Evaluating the Utility of RNAseq in Prenatal Diagnostics: Expression Profiles of Cultured Chorionic Villus and Amniotic Fluid Samples

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OBJECTIVE: While RNAseq has enhanced variant interpretation in postnatal cases, its potential in the prenatal setting remains underexplored. This study investigates the utility of RNAseq in prenatal diagnostics by analyzing the expression profiles of cultured chorionic villus samples (cCVS) and amniotic fluid (cAF) samples. METHODS: We performed RNAseq on 25 prenatal samples (10 cCVS and 15 cAF) and compared their expression profiles with those of postnatal tissues-blood and skin fibroblasts. RESULTS: To evaluate the clinical relevance of gene expression in these samples, we curated a list of genes associated with fetal-onset genetic disorders (n = 375). Using this curated list as a reference, our analysis revealed that cAF samples have the highest proportion of highly expressed genes (60%), surpassing cCVS (54%), fibroblasts (54%), and blood (34%). Differential expression analysis identified unique gene expression patterns in cCVS and cAF samples, reflecting their distinct tissue origins. Specifically, cAF samples showed elevated expression of genes involved in fetal kidney development, whereas cCVS samples were enriched for genes related to trophoblast function. CONCLUSIONS: These findings demonstrate that prenatal RNAseq reliably detects clinically relevant gene expressions, offering insights into prenatal conditions and fetal organ development. This underscores the potential of prenatal RNAseq as a valuable tool for supporting genetic variant interpretation.

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