Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253597 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1460750_1.fastq.gz | Fastqsanger.gz | |||
| SRR1460750_2.fastq.gz | Fastqsanger.gz | |||
| SRR1460751_1.fastq.gz | Fastqsanger.gz | |||
| SRR1460751_2.fastq.gz | Fastqsanger.gz | |||
| SRR1460752_1.fastq.gz | Fastqsanger.gz |
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Project description:While chromosomal microarray analysis (CMA) is increasingly utilized in prenatal diagnosis, most research focuses on mid-to-late pregnancy amniotic fluid samples. Chorionic villus samples (CVS) from the first trimester possess distinct biological characteristics. To evaluate the efficacy of CMA in early pregnancy prenatal diagnosis, we performed a genomic analysis of CVS from high-risk pregnancies.We conducted a single-center cohort study of singleton pregnancies that underwent CVS between 11⁺⁰ and 13⁺⁶ weeks of gestation. Indications for testing included advanced maternal age, ultrasound-detected soft markers or structural anomalies, abnormal first-trimester serum screening, or adverse obstetric history. All villus samples were analyzed using CMA (Affymetrix CytoScan 750K arrays). Among the samples analyzed by CMA, 16.6% showed chromosomal abnormalities, with CNVs accounting for 58.9% of these cases. Compared with other indicators, the detection rate was significantly higher in the group with ultrasound abnormalities. Complex ultrasound abnormalities, in particular, hold greater clinical significance. This study demonstrates the utility of CMA for detecting chromosomal abnormalities in first-trimester CVS. Our findings support the integration of CMA into early prenatal diagnostic protocols.
2025-12-04 | GSE306863 | GEO
Project description:Placental gene expression is a finely controlled process, yet little is known about the factors that regulate it, including epigenetic factors such as DNA methylation. In this study, we quantified the effects of DNA methylation on placental gene expression. Using targeted high throughput sequencing, we generated methylation profiles of 3.7 million CpG dinucleotides from 6 karyotypically normal CVS samples and compared these to gene expression data obtained from a publically available database. We found a broad association between methylation and gene expression at both the chromosome and individual gene levels. At the chromosome level, we found alternating domains of high and low methylation. Within each gene, we found distinct methylation patterns at different regulatory genetic elements. For example, the promoters of highly expressed genes were neither highly methylated, nor completely unmethylated. Rather, they had < 50% of the CG dinucleotides in their sequences in the methylated state. In contrast, promoters of unexpressed genes tended to be either highly methylated or fully unmethylated. Similarly, patterns of methylation in exons and introns differed between highly expressed and unexpressed genes. Our data show that the relationship between DNA methylation and gene expression is nuanced: highly expressed and unexpressed genes differ, not only by their extent of methylation, but also by minute changes in the locations of their methylation sites. DNA methylation analysis of placental genes may help predict abnormal placental gene expression and pregnancy complications, making it a possible tool for prenatal diagnosis. DNA from 6 chorionic villus samples from the 1st trimester (from 3 male and 3 female fetuses) as well as 3 maternal blood cell samples was extracted, hybridized to probes in the Agilent SureSelectXT Methyl-Seq Target Enrichment kit, targeting 84Mb of the genome and then bisulfite converted before sequencing.
2016-06-25 | E-GEOD-58826 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples. Bisulphite converted DNA from the 54 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.
2015-03-31 | E-GEOD-66210 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples.
2015-03-31 | GSE66210 | GEO
Project description:Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples We performed a genome wide analysis of DNA methylation first trimester CVS samples and gestational age matched MBCs. We analyzed DNA samples obtained from 12 CVS samples and 12 MBC samples. Data were generated using two high-throughput approaches: the Infinium “humanmethylation27” platform marketed by Illumina and a custom Agilent-based platform. We then compared these data with genome wide transcription data for the same tissues. This Series covers only the Illumina HumanMethylation27 part of the study.
2010-07-31 | E-GEOD-23311 | biostudies-arrayexpress
Project description:Human placenta bulk small RNA-seq from healthy pregnancies without infertility, from n=113 first trimester (58 female, 55 male) and n=47 third trimester (19 female, 28 male) tissue samples. Tissue was collected at Cedars-Sinai Medical Center in Los Angeles, California, USA. First trimester placenta was collected at 70-102 days of gestation from leftover chorionic villus sampling for prenatal genetic diagnosis. Third trimester placenta was collected after delivery at 254-290 days gestation from the fetal side near the umbilical cord insertion site beneath the amnion. Mothers with pre-existing diabetes or hypertension were excluded. All pregnancies were conceived without fertility treatments, were normal karyotype, and resulted in live singleton births. The average parental age was advanced (over 35 years old) but PCA analysis did not show clustering by either maternal or paternal age. Gonzalez et al 2021 [PMID: 34030457] analyzes similarities and differences between first and third trimester miRNA expression overall. Flowers et al 2021 focuses on the effect of fetal sex on miRNA expression across gestation.
