Improving the Positive Predictive Value of Non-invasive Prenatal Screening (NIPS)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE84810 | GEO | 2017/05/22
SECONDARY ACCESSION(S): PRJNA331174
REPOSITORIES: GEO
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Project description:We evaluated performance characteristics of a laboratory-developed, non-invasive prenatal screening (NIPS) assay for fetal aneuploidies. This assay employs massively parallel shotgun sequencing with full automation. GC sequencing bias correction and statistical smoothing were performed to enhance discrimination of affected and unaffected pregnancies. Maternal plasma samples from pregnancies with known aneuploidy status were used for assay development, verification, and validation. Assay verification studies using 2,085 known samples (1873 unaffected, 69 trisomy 21, 20 trisomy 18, 17 trisomy 13) demonstrated complete discrimination between autosomal trisomy (Z scores >8) and unaffected (Z scores <4) singleton pregnancies. A validation study using 552 known samples (21 trisomy 21, 10 trisomy 18, 1 trisomy 13) confirmed complete discrimination. Twin pregnancies showed similar results. Follow-up of abnormal results from the first 10,000 clinical samples demonstrated PPVs of 98% (41/42) for trisomy 21, 92% (23/25) for trisomy 18, and 69% (9/13) for trisomy 13. Adjustment for causes of false-positive results identified during clinical testing (eg, maternal duplications) improved PPVs to 100% for trisomy 21 and 96% for trisomy 18. This NIPS test demonstrates excellent discrimination between trisomic and unaffected pregnancies. The PPVs obtained in initial clinical testing are substantially higher than previously reported NIPS methods.
| S-EPMC5382935 | biostudies-literature
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:Maternal exposure to stress during pregnancy is associated with an increased risk of psychiatric disorders in the offspring in later life. The mechanisms through which the effects of maternal stress are transmitted to the fetus are unclear, however the placenta, as the interface between mother and fetus, is likely to play a key role. Using a rat model, we investigated a role for placental oxidative stress in conveying the effects of maternal social stress to the fetus and the potential for treatment using a nanoparticle-bound antioxidant to prevent adverse outcomes in the offspring. Maternal psychosocial stress increased circulating corticosterone in the mother, but not in the fetuses. Maternal stress also induced oxidative stress in the placenta, but not in the fetal brain. Blocking oxidative stress using an antioxidant prevented the prenatal stress-induced anxiety phenotype in the male offspring, and prevented sex-specific neurobiological changes, specifically a reduction in dendrite lengths in the hippocampus, as well as reductions in the number of parvalbumin-positive neurons and GABA receptor subunits in the hippocampus and basolateral amygdala of the male offspring. Importantly, many of these effects were mimicked in neuronal cultures by application of placental-conditioned medium or fetal plasma from stressed pregnancies, indicating molecules released from the placenta may mediate the effects of prenatal stress on the fetal brain. Indeed, both placenta-conditioned medium and fetal plasma contained differentially abundant microRNAs following maternal stress, and their predicted targets were enriched for genes relevant to nervous system development and psychiatric disorders. The results highlight placental oxidative stress as a key mediator in transmitting the maternal social stress effects on the offspring's brain and behaviour, and offer a potential intervention to prevent stress-induced fetal programming of affective disorders.
2020-12-01 | GSE130573 | GEO
Project description:With the advancement of molecular technology, fetal talipes equinovarus (TE) is believed to be not only associated with chromosome aneuploidy, but also related to chromosomal microdeletion and microduplication. The study aimed to explore the molecular etiology of fetal TE and provide more information for the clinical screening and genetic counseling of TE by CMA.This retrospectively study included 131 fetuses with TE identified by ultrasonography. Conventional karyotyping and SNP array analysis were performed for all the subjects. They were divided into isolated TE group (n=55) and complex group (n=76) according to structural anomalies.Among the total of 131 fetuses, karyotype analysis found 12(9.2%) abnormal results, while SNP array found 27 (20.6%) cases. Trisomy 18 was detected most frequently among abnormal karyotypes. The detection rate of SNP array was significantly higher than that of traditional chromosome karyotype analysis.SNP array detected 15 (11.5%) cases of submicroscopic abnormalities that karyotype analysis did not find. The most common CNV was the 22q11.2 microdeletion. For both analyses, the overall detection rates were significantly higher in the complex TE group than in the isolated TE group. The incremental yield of chromosomal abnormalities in fetuses with unilateral TE (22.0%) was higher than in fetuses with bilateral TE (19.8%), but this difference was not statistically significant.Abnormal chromosomes were most frequently detected in fetuses with TE plus cardiovascular system abnormalities.Fetal TE is related to chromosomal microdeletion or microduplication. Prenatal diagnosis is recommended for fetuses with TE, and CMA testing is preferred. CMA can improve the detection rate of chromosomal abnormalities associated with fetal TE, especially in pregnancies with complex TE.
