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14 results for “EWAS”
Training Data for 'ewas_suite' Analysis
<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes EWAS data from a study published by Hugo, Willy, et al., 2015 (DOI: <a href="https://doi.org/10.1016/j.cell.2015.07.061">10.1016/j.cell.2015.07.061</a>) to identify differentially methylated regions and positions associated with melanoma MAPKi resistance.</p>
Baseline of the WEAI for East and West African case studies within EWA-BELT Project
<p>The Women’s Empowerment in Agriculture Index (WEAI) is a survey-based tool that measures women’s empowerment and inclusion in agricultural activities.</p> <p>This database contained the baseline "pre-project activities" collected from October 2022 to January 2023 in 40 households per each Country involved (Ethiopia, Kenya, Tanzania, Burkina, Ghana). A total of 219 households were involved collecting 381 interviews, in 65 households the primary respondent was a woman, so we had not to interview a male secondary respondent. </p> <p>There are 3 types of surveys to calculate the WEAI: the original WEAI, the Accelerated WEAI (A – WEAI) and the PRO WEAI. The original WEAI is the first developed by IFPRI, the A-WEAI is a shorter and faster version, while the PRO WEAI is an extended version aimed to cover more areas of empowerment. We chose A-WEAI because it was faster and simpler to administer, considering that it is the first time for most of the partners to work on this survey and that the participants have already answered to many surveys, hence they might answer with more attention to a short and fast survey.</p>
EWAS associations between DNAm and general cognitive score, perceptive performance score, and verbal score
<p><strong><span>Evaluating the association between placenta DNA methylation and cognitive functions in the offspring </span></strong></p> <p><a name="_Hlk141095040"></a><span>Placenta plays a crucial role protecting the foetus from environmental harm and supports the development of its brain. In fact, compromised placental function could predispose an individual to neurodevelopmental disorders</span><span><span>. Placental epigenetic modifications, including DNA methylation, could be considered a proxy of placental function and thus plausible mediators of the association between intrauterine environmental exposures and genetics, and childhood and adult mental health. Although neurodevelopmental disorders such as autism spectrum disorder have been investigated in relation to placenta DNA methylation, no studies have addressed the association between placenta DNA methylation and child’s cognitive functions. </span><span>Thus, our goal here was to investigate whether placental DNA methylation profile measured using the Illumina EPIC array is associated with three different cognitive domains (namely verbal score, perceptive performance score, and general cognitive score) assessed by the McCarthy Scales of Children’s functions in childhood at age 4. To this end, we conducted epigenome-wide association analyses including data from 255 mother-child pairs within the INMA project and performed a follow-up functional analysis to help the interpretation of the findings. After multiple-testing correction, we found that methylation at 4 CpGs (cg1548200, cg02986379, cg00866476 and cg14113931) was significantly associated with the general cognitive score, and 2 distinct differentially methylated regions (DMRs) (including 27 CpGs) were significantly associated with each cognitive dimension. <a name="_Hlk168395284"></a><a name="_Hlk168394861"></a><span>Interestingly, the genes annotated to these CpGs, <span>such as <em>DAB2, CEP76</em>, <em>PSMG2,</em> or <em>MECOM,</em> </span>are involved in placenta, foetal, and brain development</span><span>. </span>Moreover, functional enrichment analyses of suggestive CpGs (<em>p</em><1x10<sup>-4</sup>) revealed gene-sets involved in placenta development, foetus formation and brain growth. These findings suggest that placental DNAm could be a mechanism contributing to the alteration of important pathways in the placenta that have a consequence on the offspring’s brain development and cognitive function. </span></span></p>
EWAS results "Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer"
<p>Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts.</p> <p>DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an Epigenome Wide Association Study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip, and subject as random effect.</p> <p>The full analyses results are deposited here.</p>
The EWAS Catalog manuscript: Extended data
<p>Epigenome-wide association studies (EWAS) of 387 traits were conducted within the Accessible Resource for Integrated Epigenomic Studies (ARIES). These results were uploaded to The EWAS Catalog: http://www.ewascatalog.org/. The table presented here represents the extended data in The EWAS Catalog manuscript. </p>
The EWAS Catalog manuscript: Underlying data
<p>Epigenome-wide association studies (EWAS) of 40 traits were conducted using publically available data from the Gene Expression Omnibus (GEO) online repository. These results were uploaded to The EWAS Catalog: http://www.ewascatalog.org/. The table presented here represents the underlying data in The EWAS Catalog manuscript and contains the traits along with the corresponding GEO accession numbers and PubMed IDs.</p>
Impact of BMI and waist circumference on epigenome-wide DNA methylation and identification of epigenetic biomarkers in blood: an EWAS in multi-ethnic Asian individuals
<p>The datasets contains summary statistics from meta-analysis of EWAS on BMI and WC in 409 multi-ethnic Asians.</p>
Epigenetic analysis of psychosocial stress among mother-newborn dyads in the Democratic Republic of Congo (EWA reanalysis)
GEO Series GSE224364. Homo sapiens. 356 samples. Type: Methylation profiling by array.
