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412 results for “genetic risk”

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zenodo44/100

Online Appendix for PhD Thesis Titled "Dissecting Causal Relationships and Molecular Mechanisms in Disease using Genetic Risk Profiles"

<p>This repository contains 23 tables and two figures, which are too big to be included in the Appendix section of my thesis document.</p> <p>The second version includes additional summary statistics of metabolite-PGS associations which can be found at http://mrcieu.mrsoftware.org/metabolites_PRS_atlas/.</p>

opencc-by-4.0Nov 2023View details →
zenodo44/100

Tree mortality risks under climate change in Europe: assessment of silviculture practices and genetic conservation networks

<p>General context: Climate change can positively or negatively affect abiotic and biotic drivers of tree mortality. Process-based models integrating these climatic effects are only seldom used at species distribution scale.</p> <p>Objective: The main objective of this study was to investigate the multi-causal mortality risk of five major European forest tree species across their distribution range from an ecophysiological perspective, to quantify the impact of forest management practices on this risk and to identify threats on the genetic conservation network.</p> <p><br> Methods: We used the process-based ecophysiological model CASTANEA to simulate the mortality risk of \textit{Fagus sylvatica}, \textit{Quercus petraea}, \textit{Pinus sylvestris}, \textit{Pinus pinaster} and \textit{Picea abies} under current and future climate conditions, while considering local silviculture practices. The mortality risk was assessed by a composite risk index \textit{(CRIM)} integrating the risks of carbon starvation, hydraulic failure and frost damage. We took into account extreme climatic events with the \textit{CRIM$_{max}$}, computed as the maximum annual value of the \textit{CRIM}.</p> <p><br> Results: The physiological processes&#39; contributions to \textit{CRIM} differed among species: it was mainly driven by hydraulic failure for \textit{P. sylvestris} and \textit{Q. petraea}, by frost damage for \textit{P. abies}, by carbon starvation for \textit{P. pinaster}, and by a combination of hydraulic failure and frost damage for \textit{F. sylvatica}. Under future climate, projection showed an increase of \textit{CRIM} for \textit{P. pinaster} but a decrease for \textit{P. abies}, \textit{Q. petraea} and \textit{F. sylvatica}, and little variation for \textit{P. sylvestris}. Under the harshest future climatic scenario, forest management decreased the mean \textit{CRIM} for \textit{P. sylvestris}, increased it for \textit{P. abies} and \textit{P. pinaster} and had no major impact for the two broadleaved species. By the year 2100, 38\% to 90\% of the conservation units are at extinction threat (\textit{CRIM$_{max}$}=1), depending on the species.</p> <p><br> Conclusions: Using a process-based ecophysiological model allowed us to disentangle the multiple drivers of tree mortality under current and future climate. Taking into account the positive effect of increased CO$_2$ on fertilization and water use efficiency, the average risks may increase or decrease in the future depending on species and sites. However, considering extreme climatic events, future projections are as pessimistic than those obtained with bioclimatic niche models.</p> <p>&nbsp;</p> <p>Abbreviation for column:</p> <p>X&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Longitude<br> Y&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Latitude<br> LAImax&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Leaf area index max reach<br> Nha&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Density per hectar<br> Vha&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Volume per hectar<br> NEE&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Net ecosystem exchange<br> NPP&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;net primary production<br> Reco&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Respiration ecosystem<br> GPP&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Gross primary production<br> Etveg&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Evapotranspiration canopy<br> Etsol&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Evapotranspiration sol<br> TR&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;tree transpiration<br> ETP&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;evapotranspiration potentiel<br> BiomassOfReserves&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Biomass of reserve<br> rw&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;ring width<br> dbh&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;diameter at breast heast<br> height&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;height<br> BBday&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Budburst date<br> rFD&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;risk of frost<br> CRIM_max&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Maximum combined risk index of mortality reach<br> rNSC&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;risk of carbon starvation<br> rPLC&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;risk of embolism<br> rPLC_max&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Maximum risk of embolism reach<br> CRIM&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;combined risk index of mortality<br> Climate&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Climatic model<br> rNSC_max&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;maximum risk of carbon starvation reach<br> rFD_max&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Maximum risk of frost&nbsp; reach<br> Scenario_Sylvicol&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;null means no silvulcture simulated<br> species&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;species<br> Country&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Country<br> alt_watch&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;altitude of climate simulated<br> grid_watch&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;number of the pixel point of WATCH<br> grid_eurocordex&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;number of the pixel point of Eurocordex<br> Pinus_sylvestris&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0 abscence&nbsp;; 1 presence<br> Fagus_sylvatica&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0 abscence&nbsp;; 1 presence<br> Quercus_petraea&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0 abscence&nbsp;; 1 presence<br> Picea_abies&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0 abscence&nbsp;; 1 presence<br> Pinus_pinaster&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0 abscence&nbsp;; 1 presence</p> <p>&nbsp;</p>

