Abstract
PURPOSE: Fetal cells in maternal blood are a pure source of fetal genomic DNA for noninvasive prenatal testing (NIPT), if successfully isolated. We assessed whether single-cell genome and transcriptome sequencing (G&T-seq) can be applied to efficiently isolate fetal nucleated red blood cells (fNRBCs) suitable for genetic testing. METHODS: Using umbilical cord blood as a model, we isolated 165 single NRBC candidates from four samples and 12 single lymphocytes as controls from one sample. G&T-seq was used to estimate the maturation stage of each NRBC candidate from the transcriptome data, and genomic integrity was assessed using shallow whole-genome sequencing (WGS) data. RESULTS: Multi-dimensional scaling (MDS) of the transcriptome data revealed that five NRBC candidates clustered separately, classifying them as primitive NRBCs. Two of these cells showed high yields of WGS libraries and high mapping rates comparable to control lymphocytes, suggesting an intact nuclear genome. CONCLUSIONS: G&T-seq effectively identified primitive NRBCs with high-quality DNA among candidate cells dominated by mature RBCs. Single-cell multi-omics technology may advance the development of fNRBC-based NIPT.