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Creating basis for introducing NIPT in the Estonian public health setting

By Olga Žilina, Kadri Rekker, Lauris Kaplinski, Martin Sauk, Priit Paluoja, Hindrek Teder, Eva-Liina Ustav, Neeme Tõnisson, Konstantin Ridnõi, Priit Palta, Kaarel Krjutškov, Ants Kurg, Andres Salumets

Posted 03 Oct 2018
bioRxiv DOI: 10.1101/431924

Objective: The study aimed to validate a whole-genome sequencing-based NIPT method and our newly developed NIPTmer analysis software with the potential to integrate the pipeline into prenatal clinical care in Estonia. Method: In total, 447 maternal blood samples were included to the study. Analysis pipeline involved whole-genome library preparation and massively parallel sequencing on Illumina NextSeq 500. Aneuploidy status was determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data. To estimate fetal fraction (FF) from total cell-free DNA SeqFF was implemented. Results: NIPTmer software allowed to identify correctly all samples of non-mosaic T21 (15/15), T18 (9/9) and T13 (4/4) cases. However, one mosaic T18 remained undetected. Six false positive results were observed, including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). FF < 4% (2.8-3.99%) was estimated in eight samples, including two samples with T13 and T18. Despite low FF, these two samples were determined as aneuploid with NIPTmer software. Conclusion: Our NIPT analysis pipeline proved to perform efficiently in detecting common fetal aneuploidies T21, T18 and T13 and is feasible for implementation into clinical service in Estonia.

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