Non-Invasive Whole Genome Sequencing of a Human Fetus
Ontology highlight
ABSTRACT: The overall purpose of this study was to demonstrate the feasibility of producing haplotype-phased whole genome sequence data from a fetus using free fetal DNA isolated from maternal plasma collected during the first half of gestation.
SECONDARY ACCESSION(S): PRJNA168048PRJNA168047
REPOSITORIES: dbGaP
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| GapExchange_phs000500.v1.p1.xml | Xml | |||
| dbGaPEx2.1.5.xsd | Other | |||
| Study_Report.phs000500.Fetal_Genome.v1.p1.MULTI.pdf | ||||
| manifest_phs000500.Fetal_Genome.v1.p1.c1.GRU.pdf | ||||
| datadict_v2.xsl | Other |
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Similar Datasets
Project description:<p>The overall purpose of this study was to demonstrate the feasibility of producing haplotype-phased whole genome sequence data from a fetus using free fetal DNA isolated from maternal plasma collected during the first half of gestation.</p>
| phs000500.v1.p1 | EGA
Project description:Pregnancy is a time of extreme metabolic demand that requires coordinated adaptations between mother and fetus. To determine the contributions of maternal and fetal metabolism to metabolic plasticity during gestation, mice with a liver-specific Carnitine Palmitoyltransferase-2 knockout mice (Cpt2-/-), or Pparα KO mice were subjected to late-gestation nutrient stress, a 24hr fast from E16.5 to E17.5. The fetal response to maternal fasting was dominated by maternal lipid metabolism as the loss of maternal hepatic fatty acid oxidation or Pparα signaling accelerated fetal liver transcriptional programing. These data show that maternal nutritional environment is a major driver of perinatal metabolic programing and plasticity.
2019-09-20 | GSE129368 | GEO
Project description:We used the rhesus monkey (Macaca mulatta) as our animal model for the current study with two goals: to characterize the changes in histology and gene expression from early to late gestation (prenatal uterine organogenesis) and to determine if there are effects of prenatal exposure to bisphenol A (BPA) on the developing female uterus. Pregnant rhesus monkeys carrying a female fetus (N=22) were divided into two experimental groups, based on gestational timing: 'early' (N=10) and 'late' (N=12). These groups were then equally sub-divided into control (unexposed) and BPA (exposed) groups (5 Early Control, 5 Early BPA-exposed, 6 Late Control and 6 Late BPA-exposed.) The BPA-exposed monkeys received a deuterated BPA (dBPA, CDN Isotopes, Quebec, Canada) fruit treat on a daily basis, at a dose of 400ug/kg/day). The dosing was aimed at achieving serum levels of BPA detected in adult human biomonitoring studies. The control animals received a vehicle control on a daily basis. The 'early' time period (mid-gestation) referred to gestational days 50-100, approximating the second trimester of human gestation. The fetal monkeys in the 'early' group were delivered via cesarean section on gestation day 100 and euthanized. Samples of maternal and fetal blood and amniotic fluid were obtained. Maternal and fetal weights were also recorded. The 'late' time period referred to gestational days 100-165, approximating the third trimester of human gestation. The fetal monkeys in the 'late' group were delivered vaginally and euthanized. There were five idiopathic stillbirths (2 Control, 3 BPA-exposed) in the late group. Samples of maternal and fetal blood and amniotic fluid were obtained. Maternal and fetal weights were also recorded. After delivery, the fetal uterus was excised and cut sagitally from fundus to cervix; one side was fixed for histological evaluation and the other half was frozen for analysis of gene expression by microarray. The stillbirths were excluded from the microarray.
2014-05-22 | E-GEOD-38421 | biostudies-arrayexpress
Project description:Activation of the maternal immune system during pregnancy can fetal development, which can lead to postnatal susceptibility to a wide range of diseases, including cardiovascular, metabolic and psychiatric disorders. During maternal immune activation (MIA), the maternal body must balance its ressources between mounting an immune response and investing resources into continued metabolism and growth : both essential for survival of the fetus and a successful pregnancy. How the placenta responds to MIA over time and how it can protect the fetus is not well understood, and neither are the fetal consequences of MIA. Here, we characterised the response to an induced acute inflammation in maternal lungs over time across maternal and fetal organs, using a combination of omics-methods, imaging and integrative computational analysis. We found that the placenta, unlike other maternal organs, did not react by inducing a typical inflammatory response, but instead initially induced genes associated to strengthen tissue integrity and simultaneously reduced growth to prevent exposure to potential infections. Afterwards, a return to homeostasis was observed, with heightened biosynthesis and expression of endoplasmic reticulum (ER) stress genes. This mechanism likely protects the fetus from inflammation, as we observed no immune response in the fetal liver transcriptome. Instead, we observed metabolic adaptations in the fetus, including a release of docosahexaenoic acid (DHA) Notably, DHA has a crucial function for fetal brain development , and levels of triglyceride and phosphatidylcholine lipids that are necessary for transportation of DHA to the brain were also increased. This metabolic response is likely a combination of the placental MIA response and temporary maternal fasting, caused by MIA-induced fever and lack of nutrient intake. Our study shows, for the first time, the temporal and systemic response to MIA in lungs across maternal and fetal organs.