opencc-by-4.0Dec 2020View details →
zenodo40/100

FIGURE 2 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)

FIGURE 2: (Left) Maximum clade credibility tree depicting the phylogenetic position of Pristimantis penelopus within the P. ridens series. Numbers on nodes indicate posterior probabilities. Numbers below nodes represent nodal support using the ultrafast bootstrap (see methods). Asterisks indicate nodal support above 95% in both Bayesian and ML methods. (Right) Haplotype network based on 460 bp of the COI region. Numbers of mutational steps are shown on the lines connecting haplotypes. Colors refer to geographic locations shown in Figure 1.

opencc-by-4.0Mar 2017View details →
zenodo40/100

FIGURE 4 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)

FIGURE 4: Potential distribution of Pristimantis penelopus based on ecological niche modeling (red). Yellow dots represents occurrence localities used to calibrate the model. See main text for details.

opencc-by-4.0Mar 2017View details →
zenodo40/100

FIGURE 1 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)

FIGURE 1: Geographic sampling of Pristimantis penelopus. Colored circles indicate sequenced specimens. Different colors represent the populations used in the genetic analysis (see Figure 2 for color codes).

opencc-by-4.0Mar 2017View details →
zenodo40/100

FIGURE 3 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)

FIGURE 3: Phenotypic variation of Pristimantis penelopus across its distribution. Localitites are shown in Appendix 1.

opencc-by-4.0Mar 2017View details →
zenodo40/100

Literature Review 13/02/2018: Genetic risk of Parkinson's disease dementia due to APOE4 or MAPT

<p>Literature review assessing&nbsp;genetic risk of dementia due to <em>APOE4</em> or <em>MAPT </em>in Parkinson&#39;s disease,&nbsp;performed on the 13<sup>th</sup> February 2018. All studies had to fulfil three<em> a priori </em>inclusion criteria:</p> <p>1) Case control studies using clinically diagnosed or pathologically confirmed PD and PDD.</p> <p>2) Time between motor diagnosis and experimental assessment could be defined or estimated.</p> <p>3) Genotype information supplied, allowing the odds ratio (OR) and confidence intervals (CI) to be calculated that aligned with the genotype categories used in this work.</p> <p>For <em>MAPT</em>, a PubMed search for the term &ldquo;<em>MAPT Parkinson&rsquo;s dementia</em>&rdquo; identified 105 potential matches, of which 9 met the inclusion criteria. For <em>APOE4</em>, a PubMed search for the term &ldquo;<em>APOE Parkinson&rsquo;s dementia</em>&rdquo; identified 188 potential matches, of which 19 met the inclusion criteria. Note, the review includes&nbsp;several publications arising from the CamPaIGN cohort;&nbsp;As we were interested in genetic risk as a function of time from diagnosis, we included each unique study time-point.&nbsp;</p>

opencc-by-4.0Jul 2018View details →
zenodo40/100

Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies

<p>GWAS summary results from the paper</p> <p>The Lancet Respiratory Medicine: http://dx.doi.org/10.1016/S2213-2600(19)30055-4</p> <p>Preprint: https://doi.org/10.1101/427427</p>

opencc-by-4.0Jun 2019View details →
zenodo40/100

Integrative genetic analyses illuminates ALS heritability and identifies novel risk genes

