMar 2024View details →

Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.

opencc-zeroJan 2022View details →

Post-association barrier to host switching maintained despite strong selection in a novel mutualism

Following a host shift, repeated co-passaging of a mutualistic pair is expected to increase fitness over time in one or both species. Without adaptation, a novel association may be evolutionarily short-lived as it is likely to be outcompeted by native pairings. Here we test whether experimental evolution can rescue a low-fitness novel pairing between two sympatric species of Steinernema nematodes and their symbiotic Xenorhabdus bacteria. Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations. We selected the most productive infections, co-passaging this novel mutualism nine times to determine whether selection could improve fitness of either or both partners. We found that neither partner showed increased fitness over time. Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift. Thus, post-association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists.