Detection of fetal DNA in maternal plasma by microarray coupled with emulsions PCR

The presence of fetal DNA in maternal plasma made non-invasive prenatal diagnosis possible. Although fetal DNA has been used in several genetic disease diagnoses, many challenges remained in the detection methods. We attempted to develop a sensitive and reliable microarray coupled with emulsions PCR method to detect the fetal DNA in the plasma of pregnant women.

Fetal DNAs extracted from the plasma of pregnant women were amplified in emulsions, and fluorescence was labeled at the same time. The labeled target DNAs were hybridized and detected by the capturing DNA probes on a modified slide. Six Y chromosome special sequences in gene of SRY, DYS and DYZ as the marker of fetal DNAs were detected simultaneously in this study, and the beta-globin gene was detected as marker of total DNA from maternal plasma. An unrelated sequence was also detected as negative control in this study. 76 pregnant women in the first trimester of gestation joined in this study. Conventional PCR and real time PCR were also carried out for comparison.

We could detect the fetal DNAs reliably with this method in early stage of gestation. The 6Y chromosome sequences were detected in 40 of the 42 male fetus carrier samples, and no Y special sequence was detected in the female fetus carrier samples. The earliest plasma sample which we could detect in this study was collected on the 31st day after pregnancy.

The results suggest that the microarray coupled with emulsions PCR method could be used for fetal DNA detections, and emulsions were useful in DNA amplification as reaction media to overcome the primer incompatibility which frequently encounters in multiplex PCR amplification. Our methods have the potential in high-throughput assays and could be widely used in clinical researches and diagnosis.