<p>Amyotrophic lateral sclerosis (ALS), the major adult onset motor neuron disease, has substantial heritability, in part shared with fronto-temporal dementia (FTD). We show here that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA binding proteins including TDP-43 and FUS. A discovery and replication transcriptome wide association study (TWAS) identified 6 loci associated with ALS, 3 in known ALS loci (<em>C9ORF72, SCFD1, SLC9A8</em>) and 3 novel loci including <em>NUP50 </em>encoding for the nucleopore basket protein NUP50 In our meta-analysis of TWAS cohorts, <em>NUP50 </em>common variant was associated with ALS and to decreased expression of <em>NUP50 </em>in the central nervous system. Independently, we further show association of rare variants in <em>NUP50</em> with ALS risk (<em>P</em> = 3.71.10<sup>-03</sup>; odds ratio&nbsp; = 3.29; 95%CI, 1.37 to 7.87) in a cohort of 9,390 ALS/FTD patients and 4,594 controls. Cells from one patient carrying a <em>NUP50 </em>frameshift mutation displayed a decreased levels of NUP50. Loss of NUP50 leads to neuronal death in cultured neurons, and motor defects in <em>Drosophila </em>and zebrafish models. Thus, our study identifies alterations in splicing in neurons as a critical pathogenic process in ALS, uncovers several new loci potentially contributing to ALS, and provides genetic evidence linking nuclear pore defects to ALS.</p>

opencc-by-4.0Dec 2021View details →
zenodo40/100

Parent-reported child appetite moderates relationships between child genetic obesity risk and parental feeding practices

<p>Data used in the manuscript &quot;Parent-reported child appetite moderates relationships between child genetic obesity risk and parental feeding practices&quot; by Jansen E.,&nbsp;Naymik M.,&nbsp;Thapaliya G.,&nbsp;Huentelman M.,&nbsp;Beauchemin J.,&nbsp;D&#39;Sa V.,&nbsp;Lewis C.R.,&nbsp;Deoni S.,&nbsp;RESONANCE consortium, &amp; Carnell S.</p>

opencc-by-4.0Apr 2023View details →
zenodo36/100

Interaction of Genetic Variations in NFE2L2 and SELENOS Modulates the Risk of Hashimoto's Thyroiditis

<p>This is a dataset for the following paper:&nbsp; doi: 10.1089/thy.2018.0480. PMID: 31426718</p> <p>Each book in the excel file refers to the paper&#39;s&nbsp;figure panel specified.</p> <p>For more info do not hesitate to contact me directly at gerasimos.sykiotis@chuv.ch</p>

opencc-by-4.0Dec 2019View details →
dryad36/100

Genetic architecture of alcohol consumption identified by a genotype-stratified GWAS, and impact on esophageal cancer risk in Japanese

<p><span>An East Asian-specific variant on <em>aldehyde</em> <em>dehydrogenase</em> <em>2</em> (<em>ALDH2</em> rs671, G&gt;A) is the major genetic determinant of alcohol consumption. We performed an rs671 genotype-stratified genome-wide association study (GWAS) meta-analysis in up to 175,672 Japanese individuals to uncover additional loci associated with alcohol consumption in an rs671-dependent manner. Three loci (<em>GCKR</em>, <em>KLB</em>, and <em>ADH1B</em>)</span> <span>satisfied the genome-wide significance threshold in wild-type homozygotes (GG), whereas six loci (<em>GCKR</em>, <em>ADH1B</em>, <em>ALDH1B1</em>, <em>ALDH1A1</em>, <em>ALDH2</em>, and <em>GOT2</em>) did so in heterozygotes (GA). Of these, five loci showed genome-wide significant interaction with rs671. Genetic correlation analyses revealed ancestry-specific genetic architecture in heterozygotes. Subsequent polygenic risk scoring depicted interactions highlighted by stratified GWAS. Further, most discovered loci showed significant effects on risk of esophageal cancer, a representative alcohol-related disease, and multiple other phenotypes. Our results identify the genotype-specific genetic architecture of alcohol consumption and reveal its potential impact on alcohol-related disease risk.</span></p>

