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  •   DSpace @University of Tartu
  • Loodus- ja täppisteaduste valdkond
  • LT Euroopa Liidu rahastatud projektid
  • WIDENLIFE - Widening the Scientific Excellence for Studies on Women’s and Fetal Health and Wellbeing
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  •   DSpace @University of Tartu
  • Loodus- ja täppisteaduste valdkond
  • LT Euroopa Liidu rahastatud projektid
  • WIDENLIFE - Widening the Scientific Excellence for Studies on Women’s and Fetal Health and Wellbeing
  • View Item
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NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies

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Supplementary files 5, 6, 7 (540.3Kb)
Date
2018
Author
Sauk, M.
Žilina, O.
Kurg, A.
Ustav, EL.
Peters, M.
Paluoja, P.
Roost, AM.
Teder, H.
Palta, P.
Brison, N.
Vermeesch, JR.
Krjutškov, K.
Salumets, A.
Kaplinski, L.
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Abstract
Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool – NIPTmer – is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/.
URI
https://doi.org/10.1038/s41598-018-23589-8
http://hdl.handle.net/10062/63421
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  • WIDENLIFE - Widening the Scientific Excellence for Studies on Women’s and Fetal Health and Wellbeing [45]

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