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opencc-by-4.0Sep 2022View details →

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)

This vcf file constitute underlying raw data material for the manuscript "Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)".  The SNP genotype data came from a whole-genome resequencing and were called using the Nipponbare IRGSP 1.0 rice reference genome. SNPs with a miss rate greater than 30% and minor allele frequency (MAF) less than 5% were removed. Heterozygous alleles were also excluded. Finally, 160,498 SNPs were selected and used in the GWAS analysis.

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

opencc-zeroMay 2024View details →

Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.

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-4.0Sep 2019View details →

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions" Multiple sclerosis (MS) is the most common neurological disorder in young adults. Despite extensive studies, only a fraction of MS heritability has been explained, with association studies focusing primarily on protein-coding genes, essentially for the difficulty of interpreting non-coding features. However, non-coding RNAs (ncRNAs) and functional elements, such as super-enhancers (SE), are crucial regulators of many pathways and cellular mechanisms, and they have been implicated in a growing number of diseases. In this work, we searched for possible enrichments in non-coding elements at MS genome-wide associated loci, with the aim to highlight their possible involvement in the susceptibility to the disease. We first reconstructed the linkage disequilibrium (LD) structure of the Italian population using data of 727,478 single-nucleotide polymorphisms (SNPs) from 1,668 healthy individuals. The genomic coordinates of the obtained LD blocks were intersected with those of the top hits identified in previously published MS genome-wide association studies (GWAS). By a bootstrapping approach, we hence demonstrated a striking enrichment of non-coding elements, especially of circular RNAs (circRNAs) mapping in the 73 LD blocks harboring MS-associated SNPs. In particular, we found a total of 482 circRNAs (annotated in publicly available databases) vs. a mean of 194 ± 65 in the random sets of LD blocks, using 1,000 iterations. As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP. Finally, by evaluating RNA-seq data of two cell lines, SH-SY5Y and Jurkat cells, representing tissues relevant for MS, we identified 18 (two novel) circRNAs derived from MS-associated genes. In conclusion, this work showed for the first time that MS-GWAS top hits map in LD blocks enriched in circRNAs, suggesting circRNAs as possible novel contributors to the disease pathogenesis. GEO database URL: <a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a> Numero di accesso del dataset: GSE110525

opencc-by-4.0Oct 2022View details →

Online Supplemental Tables - An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index

Summary statistics of metabolite-gene expression associations and mediation analyses of effects on body mass index. The corresponding publication is currently under revision. <ul> <li>Online Supplemental Table 1: Gene expression-metabolite association summary statistics from 97 metabolites and metabolite ratios and up to 15175 genes calculated seperately in the LIFE-Adult, LIFE-Heart, LIFE-AMI and the Sorb studies. Associations were adjusted for six covariates.</li> <li>Online Supplemental Table 2: Random-effects meta-analyzed gene expression-metabolite association summary statistics. P-Values were adjusted for multiple testing using a hierarchical adjustment procedure both on local (within phenotypes) and on global (across phenotypes) level.</li> <li>Online Supplemental Table 3: Single-study association results needed for checking mediation analysis assumptions and for calculating mediation statistics. Only gene expression probe-metabolite pairs that associated significantly at hierarchical FDR=5% in the gene-expression-metabolite association meta-analysis qualified for these associations.The following Associations were tested: gene expression probes ~ metabolites, log-BMI ~ metabolites log-BMI ~ gene expression, log-BMI ~ gene expression + metabolite. Associations were adjusted for six covariates. P-values</li> <li>Online Supplemental Table 4: Meta-analyzed association results needed for checking mediation analysis assumptions and for calculation mediation statistics.</li> <li>Online Supplemental Table 5: Mediation analysis summary statistics. Mediations of gene expression effects (exposure) via metabolite effects (mediatior) and of metabolite effects (exposure) via gene expression effects (mediator) on body mass index (outcome) were tested.</li> </ul>

opencc-by-4.0Nov 2022View details →

Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow

Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform clade. H. numata is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics. Butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages. We show that H. numata populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of a supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

opencc-by-4.0Nov 2022View details →

Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)