opencc-zeroOct 2023View details →
zenodo36/100

Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease

<p>Connectome, traits and behavior data for APOE234 mice.</p> <ul> <li>1. connectome.zip: mouse brain structural connectivity matrices from diffusion MRI.</li> <li>2. FAGNN_Phenotype.csv: a sheet of trait information of mice used in the study.</li> </ul> <p>columns: winding numbers, total distance, normalized NE time, normalized NE distance, normalized NW time, normalized NW distance, normalized SE time, normalized SE distance, normlaized SW time, normalized SW distance, island latency to first entry, island entries, normalized thigmataxis time, and normalized thigmotaxis distance</p> <div>rows: 4 trials for each day from day 1 to day 5 with 1 probing test each at day 5 and day 8</div> <ul> <li>3. mouse_anatomy.csv: brain region information regarding the connectivity matrix.</li> <li>4. behavior.zip: behavioral data for each mouse from Morris Water Maze experiments.</li> </ul>

opencc-by-4.0Dec 2023View details →
dryad36/100

Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation

<p>Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically variation in demographic history or environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analysed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found strong negative associations between genetic diversity and extinction when heterozygosity was included alone in models. However, this association was no longer present when ecological covariates were included. Interactions between heterozygosity and demographic variables revealed that associations are context-dependent or only detectable when confounding factors are controlled. For example, extinction declined with increasing heterozygosity in large but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting &gt;25% increase in extinction beyond ecological factors in certain contexts. This highlights that inferences about the importance of genetic diversity should not rely on genomic data alone but requires investments in obtaining demographic and environmental data from natural populations to jointly assess their impact on population extinction risk.</p>

opencc-zeroMar 2024View details →
zenodo36/100

DArTseq genetic dataset associated with the article "Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia"

<p>Description: This file stores genetic information on the single nucleotide polymorphism markers (SNPs) in the examined alkali grasses (Poaceae: Puccinellia). The dataset was generetad by Genome-Wide Restriction Fragment Analysis via the DArTseq platform (Diversity Arrays Technology Pty Ltd, Canberra, Australia), which combines complexity reduction methods, fragment size selection, and high-throughput sequencing, optimised for a target organism. The file contains raw data.<br>&nbsp;<br>Usage notes: We used R (version 4.2.2, 2022-10-31; https://www.R-project.org/) and RStudio (version 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06; http://www.rstudio.com/) on Windows 8.1 to handle this file. We used the dartR R-package (version 2.7.2) with necessary dependencies to import, proccess and analyse this data file as an object of a class genlight (dartR) in the R environment. You may also handle the file as an object of a class genlight using the adegenet and ade4 R-packages. To learn more about installation procedure and how to use of the R-packages visit: https://cran.r-project.org/web/packages/available_packages_by_name.html.<br>&nbsp; &nbsp;&nbsp;</p>

opencc-by-4.0Apr 2024View details →
zenodo36/100

Supplementary data for manuscript "Genetic risk converges on regulatory networks mediating early type 2 diabetes"

<p>Supplementary data for manuscript "Genetic risk converges on regulatory networks mediating early type 2 diabetes" Nature 624, 621&ndash;629 (2023). <a href="https://doi.org/10.1038/s41586-023-06693-2">https://doi.org/10.1038/s41586-023-06693-2</a></p> <p>Brief description of the included files is given below. Please visit the manuscript website for latest updates:&nbsp;<a href="http://theparkerlab.org/manuscripts/2021_islet-rfx6/">http://theparkerlab.org/manuscripts/2021_islet-rfx6/</a></p>

openMay 2022View details →
zenodo36/100

Interpretation of inherited risk signals using genetic algorithms

<p>This tarball contains the pre-processed data in .Rda files and code in .Rmd file required to execute the genetic algorithm model and compile figures in this study.</p>

opencc-by-4.0Sep 2024View details →
zenodo36/100

Trans-eQTL effects on risk of type 1 diabetes: a test of the sparse effector (omnigenic) hypothesis of complex trait genetics (supplementary data)

