Fragmentation of cell-free fetal DNA in plasma and urine of pregnant women

Objectives We assessed the effect of freezing on fragmentation of fetal DNA in maternal plasma and differences in DNA fragmentation between plasma and urine from pregnant women. Methods 1. We prepared seven kinds of real-time PCR assays to amplify different-sized amplicons targeting the SRY gene. Fragmentation of fetal DNA in maternal plasma was compared between new (n = 10) and 4-year-old samples (n = 10). 2. To investigate differences in fragmentation of fetal DNA between plasma and urine from pregnant women, we amplified three different-sized amplicons and compared DNA fragmentation between plasma and urine (n = 7). Results 1. Relative concentrations of fetal DNA compared to a 63-bp amplicon in new samples were 53.1, 42.0, 9.2 and 2.0% (median) for PCR amplicons of 107, 137, 193 and 313 bp, respectively. Concentrations in 4-year-old samples were 70.4, 40.9, 11.9 and 2.3%, respectively. 2. Although fetal DNA in urine was not detected for 107- and 137-bp amplicons of the SRY sequence, fetal DNA using a 63-bp amplicon was detectable in five of seven cases (71.4%). Conclusion Cell-free fetal DNA in maternal plasma is stable under cryopreservation at -20 degrees C for at least 4 years. Approximately, 60% of fetal DNA in maternal plasma was fragmented to < 100-bp long, and fetal DNA in urine was further fragmented. Maternal urine may be usable for detection of fetal DNA, although smaller target size is more important for PCR amplification of fetal DNA in urine than in the analysis of plasma from pregnant women. Copyright (c) 2005 John Wiley & Sons, Ltd.