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The Capital Region of Denmark - a part of Copenhagen University Hospital

Open source non-invasive prenatal testing platform and its performance in a public health laboratory

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OBJECTIVE: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis.

METHODS: Plasma-derived DNA from a total of 375 pregnant women (divided into three datasets) was whole-genome sequenced on the Ion Proton™ platform and analyzed using a pipeline based on WISECONDOR for fetal autosomal aneuploidy detection and SeqFF for fetal DNA fraction estimation. We furthermore validated a fetal sex determination analysis.

RESULTS: The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong correlation (R(2)  = 0.72) to Y-chromosomal content of the male fetus samples.

DISCUSSION: We have implemented NIPT into Danish health care using published open source scripts for autosomal aneuploidy detection and fetal DNA fraction estimation showing excellent false negative and false positive rates. SeqFF provides a good estimation of fetal DNA fraction. This coupled with an analysis of fetal sex that provides a complete NIPT workflow, which may easily be adapted for implementation in other public health laboratories. © 2016 John Wiley & Sons, Ltd.

Original languageEnglish
JournalPrenatal Diagnosis
Issue number6
Pages (from-to)530-6
Number of pages7
Publication statusPublished - Jun 2016

    Research areas

  • Journal Article

ID: 49586108