<p>This repository contains summary-level data generated by performing&nbsp;<a href="https://github.com/molepi-precmed/trans-qtls">Genomewide aggregated trans- effects (GATE) analysis</a>&nbsp;in case-control study of Type 1 Diabetes (T1D).</p>

opencc-by-4.0Mar 2023View details →
zenodo36/100

Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

<p>All full-sample files contain results generated in coronary artery tissue from 138 American adults. Subset analyses utilized 80 individuals selected from the original 138. Scripts accompanying some of these data in downstream analyses can be viewed on our Github, which also contains a link to the current version of our accompanying manuscript: https://github.com/MillerLab-CPHG/CAD_QTL</p> <p>Full summary statistics for eQTL associations using mixQTL (https://github.com/hakyimlab/mixqtl/wiki) by chromosome are located in UVA_coronary_mixQTL_sumstats_by_chromosome.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the subset of 100% European-ancestry study sample members by chromosome are located in Hodonsky_mixQTL_Euro_sumstats.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the genetically diverse downsampled subset by chromosome are located in Hodonsky_mixQTL_downsample_sumstats.zip</p> <p>Full summary statistics for nominal pass for all genes identified as significant in the permutation pass using QTLtools (https://qtltools.github.io/qtltools/) adjusting for local ancestry by gene by chromosome are located in Local_ancestry_UVA_coronary_QTLtools_nominal_sumstats.zip</p> <p>Full summary statistics for sQTL associations with splice junctions using QTLtools by gene are located in sQTL_results_UVA_coronary_full_sumstats.zip</p>

opencc-by-4.0Jan 2023View details →
dryad36/100

Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian Horse

<p class="MsoNormal"><strong>Introduction</strong>: Spontaneous rupture of tendons and ligaments is common in several species including humans. In horses, degenerative suspensory ligament desmitis (DSLD) is an important acquired idiopathic disease of a major energy-storing tendon-like structure. DSLD risk is increased in several breeds, including the Peruvian Horse. Affected horses have often been used for breeding before the disease is apparent. Breed predisposition suggests a substantial genetic contribution, but heritability and genetic architecture of DSLD have not been determined.</p> <p class="MsoNormal"><strong>Methods</strong>: To identify genomic regions associated with DSLD, we recruited a reference population of 183 Peruvian Horses, phenotyped as DSLD cases or controls, and undertook a genome-wide association study (GWAS), a regional window variance analysis using local genomic partitioning, a signatures of selection (SOS) analysis, and polygenic risk score (PRS) prediction of DSLD risk. We also estimated trait heritability from pedigrees.</p> <p class="MsoNormal"><strong>Results</strong>: Heritability was estimated in a population of 1,927 Peruvian horses at 0.22±0.08. After establishing a permutation-based threshold for genome-wide significance, 151 DSLD risk single nucleotide polymorphisms (SNPs) were identified by GWAS. Multiple regions of enriched local heritability were identified across the genome, with strong enrichment signals on chromosomes 1, 2, 6, 10, 13, 16, 18, 22, and the X chromosome. With SOS analysis, there were 66 genes with a selection signature in DSLD cases that was not present in the control group that included the <em>TGFB3</em> gene. Pathways enriched in DSLD cases included proteoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways that included the hedgehog signaling pathway. The best PRS predictive performance was obtained when we fitted 1% of top SNPs using a Bayesian Ridge Regression model which achieved the highest mean of R<sup>2</sup> on both the probit and logit liability scales, indicating a strong predictive performance.</p> <p><strong>Discussion</strong>: We conclude that within-breed GWAS of DSLD in the Peruvian Horse has further confirmed that moderate heritability and a polygenic architecture underlies the trait and identified multiple DSLD SNP associations in novel tendinopathy candidate genes influencing disease risk. Pathways enriched with DSLD risk variants include ones that influence glycosaminoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways.</p>

opencc-zeroJul 2023View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

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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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record