QF-PCR rapid aneuploidy screen and aCGH analysis of cell free fetal (cff) DNA in supernatant of compromised amniotic fluids (AF)

Abstract

Objective: The aim of this study was to determine whether cell free fetal (cff) DNA in residual amniotic fluid (AF) supernatant obtained from bloody, low-volume and late gestation samples can be used for prenatal diagnosis by quantitative fluorescence polymerase chain reaction (QF-PCR) and array comparative genomic hybridization (aCGH). Method: A total of 49 compromised AFs were analyzed in this case-control, double-blinded study. The samples were processed through: a conventional cytogenetic approach utilizing Fluorescence in situ Hybridization and/or karyotype (Approach I); QF-PCR analysis to establish the presence of maternal cell contamination (MCC) (Approach II) and a newly proposed approach using AF supernatant cff DNA (Approach III). Data on clinical impact and turn-around-time was collected. Results: Evidence of MCC was not detected in any of the cff DNA samples, and informative results were provided for all cases, including nine aneuploidies. In contrast, the conventional approach (I) failed to provide results either due to MCC or culture failure in a significant proportion of cases. An adequate amount of quality cff DNA was obtained for successful aCGH testing. Conclusion: We have shown that it is feasible to isolate pure cff DNA from routinely discarded AF supernatant to perform QF-PCR and microarray analyses, providing timely and informative results even for problematic grossly bloody and otherwise compromised AF samples or culture failures.