Ontology highlight
ABSTRACT:
PROVIDER: PRJNA882936 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of high cost. Building upon previous knowledge that placenta, the main source of fetal circulating DNA, is hypomethylated in comparison to maternal tissue counterparts of cfDNA, we propose that targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches fetal genetic material and reduces numbers of required analytical sequencing reads thereby decreasing cost of a test.
2020-10-20 | GSE148964 | GEO
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:Whereas non-invasive prenatal testing for aneuploidies (NIPT-A) is widely implemented, non-invasive prenatal testing for monogenic diseases (NIPT-M) is lagging. By capturing and targeted sequencing of 250000 polymorphic SNP loci from maternal plasma circulating cell-free DNA (cfDNA) and DNA from relatives, the fetal haplotype and chromosomal copy numbers are deduced. In all families tested, the cfDNA derived haplotypes are on average 97% concordant with the neonatal and embryo haplotype. This generic non-invasive prenatal diagnostic approach allows cost efficient scrutinizing the fetal genome for the presence of any inherited monogenic disease or trait.
| EGAS00001003634 | EGA
Project description:Improving the Positive Predictive Value of Non-invasive Prenatal Screening (NIPS)
| PRJNA331174 | ENA
Project description:Down Syndrome (DS) is a relatively severe chromosomal disorder associated with many significant clinical anomalies. Nowadays, it is still challenging to collect DS samples for studies in clinical settings. In addition, there are no perfect animal models for DS. Therefore, we constructed disease-specific induced pluripotent stem cells（iPSCs）to explore a new modality for non-invasive prenatal diagnosis of DS.
2025-11-01 | GSE280849 | GEO
Project description:Down syndrome is characterized by trisomy 21 or partial duplication of chromosome 21. There have been extensive studies focusing on the identification of the Down Syndrome Critical Region (DSCR). Our case aims in providing evidence that duplication of 21q21.1-q21.2 is not included in the DSCR and that it has no clinical consequences on the phenotype. Due to missing the appropriate gestational age for serological screening, Non-Invasive Prenatal Testing (NIPT) analysis was performed for a pregnant woman with normal prenatal examinations at 22 weeks of gestation. The result of NIPT revealed a 5.8Mb maternally inherited duplication of 21q21.1-q21.2. To test whether the fetus also carried this duplication, ultrasound-guided amniocentesis was conducted and the result of chromosomal microarray analysis (CMA) with amniotic fluid showed a 6.7Mb duplication of 21q21.1-q21.2 (ranging from position 18,981,715 to 25,707,009) for the fetus. This partial duplication of 21q21.1-q21.2 for the fetus was maternally inherited. The pregnant woman and her family decided to continue the pregnancy after genetic counseling. This case clearly indicates that 21q21.1-q21.2 duplication is not included in the DSCR and most probably has no clinical consequences on the phenotype.
2021-06-05 | GSE176138 | GEO
Project description:This study was designed to identify non-invasive biomarkers for the diagnosis of MASH in patients with type 2 diabetes. The progression from simple steatosis to MASH in diabetic patients represents a critical clinical challenge, as it significantly increases the risk for cirrhosis and hepatocellular carcinoma. Current diagnostic methods are invasive and unsuitable for broad screening. We hypothesized that circulating exosomes contain a specific microRNA (miRNA) signature that can distinguish between diabetic patients with and without MASH. To test this, we isolated serum exosomes from both patient groups and performed small RNA sequencing to comprehensively profile their miRNA content. The goal of this dataset is to provide a resource of differentially expressed exosomal miRNAs that can serve as a foundation for the development of novel, non-invasive diagnostic tools for MASH in this high-risk population.
2025-11-21 | GSE303156 | GEO
Project description:Non-invasive prenatal testing (NIPT) using cell free fetal DNA has transformed prenatal care by allowing risk assessment for a number of fetal genetic conditions without posing risk to the pregnancy. However, its limitations, including low fetal fraction and high DNA fragmentation, restrict its capacity for comprehensive genomic analysis. As an alternative, cell-based NIPT offers the potential to capture intact fetal cells for more detailed genetic interrogation. Cervical mucosa is a promising source for fetal DNA as it can be collected non-invasively as early as 5 weeks into the pregnancy and contains intact fetal cells. We performed single cell mRNA squencing of transcervical swabs and placental samples from pregant donors at multiple gestational ages to identify potential fetal cells.
2026-05-31 | E-MTAB-15846 | biostudies-arrayexpress
Project description:Currently, the majority of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) present with locally invasive and/or metastatic disease, resulting in five-year survival of less than 5%. The development of an early diagnostic test is, therefore, expected to significantly impact the patient’s prognosis. In this feasibility study, we demonstrate for the first time the utility of miRNA biomarkers for non-invasive, early detection of PDAC in urine specimens.
2016-01-28 | GSE71962 | GEO