Some caveats in PCR-based prenatal diagnosis on direct amniotic fluid versus cultured amniocytes.

The polymerase chain reaction (PCR) offers new advances in prenatal genetic diagnosis particularly with limitations in amount of sample, turn-around time of results, and costs. However, maternal contamination is a concern in any fetal sampling, and even more so with PCR given its potential to detect at the level of a few cells. We report our experience with 53 matched pairs of direct and cultured amniocytes using three independent DNA markers amplified by PCR within the setting of a service molecular diagnostic laboratory. Despite 15/53 (30 per cent) of the amniotic fluids showing visible red blood cells prior to culturing, only 5/53 (9 per cent) showed trace PCR contamination. Of note, this was found on only one marker with a particularly robust PCR product of small size and at such a low level that it was unlikely to have resulted in ambiguous interpretation. One of the cultures also showed a similar type of contamination with this same marker. However, in addition, there were 2/53 (3.7 per cent) cultures which showed substantial maternal contamination detected by all three PCR markers, but not visualized on the originating direct samples. Our results suggest that the careful use of direct amniocytes for molecular genetic testing by PCR is reliable and reproducible in most cases.