Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA241416 | ENA |
REPOSITORIES: ENA
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Project description:Motivation: The need of identifying genetic determinants that disclose the heritability of complex traits as well as pinpoint causative genetic effects in some complex diseases has propelled large-scale, systematic fashion bred epigenome-wide studies. With the very dynamic nature of epigenome and much reduced cost in microarray and sequencing experiments, more and more researchers are now studying epigenomic at multiple time points, i.e. multiple measurement and/or longitudinal study design. However, the popular site-by-site multiple testing as commonly used in genome-wide studies may impair the value of multiple measurements because it leads to underpowered analyses by ignoring the inherent dependent structure, which has called for new methods to address the statistical challenges. Results: We have proposed a penalized regression model incorporating with grid search method (PGS), for analyzing epigenome-wide multiple measurement data. The development of this analytical framework was motivated by a real-world micro RNA dataset. Comparisons between PGS and the site-by-site testing approach reveal that PGS provides smaller phenotype prediction errors and higher enrichment of phenotype-related biological pathway than the site-by-site testing approach. Our approach is also useful for epigenome-wide data of DNA methylation and histone modifications.
2017-12-21 | GSE55950 | GEO
Project description:Epigenome-Wide Association Study in multiple system atrophy (MSA)
| PRJNA599119 | ENA
Project description:Background: Maternal smoking during pregnancy is a major risk factor for adverse health outcomes. The main objective of the study was to assess the impact of in utero tobacco exposure on DNA methylation in children born at term with appropriate weight at birth. Methods: Twenty mother-newborn dyads, after uncomplicated pregnancies, in the absence of perinatal illness were included. All mothers were healthy with no cardiovascular risk factors, except for the associated risks among those mothers who smoked. Umbilical cord blood (for methylation arrays) and maternal peripheral venous blood (for cotine level measurement) were collected and an epigenome-wide association study was performed using a 450K epigenome-wide scan (Illumina Infinium HumanMethylation 450BeadChip) with adjustment to normalize the DNA methylation for data cell variability in whole blood. Results: The maternal plasmatic cotinine levels ranged from 10.70-115.40 ng/ml in the exposed group to 0-0.59 ng/ml in the non-exposed group. After adjusting for multiple comparisons in 427102 probes, statistically significant differences for 31 CpG sites, associated to 25 genes were observed. There was a greater than expected proportion of statistically-significant loci located in CpG islands (FisherM-bM-^@M-^Ys exact test, p=0.029) and of those CpG islands, 90.3% exhibit higher methylation levels in the exposed group. The most striking and significant CpG site, cg05727225, is located in the chromosome 11p15.4, within the adrenomedullin gene. Conclusions: In utero tobacco exposure, even in the absence of fetal growth restriction, may alter the epigenome, contributing to global DNA hypomethylation. Therefore, DNA status can be used as a biomarker of prenatal insults. Considering the possibility to reverse epigenetic modifications, a window of opportunity exists to change the programmed chronic disease. Twenty mother-newborn dyads, after uncomplicated pregnancies, in the absence of perinatal illness were included. All mothers were healthy with no cardiovascular risk factors, except for the associated risks among those mothers who smoked. Umbilical cord blood were collected and an epigenome-wide association study was performed using a 450K epigenome-wide scan (Illumina Infinium HumanMethylation 450BeadChip) with adjustment to normalize the DNA methylation for data cell variability in whole blood.
2015-02-16 | E-GEOD-64316 | biostudies-arrayexpress
Project description:VitGene Generalized Vitiligo Genetics Study
| PRJNA75597 | ENA
Project description:Here we designed a search-engine for single-cell epigenome profiles. We tested different application of search-engine using different data-sets including mESC scATAC-seq profile.
2022-12-27 | GSE192644 | GEO
Project description:SEARCH ProDIGY Exome Sequencing Study
| PRJNA422645 | ENA
Project description:SEARCH ProDIGY Exome Sequencing Study
| PRJNA422646 | ENA
Project description:Patient with multiple sclerosis improves during pregnancy while temporarily worsening post-partum. The reasons behind the disease modulation during pregnancy remain unknown. In this study, we have investigated the effect of pregnancy on circulating CD4+ and CD8+ T cells from patients with multiple sclerosis and healthy controls to gain a deeper understanding why patients with multiple sclerosis improves during pregnancy. We assessed epigenome-wide DNA methylation in CD4+ and CD8+ T cells obtained during (1st, 2nd and 3rd trimester) and after pregnancy (6 weeks post-partum), using the Infinium MethylationEPIC 850K array.
2023-09-23 | E-MTAB-12250 | biostudies-arrayexpress
Project description:Background: Maternal smoking during pregnancy is a major risk factor for adverse health outcomes. The main objective of the study was to assess the impact of in utero tobacco exposure on DNA methylation in children born at term with appropriate weight at birth. Methods: Twenty mother-newborn dyads, after uncomplicated pregnancies, in the absence of perinatal illness were included. All mothers were healthy with no cardiovascular risk factors, except for the associated risks among those mothers who smoked. Umbilical cord blood (for methylation arrays) and maternal peripheral venous blood (for cotine level measurement) were collected and an epigenome-wide association study was performed using a 450K epigenome-wide scan (Illumina Infinium HumanMethylation 450BeadChip) with adjustment to normalize the DNA methylation for data cell variability in whole blood. Results: The maternal plasmatic cotinine levels ranged from 10.70-115.40 ng/ml in the exposed group to 0-0.59 ng/ml in the non-exposed group. After adjusting for multiple comparisons in 427102 probes, statistically significant differences for 31 CpG sites, associated to 25 genes were observed. There was a greater than expected proportion of statistically-significant loci located in CpG islands (Fisher’s exact test, p=0.029) and of those CpG islands, 90.3% exhibit higher methylation levels in the exposed group. The most striking and significant CpG site, cg05727225, is located in the chromosome 11p15.4, within the adrenomedullin gene. Conclusions: In utero tobacco exposure, even in the absence of fetal growth restriction, may alter the epigenome, contributing to global DNA hypomethylation. Therefore, DNA status can be used as a biomarker of prenatal insults. Considering the possibility to reverse epigenetic modifications, a window of opportunity exists to change the programmed chronic disease.
2015-02-16 | GSE64316 | GEO