Initial filtered ddRADseq dataset with highly variable SNP markers from native American and Hungarian Robinia pseudoacacia L. individuals

opencc-by-4.0Dec 2022View details →

Multivariate Genome-wide association summary statistics for shared aging factor

This dataset contains genome-wide summary statistics (autosomal variants) computed from a multivariate genome-wide association study of five aging-related phenotypes using Genomic Structural Equation Modeling (https://github.com/GenomicSEM/GenomicSEM).  The effective sample size is calculated to be 1,958,774.  Column descriptions are included in the accompanying README file.   The summary statistics are provided on an "AS-IS" basis, without any type of warranty, expressed or implied, including but not limited to any warranty as to their performance, merchantability, or fitness for any particular purpose. If investigators use these data, any and all consequences are entirely their responsibility.  The user agrees that to cite the appropriate publication in any communications or publications arising directly or indirectly from these data by downloading and and using these data,.  The user also agrees to respect the requested responsibilities of resource users under 2003 Fort Lauderdale principles and also agree that they will never attempt to identify any participant.

opencc-zeroAug 2023View details →

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana

<div> <div>Plant life-history traits, such as size and flowering, contribute to shaping variation in herbivore abundance. Although plant genes involved in physical and chemical traits have been well studied, less is known about the loci linking plant life-history traits and herbivore abundance. Here, we conducted a genome-wide association study (GWAS) of aphid abundance in a field population of Arabidopsis thaliana. This GWAS of aphid abundance detected a relatively rare but significant variant on the third chromosome of A. thaliana, which was also suggestively but non-significantly associated with the presence or absence of inflorescence. Out of candidate genes near this significant variant, a mutant of a ribosomal gene (AT3G13882) exhibited slower growth and later flowering than a wild type under laboratory conditions. A no-choice assay with the turnip aphid, Lipaphis erysimi, found that aphids were unable to successfully establish on the mutant. Our genome-wide association study of aphid abundance unexpectedly found a locus affecting plant growth and flowering.</div> </div>

opencc-by-4.0Jun 2023View details →

Associated Dataset for Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

The dataset contains the final methylation call set (n=14,627,533), variant calling file for population genomics analyses, analysis codes/scripts, and other associated files related to the research (Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble bee Bombus vosnesenskii). Raw WGBS reads generated in this study have been deposited and are currently available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under NCBI BioProject PRJNA956115.

publicMay 2024View details →

Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

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publicFeb 2022View details →

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

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publicAug 2023View details →

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana

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zenodo36/100

Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis: Summary stats

Summary stats of the genome-wide meta-analysis with METAL software in the article "Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis."

opencc-by-4.0Dec 2019View details →

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.

opencc-zeroSep 2021View details →

Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

Type 2 diabetes (T2D) is a global public health challenge. Whilst the advent of genome-wide association studies has identified >400 genetic variants associated with T2D, our understanding of its biological mechanisms and translational insights is still limited. The EPIC-InterAct project, centred in 8 countries in the European Prospective Investigations into Cancer and Nutrition study, is one of the largest prospective studies of T2D. Established as a nested case-cohort study to investigate the interplay between genetic and lifestyle behavioural factors on the risk of T2D, a total of 12,403 individuals were identified as incident T2D cases and a representative sub-cohort of 16,154 individuals was selected from a larger cohort of 340,234 participants with a follow-up time of 3.99 million person-years. We describe the results from a genome-wide association analysis between more than 8.9 million SNPs and T2D risk among 22,326 individuals (9,978 cases and 12,348 non-cases) from the EPIC-InterAct study. The summary statistics to be shared provide a valuable resource to facilitate further investigations into the genetics of T2D.

opencc-zeroDec 2017View details →

Data from: Genome-wide association analyses in the model rhizobium Ensifer meliloti

Genome-wide association studies (GWAS) can identify genetic variants responsible for naturally occurring and quantitative phenotypic variation and therefore provide a powerful complement to approaches that rely on de novo mutations for characterizing gene function. Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which non-independence among genomic variants (e.g. linkage disequilibrium, LD) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. We apply association analyses to identify candidate genes underlying variation in 20 biochemical, growth, and symbiotic phenotypes among 153 stains of Ensifer meliloti. For 10 traits we find genotype-phenotype associations that are stronger than expected by chance, with the candidates in relatively small linkage groups, indicating that LD does not preclude resolving association candidates to relatively small genomic regions. The significant candidates show an enrichment for nucleotide polymorphisms (SNPs) over gene presence-absence variation (PAV), and for five traits, candidates are enriched in large linkage groups, a possible signature of epistasis. Many of the variants most strongly associated with symbiosis phenotypes were in genes previously known to be involved in nitrogen-fixation or nodulation. For other traits, apparently strong associations were not stronger than the range of associations detected in permuted data. In sum, our data show that GWAS in bacteria may be a powerful tool for characterizing genetic architecture and identifying genes responsible for phenotypic variation, however, careful evaluation of candidates is necessary to avoid false signals of association.