OP22.07: Validation of NIPT as a screening test for Trisomy 21, 18, 13 and fetal sex performed at Hvidovre Hospitals NIPT Centre, Copenhagen, Denmark

Abstract

The objective of this study was to establish an open source platform for NIPT based on Massive Parallel whole-genome Sequencing (MPS) in a public setting. MPS was performed on circulating cell-free DNA from 205 selected pregnant women with known fetal karyotypes. The pipeline included automated library preparation and sequencing on a HiSeq1500 (Illumina). WISECONDOR and SeqFF were used for data analysis of aneuploidies, fetal sex and fetal fraction (FF). Data analysis for aneuploidy and fetal sex were accepted in samples with FF above 0.02 and 0.025, respectively. Samples with FF below cut-off were described as 'no-calls'. The NIPT results were positive for T21 in 44 of 46 T21 cases. The two negative T21 cases were 'no-calls' due to low FF. Among 19 T18 cases 14 were NIPT positive of which two cases were identified even though FF were too low. Two samples were 'no-calls' and three samples were false negative, which could be explained by a vanished twin or IVF treatment. Finally, seven out of eight T13 cases were positive, though one case had a low FF. The false negative T13 sample is probably explained by a vanished twin. Among normal karyotypes we found four false positive cases. Fetal sex was analysed in 189 samples (FF<0.025 excluded) and was correctly identified in all 94 females. Fetal sex was correctly identified in 92 out of 95 male fetuses. Two of the incorrectly results might be due to a vanished twin and a very high maternal BMI. Our study shows that screening for fetal aneuploidy and sex can be done by our fully automated NIPT pipeline. The sensitivity for T21 was 100% but lower for T18 and T13. This study demonstrates that FF, a vanished twin, BMI and perhaps IVF are important factors that should be taken into consideration in the interpretation of NIPT results.