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Creating basis for introducing NIPT in the Estonian public health setting

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
doi: https://doi.org/10.1101/431924
Olga Žilina
1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Kadri Rekker
2Competence Centre on Health Technologies, Tartu, Estonia
3Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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Lauris Kaplinski
1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Martin Sauk
1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Priit Paluoja
2Competence Centre on Health Technologies, Tartu, Estonia
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Hindrek Teder
2Competence Centre on Health Technologies, Tartu, Estonia
4Department of Biomedicine, Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
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Eva-Liina Ustav
3Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
5Women’s Clinic, Tartu University Hospital, Tartu, Estonia
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Neeme Tõnisson
6Institute of Genomics, University of Tartu, Tartu, Estonia
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Konstantin Ridnõi
7Center for Perinatal Care, Women’s Clinic, East-Tallinn Central Hospital, Tallinn
8Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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Priit Palta
6Institute of Genomics, University of Tartu, Tartu, Estonia
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Kaarel Krjutškov
2Competence Centre on Health Technologies, Tartu, Estonia
9Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
10Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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Ants Kurg
1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Andres Salumets
2Competence Centre on Health Technologies, Tartu, Estonia
3Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
4Department of Biomedicine, Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
11Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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  • For correspondence: andres.salumets@ccht.ee
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Abstract

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 03, 2018.
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Creating basis for introducing NIPT in the Estonian public health setting
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
bioRxiv 431924; doi: https://doi.org/10.1101/431924
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Creating basis for introducing NIPT in the Estonian public health setting
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
bioRxiv 431924; doi: https://doi.org/10.1101/431924

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