Uncultured Amniocytes Enable Rapid and Clinically Informative Prenatal RNA Sequencing for Genetic Diagnosis

RNA sequencing (RNA-seq) provides transcript-level evidence for interpreting variants of uncertain significance in monogenic disorders, but its prenatal application is limited by sample availability and processing time. This study evaluated uncultured amniocytes as a practical substrate for prenatal RNA-seq. We performed RNA-seq on 15 matched paired cultured and uncultured amniocyte samples and compared their transcriptomic profiles using principal component analysis, differential expression analysis, and pathway enrichment. We then analyzed 77 uncultured amniocyte samples collected between 16+6 and 29+6 weeks of gestation to disease-related gene expression coverage and gestational-age-associated variation. Five selected cases were further analyzed to evaluate transcript-level findings relevant to variant interpretation. Cultured and uncultured amniocytes showed distinct transcriptomic profiles, with 11,234 differentially expressed genes and culture-associated transcriptional and pathway changes. Uncultured amniocytes expressed an average of 63.4% of genes across disease-associated panels, and most disease-related genes were consistently expressed across gestational stages, although stage-associated differences in gene detectability were observed. In selected cases, uncultured amniocyte RNA-seq detected aberrant expression, aberrant splicing, allelic imbalance, and expressed sequence variants. These findings support the feasibility of prenatal RNA-seq using uncultured amniocytes and further evaluation of this approach as a complementary functional assay for prenatal variant interpretation.