2024-06-13 | PXD039402 | Pride
Project description:Human epidemiological evidence has led scientists to theorize that undernutrition during gestation is an important early origin of adult diseases. Animal models have successfully demonstrated that maternal diet could contribute to some of adult diseases. Undernutrition is perceived harmful in pregnant women whereas calorie restriction is a strategy proven to extend healthy and maximum life span in adult. This diagrammatically opposite effect of nutritional condition might provide us hints to search for genes underlying health conditions. Here, we have initiated a study examining the effect of undernutrition on maternal and fetal livers, utilizing high-throughput DNA microarray analysis for screening genome-wide changes in their transcriptomes. Briefly, pregnant mice were exposed to food deprivation (FD) on gestation day (GD) 17, and caesarean section was performed on GD18. Control mice were supplied with chow ad libitum till sacrifice. Total RNA extracted from mother and fetal livers for each control and treatment (FD) was analyzed with an Agilent mouse whole genome DNA chip. Total of 3058 and 3126 up (>1.5 fold)- and down (<0.75 fold)-regulated genes, and 1475 and 1225 up- (>1.5 fold)- and down (<0.75 fold)-regulated genes showed differential expression at the mRNA level, in the maternal and fetal livers, respectively. Interestingly, 103 genes up-regulated in mother were down-regulated in fetus, whereas 108 down-regulated maternal genes were up-regulated in fetus; these 211 genes are potential candidates related to longevity or health. The role of some of these genes, in context of the proposed mechanisms for developmental origins of health and disease is discussed. Comparison between mouse control and FD livers in fetus and mother was performed. Five to ten biological replicates were used, and pooled total RNA from each condition (control and FD) was dye-swaped.
2011-04-01 | E-GEOD-28175 | biostudies-arrayexpress
Project description:The response to the presence of the ncpBVDV-infected PI or TI fetus is expected to provide information on the impact of the PI fetus on the immune response of the dam Fetal PI infection was induced by intranasal inoculation of pregnant heifers with ncpBVDV on day 75 of gestation. Fetal transient infection (TI) was induced by infection of pregnant heifers with ncpBVDV on day 175 of gestation. Control heifers were kept uninfected. Blood samples from pregnant heifers of the PI and control groups were collected on day 160 of gestation. Blood samples of PI, TI and healthy fetus carrying heifers were collected for microarray on day 190 of gestation.
2009-06-15 | E-GEOD-11835 | biostudies-arrayexpress
Project description:The late-gestation fetal sheep responds to hypoxia with physiological, neuroendocrine, and cellular responses that aid in fetal survival . The response of the fetus to hypoxia represents a coordinated effort to maximize oxygen transfer from the mother and minimize wasteful oxygen consumption by the fetus. While there have been many studies aimed at investigating the coordinated physiological and endocrine responses to hypoxia, and while immunohistochemical or in situ hybridization studies have revealed pathways supporting the endocrine function of the pituitary, there is little known about the coordinated cellular response of the pituitary to the hypoxia. The objective of this study was to use transcriptomics and systems analysis to determine significantly altered biological processes in the late gestation ovine fetal pituitary one hour after a 30 minute period of hypoxia, produced by lowering the inspired oxygen content in the maternal inspired gas. We found that the acute response to 30 min of transient hypoxia in the late-gestation fetus results in reduced cellular metabolism and a pattern of gene expression that is consistent with cellular oxygen and ATP starvation. The response is not consistent with gene regulation by HIF1A .
2015-10-01 | GSE69246 | GEO
Project description:Microarray of whole blood maternal samples comparing the expression of genes in the maternal blood in pregnancies where the fetus was hypoxic at birth compared to those where the fetus was normoxic at birth. Intrapartum hypoxia is associated with severe neonatal morbidity and mortality. Current techniques to assess fetal hypoxic status during labour have a poor sensitivity. At birth, the lactate level in umbilical cord blood is used to assess the degree of fetal hypoxia during birth, such that a high lactate reflects a hypoxic fetus and a low lactate a normoxic fetus. We collected maternal blood prior to delivery and compared the expression of genes in the maternal blood in women delivering a normoxic or hypoxic fetus as evidenced by umbilcal cord blood levels.
2014-05-08 | E-MTAB-2054 | biostudies-arrayexpress
Project description:Maternal stressors as psychophysical stress and obesity might share converging inflammatory/OS related pathways, disrupting fetal brain development, assuming a key role for the placenta in conveying maternal stressful mediators to the fetus. To test such hypothesis, we used two different mouse models mimicking, respectively, maternal psychophysical stress and maternal obesity and anlyased by LFQ-DIA mass spectrometry the placental tissue.
2023-07-10 | MSV000092388 | MassIVE
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