2022-08-04 | GSE184860 | GEO
Project description:Noninvasive prenatal diagnosis currently used does not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal whole blood have been explored for noninvasive prenatal detection. However, such efforts cover only chromosomal aneuploidy; fetal methylated DNA biomarkers for detecting single-gene disease remain to be discovered. To address this issue, we systematically screened significantly hypermethylated genes in fetal tissues compared with maternal blood for noninvasive prenatal diagnosis of various inherited diseases. First, Methylated-CpG island recovery assay combined with CpG island array was performed in four maternal peripheral bloods and their corresponding placental tissues. Subsequently, direct bisulfite sequencing and combined bisulfite restriction analysis (COBRA) were carried out to validate the reliability of methylation microarray analysis. As results, 310 significantly hypermethylated genes in fetal tissues were detected by microarray. Two of five randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in fetal tissue samples by direct bisulfite sequencing. All four randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in five independent amniotic fluid samples and five independent chorionic villus samples from 10 pregnant women by CORBA. In conclusions, We found a lot of hypermethylated genes and methylation sites in fetal tissues, some of which have great potential to be developed into molecular markers for noninvasive prenatal diagnosis of monogenic disorders. Further clinical study is warranted to confirm these findings. Paired experiments, placental tissues vs. maternal peripheral bloods. Biological replicates: 4 placental tissues and 4 correspoding maternal peripheral bloods.
2012-02-22 | E-GEOD-35997 | biostudies-arrayexpress
Project description:Noninvasive prenatal diagnosis currently used does not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal whole blood have been explored for noninvasive prenatal detection. However, such efforts cover only chromosomal aneuploidy; fetal methylated DNA biomarkers for detecting single-gene disease remain to be discovered. To address this issue, we systematically screened significantly hypermethylated genes in fetal tissues compared with maternal blood for noninvasive prenatal diagnosis of various inherited diseases. First, Methylated-CpG island recovery assay combined with CpG island array was performed in four maternal peripheral bloods and their corresponding placental tissues. Subsequently, direct bisulfite sequencing and combined bisulfite restriction analysis (COBRA) were carried out to validate the reliability of methylation microarray analysis. As results, 310 significantly hypermethylated genes in fetal tissues were detected by microarray. Two of five randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in fetal tissue samples by direct bisulfite sequencing. All four randomly selected hypermethylated genes detected by microarray were confirmed to be hypermethylated in five independent amniotic fluid samples and five independent chorionic villus samples from 10 pregnant women by CORBA. In conclusions, We found a lot of hypermethylated genes and methylation sites in fetal tissues, some of which have great potential to be developed into molecular markers for noninvasive prenatal diagnosis of monogenic disorders. Further clinical study is warranted to confirm these findings.
2012-02-22 | GSE35997 | GEO
Project description:Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples
2010-07-31 | GSE23311 | GEO
Project description:Preeclampsia is one of the leading causes of maternal death worldwide. While the root cause is still unknown, the underlying biology of the disorder is becoming more clear. We recently published a study showing large, significant differences in DNA methylation in 3rd trimester placental samples associated with early-onset preeclampsia (EOPET) compared to controls. In this study, to identify DNA methylation differences associated with preeclampsia that occur early in pregnancy and to further delineate common EOPET-associated differences, we utilized a genetic defect, trisomy 16 (T16), that is predisposing to preeclampsia. We ran T16 placental samples from the 1st trimester (n=5) and 3rd trimester (n=10) against gestational age matched controls on the Illumina Infinium HumanMethylation450 BeadChip. Third trimester samples were from pregnancies with T16 confined to the placenta (confined placental mosaicism 16;CPM16), and consisted of samples that were and were not associated with EOPET (n=5 each). We identified a large number of DNA methylation differences in CPM16 samples compared to controls using stringent criteria (n=2254;False Discovery Rate <0.01, ->0.15). Several of these differences (11%) overlapped differences observed in chromosomally normal EOPET using similarly stringent criteria (FDR<0.01;->0.125). Isolating EOPET-associated probes produced a similar - distribution amongst CPM16 samples, although samples associated with EOPET showed a tendency towards larger DNA methylation differences. We also identified 262 DNA methylation differences between 1st trimester T16 and 1st trimester controls. Of these, 77 overlapped differences seen in 3rd trimester CPM16. Investigating these 77 T16/CPM16 specific DNA methylation differences, we identified three probes near two genes (ARGHEF37 and JUNB) that were also present as EOPET-associated methylation differences. In summary, we identified significant overlapping DNA methylation profiles of placentas with T16 and chromosomally normal placentas associated with EOPET. Specific DNA methylation marks within these profiles may be of future clinical utility in early identification of pregnancies susceptible to EOPET. Bisulfite converted DNA from 5 1st trimester trisomy 16 placentas, 5 chromosomally normal 1st trimester placentas, 10 third trimester placentas from confined placental mosaicism placentas and 10 chromosomally normal 3rd trimester placentas
2014-01-15 | E-GEOD-49343 | biostudies-arrayexpress