Effect of Different DNA Concentration Methods on Performance of Non-Invasive Fetal Y-Chromosomal Short Tandem Repeat Profiling from Maternal Plasma

Background: The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. Materials and Methods: DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. Results: A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. Discussion: The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate.