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Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [RNA-seq]

ABSTRACT: Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [RNA-seq]

PROVIDER: PRJNA646066 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12214600.fastq.gz	Fastqsanger.gz
	SRR12214601.fastq.gz	Fastqsanger.gz
	SRR12214602.fastq.gz	Fastqsanger.gz
	SRR12214603.fastq.gz	Fastqsanger.gz
	SRR12214604.fastq.gz	Fastqsanger.gz

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Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

Project description:Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

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Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [WGBS]

Project description:Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [WGBS]

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Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [WGBS]

Project description:Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. Here we investigated cell-free DNA and RNA content of 102 maternal and 25 cord plasma samples. Employing a novel deconvolution methodology, we found that during the first trimester, placenta-specific DNA increased prior to the subsequent development of gestational diabetes with no change in patients with preeclampsia while decreasing with maternal obesity. Moreover, using cell-free RNA sequencing, APOs revealed seventy-one differentially expressed genes early in pregnancy. We noticed the upregulation of S100A8, MS4A3 and MMP8 that have been already associated with APOs but also the upregulation of BCL2L15 and the downregulation of ALPL that have never been associated with APOs. We constructed a classifier with a positive predictive ability (AUC) of 0.91 for APOs, 0.86 for preeclampsia alone and 0.64 for GDM. We conclude that placenta-specific cell-free nucleic acids during early gestation provide the possibility of predicting APOs prior to the emergence of characteristic clinical features.

2020-10-19 | GSE154348 | GEO

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes [RNA-seq]

Project description:Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. We investigated the cell-free RNA content of 102 maternal, 25 cord plasma samples and 7 non pregnant women as control. using cell-free RNA sequencing, APOs revealed seventy-one differentially expressed genes early in pregnancy. We noticed the upregulation of S100A8, MS4A3 and MMP8 that have been already associated with APOs but also the upregulation of BCL2L15 and the downregulation of ALPL that have never been associated with APOs. We constructed a classifier with a positive predictive ability (AUC) of 0.91 for APOs, 0.86 for preeclampsia alone and 0.64 for GDM. We conclude that placenta-specific cell-free nucleic acids during early gestation provide the possibility of predicting APOs prior to the emergence of characteristic clinical features.

2020-10-19 | GSE154377 | GEO

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-10-19 | GSE154378 | GEO

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes.

Project description:Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. Here we investigated cell-free DNA and RNA content of 102 maternal and 25 cord plasma samples. Employing a novel deconvolution methodology, we found that during the first trimester, placenta-specific DNA increased prior to the subsequent development of gestational diabetes with no change in patients with preeclampsia while decreasing with maternal obesity. Moreover, using cell-free RNA sequencing, APOs revealed 71 differentially expressed genes early in pregnancy. We noticed the upregulation of S100A8, MS4A3, and MMP8 that have been already associated with APOs but also the upregulation of BCL2L15 and the downregulation of ALPL that have never been associated with APOs. We constructed a classifier with a positive predictive ability (AUC) of 0.91 for APOs, 0.86 for preeclampsia alone and 0.64 for GDM. We conclude that placenta-specific cell-free nucleic acids during early gestation provide the possibility of predicting APOs prior to the emergence of characteristic clinical features.

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Adverse neonatal outcomes are associated with a sex-specific placental inflammatory profile

Project description:Background and objective: The placenta is crucial for fetal development; altered function is associated with complications and adverse neonatal outcomes. Our goal was to ascertain changes in the placental transcriptome in relation to neonatal outcome and fetal/placental sex. Study Design: 72 mother-baby dyads were included. Demographic, obstetrical, neonatal and infant health data were obtained through medical charts. Adverse neonatal outcome was defined as the presence of a pulmonary, cardiac, neurological or other health complication. Bulk RNA-sequencing of placental biopsies was obtained. P-value < 0.05 was considered statistically significant. Results: Neonates experiencing adverse outcomes were more likely to be premature or have lower birth weights. Analysis of the placental transcriptome revealed a predominant inflammatory profile in pregnancies associated with adverse neonatal outcomes with the top pathways being related to immune and inflammatory responses. Amongst differently expressed genes (DEGs), 1237 were upregulated and 239 were downregulated in adverse vs no adverse outcomes. Furthermore, sex-specific differences in gene expression were observed and indicated that male and female placentas displayed unique DEGs in association with adverse outcomes. Indeed, no DEG was observed in female placentas when comparing those without vs with adverse neonatal outcomes, as opposed to 1279 DEGs in male placentas, of which 91% were up-regulated in adverse subgroups. Conclusions: These findings highlight that inflammatory pathways are upregulated in placentas in association with adverse neonatal outcomes, and showcase the importance of the fetal sex in understanding neonatal health. The placenta provides a unique tool for early identification of high-risk infants rapidly after delivery.

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Prediction of neurological outcomes shortly after cardiac arrest

2013-06-01 | GSE29540 | GEO

Prediction of neurological outcomes shortly after cardiac arrest

Project description:Prediction of neurological outcomes shortly after cardiac arrest would represent a major breakthrough. We tested the ability of gene expression profiles of blood cells to predict outcome in cardiac arrest patients. 35 consecutive cardiac arrest patients treated with therapeutic hypothermia (33Â°C for 24h) were included in this prospective monocentre study. Cerebral Performance Category (CPC) was determined at discharge and 6 months later. All patients had blood sampling at the end of hypothermia. Gene expression profiles of blood cells were determined using 25,000~gene microarray in two groups of patients: good outcome (CPC 1-2) and bad outcome (CPC 3-5).

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Project description:Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

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