ArticlePrenatal diagnosis2014
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome.
Article in Prenatal diagnosis, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Differential Transcriptome Analysis of Intrauterine UPD6pat Fetuses With Distinct Phenotypes.Molecular genetics & genomic medicine · 2026Article
- The Role of Microarray in Modern Sequencing: Statistical Approach Matters in a Comparison Between Microarray and RNA-Seq.Biotech (Basel (Switzerland)) · 2025Article
- RNA-Seq of amniotic fluid cell-free RNA: a discovery phase study of the pathophysiology of congenital cytomegalovirus infection.American journal of obstetrics and gynecology · 2022Article
- Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing.Prenatal diagnosis · 2022Review
- The Amniotic Fluid Cell-Free Transcriptome Provides Novel Information about Fetal Development and Placental Cellular Dynamics.International journal of molecular sciences · 2021Review
- Transcriptomic Analysis of Cell-free Fetal RNA in the Amniotic Fluid of Vervet Monkeys (Comparative medicine · 2020Article
- Article
- Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition.Scientific reports · 2019Article
- Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Review
- Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele.American journal of obstetrics and gynecology · 2017Article
- Extracellular RNA in aging.Wiley interdisciplinary reviews. RNA · 2017Review
- Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity.BMC medical genomics · 2015Article
- The amniotic fluid transcriptome as a guide to understanding fetal disease.Cold Spring Harbor perspectives in medicine · 2015Review
- A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.PloS one · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
objectiveThe aim of this study was to compare the complexity of the amniotic fluid supernatant cell-free fetal transcriptome as described by RNA Sequencing (RNA-Seq) and gene expression microarrays.
methodsCell-free fetal RNA from the amniotic fluid supernatant of five euploid mid-trimester samples was divided and prepared in tandem for analysis by either the Affymetrix HG-U133 Plus 2.0 Gene Chip microarray or Illumina HiSeq. Transcriptomes were assembled and compared on the basis of the presence of signal, rank-order gene expression, and pathway enrichment using Ingenuity Pathway Analysis (IPA). RNA-Seq data were also examined for evidence of alternative splicing.
resultsWithin individual samples, gene expression was strongly correlated (R = 0.43-0.57). Fewer expressed genes were observed using RNA-Seq than gene expression microarrays (4158 vs 8842). Most of the top pathways in the 'Physiological Systems Development and Function' IPA category were shared between platforms, although RNA-Seq yielded more significant p-values. Using RNA-Seq, examples of known alternative splicing were detected in several genes including H19 and IGF2.
conclusionsIn this pilot study, we found that expression microarrays gave a broader view of overall gene expression, while RNA-Seq demonstrated alternative splicing and specific pathways relevant to the developing fetus. The degraded nature of cell-free fetal RNA presented technical challenges for the RNA-Seq approach.
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