Lipolysis regulates major transcriptional programs in brown adipocytes [3Dcultured_eWAs_RNA-seq]
GEO Series GSE202834. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
EWAS of lung function in Latinos with asthma - Summary Statistics
<p>Summary statistics generated for the manuscript entitled <strong>"Epigenome-wide association study of lung function in Latino children and youth with asthma"</strong></p> <p>Our aim was to identify DNA methylation signals associated with lung function in Latino youth with asthma and validate previous epigenetic signals from non-Latino populations. For that, we performed multiple epigenome-wide association studies (EWAS) of lung function measurements analyzing whole blood from 250 Puerto Rican (PR) and 148 Mexican American (MEX) youth with asthma from the Genes-Environment and Admixture in Latino Americans (GALA II) study. The following measurements were evaluated Pre- and post- albuterol administration: Forced expiratory volume in one second (FEV1.Meas), forced vital capacity (FVC.Meas) and their ratio (FEV1.FVC.Meas). DNA methylation was profiled with the Infinium EPIC BeadChip or the Infinium HumanMethylation450 BeadChip array (Illumina, San Diego, CA, USA). The association of methylation beta-values and raw PFT values (in liters) was tested by robust linear regressions with correction for age, sex, height, the first three genotype principal components (PCs),<em> in utero</em> maternal smoking exposure, the first six ReFACTor components, and batch, when appropriate, via limma R package. The results for individuals of the same ethnic subgroup were meta-analyzed using fixed- or random-effects models, based on Cochran's Q p-value. Version 1 is deprecated.</p> <p>The EWAS result files (*.txt) contains:</p> <ul> <li>RSID: CpG name.</li> <li>STUDY: Number of sets of individuals included in the meta-analysis.</li> <li>BETA_meta: Coefficient of the regression.</li> <li>SEBETA_meta: Standard error of the coefficient of the regression.</li> <li>PVALUE_meta: P-value for the association.</li> <li>PVALUE_Q: Cochran's Q p-value.</li> <li>Model: Fixed-effect (FE) or Random-effects (RE2) model.</li> <li>PVALUE_meta_adj: False discovery rate (Benjamini & Hochberg method).</li> </ul>
GWAS and EWAS in Patients With Erdheim-Chester Disease
ClinicalTrials.gov study NCT06332183. IPD Sharing: NO. Countries: 3. Publications: 0.
Epigenome-Wide Association Study (EWAS) Identifies Transgenerational Disease Biomarkers in Sperm Following Ancestral Exposure to the Pesticide Methoxychlor
GEO Series GSE158086. Rattus norvegicus. 28 samples. Type: Methylation profiling by high throughput sequencing.
EWA-DB – Early Warning of Alzheimer speech database
<h4>EWA-DB is a speech database that contains data from 3 clinical groups: Alzheimer's disease, Parkinson's disease, mild cognitive impairment, and a control group of healthy subjects. Speech samples of each clinical group were obtained using the EWA smartphone application, which contains 4 different language tasks: sustained vowel phonation, diadochokinesis, object and action naming (30 objects and 30 actions), picture description (two single pictures and three complex pictures).<br><br>The total number of speakers in the database is 1649. Of these, there are 87 people with Alzheimer's disease, 175 people with Parkinson's disease, 62 people with mild cognitive impairment, 2 people with a mixed diagnosis of Alzheimer's + Parkinson's disease and 1323 healthy controls.<br><br>For speakers who provided written consent (total number of 1003 speakers), we publish audio recordings in WAV format. We are also attaching a JSON file with ASR transcription, if available manual annotation (available for 965 speakers) and additional information about the speaker. For speakers who did not give their consent to publish the recording, only the JSON file is provided. ASR transcription is provided for all 1649 speakers. All 1649 speakers gave their consent to the provider to process their audio recordings. Therefore, it is possible for third party researchers to carry out their experiments also on the unpublished audio recordings through cooperation with the provider.</h4>
Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation
GEO Series GSE124366. Homo sapiens. 215 samples. Type: Methylation profiling by array.
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