Genome wide association study of severe malaria in Gambian mother-father-child trios
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ABSTRACT:
PROVIDER: EGAS00000000087 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genome-wide association study of severe malaria in Ghanain mother-farther-child trios
| EGAS00000000088 | EGA
Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ
2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress
Project description:In this project exposuere to DiethylPhosphate (DE) metabolites has been monitored in the usine of pregnant women of the French mother-child cohort PELAGIE. We performed ChIPs against H3K4me3 from male or female newborns' placenta in order to identify whether exposure to DE can affect their epigenetic landscape. Representing samples from each group were selected for genome-wide ChIP-seq analysis. Exposure and epigenetic data are compared and associated with potential effects on developmental processes.
2022-11-10 | GSE209943 | GEO
Project description:The aim of this study was to investigate how the human milk proteome relates to allergy of the mother and allergy development in the infant.
2022-10-31 | PXD034806 | Pride
Project description:This study contrasts the expression profiles of peripheral blood leukocytes from third trimester pregnant mothers, with cord blood leukocytes from their newborn children. It is a companion to (GSE21311). After normalization for RNA integrity, major principal components of the variation were found to distinguish individuals. Transmission of gene expression profiles from mother to child was documented, along with differences between gestational diabetic, obese, and normal weight mothers and their children. 56 individulas (Brisbane, Australia) were sampled for the mother-newborn study, under informed consent. 19 mothers sample were collected in the last month of pregnancy (between 30th and 36th week of pregnancy) and 37 cord blood samples were obtained at birth from newborn babies. Mothers having BMI values over 30 before pregnancy were classified as obese. From the 37 newborn babies, 10 were born to obese mothers, 8 to gestational diabetic mothers (with a wide range of body mass indices), and 19 to normal-weight mothers. There were 16 mother-newborn pairs in the dataset. RNA from each was hybridized to an Illumina HT12 array.
2011-01-01 | E-GEOD-21342 | biostudies-arrayexpress
Project description:Whole blood transcriptomes from a longitudinal study of 5 Malawian children who first present with severe Plasmodium falciparum malaria, and return in one month with mild malaria We used microarrays to identify transcripts that were associated with each clinical presentation. A blood sample was taken upon presentation during the severe and mild malaria episodes in 5 Malawian children (total n=5 pairs) followed by RNA extraction and hybridization on Affymetrix GeneChip Human Gene 1.0 ST Array, using a paired analysis
2012-01-11 | E-GEOD-33811 | biostudies-arrayexpress
Project description:This study contrasts the expression profiles of peripheral blood leukocytes from third trimester pregnant mothers, with cord blood leukocytes from their newborn children. It is a companion to (GSE21311). After normalization for RNA integrity, major principal components of the variation were found to distinguish individuals. Transmission of gene expression profiles from mother to child was documented, along with differences between gestational diabetic, obese, and normal weight mothers and their children.
2011-01-01 | GSE21342 | GEO
Project description:Whole blood transcriptomes from a longitudinal study of 5 Malawian children who first present with severe Plasmodium falciparum malaria, and return in one month with mild malaria We used microarrays to identify transcripts that were associated with each clinical presentation.
2012-01-11 | GSE33811 | GEO
Project description:Suicidal behavior (SB) has a complex etiology of genes, environment or both. One of the genetic components in SB could be copy number variations (CNVs), since CNVs are implicated in a range of neurodevelopmental disorders. However, a recently published genome-wide and case-control study failed to observe a significant role of CNVs in SB (see E-MTAB-3519). Here we complement those initial observations by conducting a brief CNV-association study, for the first time in a family-based trio-sample with severe suicide attempt (SA) outcome in offspring (n=660 trios; the \GISS\ sample, see http://www.ncbi.nlm.nih.gov/pubmed/23422793 and refs therein). For association testing, we here used the FBAT-CNV methodology (http://www.ncbi.nlm.nih.gov/pubmed/18228561), which allows for CNV association testing directly on the raw intensity values (Illumina \log R ratio\), evaluating any type of CNVs (e.g. de novo or inherited) without reliance on CNV calling algorithms and robust to control selection biases. Here we have deposited these raw logR-values for 88,450 on-chip CNV-loci of the HumanOmni1-Quad_v1 chip, arranged in a standard pedigree format used as input for FBAT-CNV analysis in SVS software (goldenhelix.com): column 1 is the family ID, column 2 is the Subject type (1 = offspring, 2 = mother, 3 = father), column 3 is the father ID (? for missing), column 4 is the mother ID (? for missing), column 5 is the sex (1 = female, 0 = male), column 6 is the affection status (1 = suicide attempt, 0 = not affected) and columns 7 and onward are the logR-values for each CNV-loci as is listed in the header row. We observed experiment-wide significant association (P ≤ 5.6 x 10-7) of two proximal CNVs at chromosome 14 (Illumina markers cnvi0108946 and cnvi0118308, with NCBI 36.3 start positions 22794779 and 22582820). However, these CNV-associations mapped to T-cell receptor regions, and therefore most likely reflect inter-individual variation in somatic rearrangements occurring in white blood cells (as our source of DNA was blood), rather than association with SA. In conclusion, our results did not suggest any major role of CNVs in SA etiology, in line with the results of the recent case-control study (see E-MTAB-3519).
2015-10-30 | E-MTAB-3744 | biostudies-arrayexpress
Project description:Genome wide transcriptome analyses could reveal whether parasites causing severe malarial disease express different genes to those causing uncomplicated malaria. This knowledge could inform therapy and vaccine design targeting severe disease. Venous samples were collected from patients with severe (n=23) and uncomplicated (n=21) malaria attending a healthcare facility in Timika, Papua Province, Indonesia. This area has unstable malaria transmission with estimated annual parasite incidence of 450 per 1000 population and symptomatic illness in all ages. Severe malaria was defined as peripheral parasitaemia with at least one modified World Health Organization (WHO) criterion of severity. Erythrocytes were immediately isolated from whole blood, solubilised in RNA preservative and frozen. Libraries were 100 bp paired end sequenced on a 2500-HT Hiseq (Illumina) using RapidRun chemistry (Illumina).
2018-02-08 | E-MTAB-5860 | biostudies-arrayexpress