2023-10-22 | GSE230532 | GEO
Project description:For many chronic diseases, translational success using the animal model paradigm has reached an impasse. Using Alzheimer's disease as an example, this review employs a networks-based method to assess repeatability of outcomes across species, by intervention and mechanism. Over 75% of animal studies reported an improved outcome. Strain background was a significant potential confounder. Five percent of interventions had been tested across animals and humans, or examined across three or more animal models. Positive outcomes across species emerged for donepezil, memantine and exercise. Repeatable positive outcomes in animals were identified for the amyloid hypothesis and three additional mechanisms. This approach supports in silico reduction of positive outcomes bias in animal studies.
| S-EPMC4417064 | biostudies-literature
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:BackgroundTwin growth discordance was demonstrated to be a risk factor for adverse perinatal outcomes, and prenatal ultrasonographic methods were utilized to predict twin growth discordance to improve outcomes. The results currently reported are not consistent due to the poor unified parameters and gestational durations.MethodsA total of 71 dichorionic twins with growth discordance and 346 dichorionic twins with normal growth were respectively included in the retrospective cohort study. The weight discordance of more than 25% was defined as a "growth discordant twin". The clinical baseline information, maternal outcomes, twin birth weights and fetal growth parameters (which were measured by ultrasound) were compared between the two groups from early gestation to late gestation. Multiple logistic regression and receiver operating characteristic curves were adopted to evaluate the predictive value of the growth parameters.ResultsCompared with normal dichorionic twins, the clinical baseline conditions were similar in the twins those finally developed growth discordance. The fetal growth parameters and the deepest volume pocket of amniotic fluid in early and mid-pregnancy showed no obvious predictive values. The fetal growth parameters in late pregnancy showed predictive values, especially the discordance of estimated fetal weight (EFW) in the early third-trimester (P?<?0.001, area under the curve, 0.822; the cut-off value, 20%; sensitivity, 66.67%; specificity, 91.30%; positive predictive value, 88.46%).ConclusionTwo assessment approaches were suggested and adopted to predict twin growth discordance in the current study. Twin growth should be assessed longitudinally and dynamically. Normal twins may show growth imbalance in the early stage. The discordance of EFW in late pregnancy may be a useful indicator for a growth discordance of more than 25%, which is required further confirmation.
| S-EPMC7388498 | biostudies-literature
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 | dbGaP
Project description:A total of 1039 stage I-III invasive lung adenocarcinoma including 186 solid subtype patients who have undergone radical resection were assessed for clinicopathologic characteristics, status of common driver mutations, pattern of recurrence, recurrence-free survival (RFS), overall survival (OS), post-recurrence survival (PRS) and predictive value for adjuvant chemotherapy and EGFR tyrosine kinase inhibitors (TKIs). Solid predominant adenocarcinomas were more likely to have initial distant recurrences than non-solid subtype invasive adenocarcinomas (P = 0.018). In univariate analysis, solid predominant adenocarcinoma patients had significantly worse RFS (P < 0.001), OS (P < 0.001) and PRS (P = 0.010). Multivariate analysis adjusting for clinicopathologic variables and mutational status showed that solid subtype was an independent poor prognostic factor (odds ratio = 1.876, 95% confidence interval: 1.291-3.158; P = 0.003) and an independent negative predictor for stage II-III patients undergoing adjuvant chemotherapy (odds ratio = 2.020, 95% confidence interval: 1.291-3.158; P = 0.002). In EGFR-mutated solid predominant lung adenocarcinoma patients who experienced disease recurrence, the response rate to EGFR TKIs was only 37.5%. In radically resected invasive lung adenocarcinoma, solid subtype was an independent poor prognostic factor and negative predictor for adjuvant chemotherapy.
| S-EPMC4650946 | biostudies-other
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