Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA30977 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method can identify pregnant women with AID during routine non-invasive prenatal screening. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.
2022-09-14 | E-MTAB-11607 | biostudies-arrayexpress
Project description:The discovery of fetal mRNA transcripts in maternal circulation holds great promise for noninvasive prenatal diagnosis. To identify potential fetal biomarkers, we studied whole blood and plasma transcripts common to term pregnant women and their newborns but reduced or absent in the postpartum mothers. In whole blood, 157 potentially-fetal transcripts were identified. RT-PCR confirmed the presence of specific transcripts, SNP analysis confirmed the presence of fetal transcripts in maternal circulation. Comparison of whole blood and plasma samples from the same women suggested that placental genes are more easily detected in plasma. We conclude that fetal and placental mRNA circulates in the blood of pregnant women.
2014-01-08 | GSE53669 | GEO
Project description:<p><b>Background</b>: Circulating cell free (ccf) fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the genetically distinct maternal and fetal DNA. Current testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA and thus support additional clinical opportunities; however, this depends on knowledge of the methylomes of ccf DNA and its cellular contributors.</p> <p><b>Results</b>: Whole genome bisulfite sequencing was performed on a set of unmatched samples including ccf DNA from 8 non-pregnant (NP) and 7 pregnant female donors and genomic DNA from 7 buffy coat and 5 placenta samples. We found CpG cytosines within longer fragments were more likely to be methylated, linking DNA methylation and fragment size in ccf DNA. Comparison of the methylomes of placenta and NP ccf DNA revealed many of the 51,259 identified differentially methylated regions (DMRs) were located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases, regions we termed placenta hypomethylated domains. DMRs identified when comparing placenta to NP ccf DNA were recapitulated in pregnant ccf DNA, confirming the ability to detect differential methylation in ccf DNA mixtures.</p> <p><b>Conclusions</b>: We generated methylome maps for four sample types at single base resolution, identified a link between DNA methylation and fragment length in ccf DNA, identified DMRs between sample groups, and uncovered the presence of megabase-size placenta hypomethylated domains. Furthermore, we anticipate these results to provide a foundation to which future studies using discriminatory DNA methylation may be compared.</p>
| phs000846 | dbGaP
Project description:Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no comprehensive and direct accuracy evaluations of these tools is published. Here, we evaluate and determine the precision of five commonly used computational NIPT aneuploidy analysis tools, considering diverse sequencing depth (coverage), arbitrary sequencing read placement, and fetal DNA fraction on clinically validated NIPT samples.
| EGAS00001005323 | EGA
Project description:The goal of the experiment was to uncover novel TTTS biomarkers using microarray gene expression analysis of cell free fetal RNA from the amniotic fluid of TTTS-affected and non-affected pregnant women.
2018-06-01 | E-MTAB-6100 | biostudies-arrayexpress
Project description:The discovery of fetal mRNA transcripts in maternal circulation holds great promise for noninvasive prenatal diagnosis. To identify potential fetal biomarkers, we studied whole blood and plasma transcripts common to term pregnant women and their newborns but reduced or absent in the postpartum mothers. In whole blood, 157 potentially-fetal transcripts were identified. RT-PCR confirmed the presence of specific transcripts, SNP analysis confirmed the presence of fetal transcripts in maternal circulation. Comparison of whole blood and plasma samples from the same women suggested that placental genes are more easily detected in plasma. We conclude that fetal and placental mRNA circulates in the blood of pregnant women. [I] We profiled whole antepartum (A), postpartum (P), and umbilical cord (U) blood samples from each of 9 mothers and their 10 newborns (1 set of twins, denoted as a and b after the sample names). [II] We also profiled plasma samples (A, P, and U) from three of those mothers to allow for a direct comparison between blood and plasma.
2014-01-08 | E-GEOD-53669 | biostudies-arrayexpress
Project description:Cell-free DNA molecules in the plasma of pregnant women exhibit nonrandom fragmentation with preferred end sites. We studied if such preferred end sites might bear any re- lationship with fragment lengths of plasma DNA. Short and long plasma DNA molecules were associated with different preferred DNA end sites. Analysis of size-tagged preferred ends could be used for measuring fetal DNA fraction and for facilitating fetal trisomy 21 detection. Fetal preferred end sites were generally located in the nucleosome cores, while the maternal ones were located in the linker regions. This con- ceptual framework provides an explanation of the relative shortness of fetal DNA in maternal plasma and brings us closer to understanding the biological mechanisms that influence plasma DNA fragmentation.
| EGAS00001002831 | EGA
Project description:Circulating cell-free RNA in the blood provides a potential window into the health, phenotype, and developmental programs of a variety of human organs. We employed high throughput methods of RNA analysis such as microarrays and next-generation sequencing to characterize the global landscape circulating RNA in a cohort of human subjects. By focusing on genes whose expression is highly specific to certain tissues, we were able to identify the relative contributions of these tissues to circulating RNA, and to monitor changes in tissue development and health. As one such application of this approach, we performed a longitudinal study on pregnant women and analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. In addition to the presence of messenger RNA, we observed and characterized non-coding species such as long non-coding RNA and circular RNA transcripts whose presence had not been previously observed in human plasma. We demonstrate that it is possible to track specific longitudinal phenotypic changes in both the mother and the fetus, and that it is possible to directly measure transcripts from a variety of fetal tissues in the maternal blood sample. We also studied the role of neuron specific transcripts in the blood of healthy adults and those suffering from the neurodegenerative disorder Alzheimer’s disease, and showed that disease specific neural transcripts are present at increased levels in the blood of affected patients. Characterization of the cell-free transcriptome in its entirety may thus provide broad insights into human health and development without the need for invasive tissue sampling. Cell-free RNA are extracted from pregnant women on the first, second and third trimester and immediately post-partum. Temporal trends are extracted from individual patients.
2014-04-18 | E-GEOD-56899 | biostudies-arrayexpress