NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies
| dc.contributor | "European Union (EU)" and "Horizon 2020" | |
| dc.contributor.author | Sauk, M. | |
| dc.contributor.author | Žilina, O. | |
| dc.contributor.author | Kurg, A. | |
| dc.contributor.author | Ustav, EL. | |
| dc.contributor.author | Peters, M. | |
| dc.contributor.author | Paluoja, P. | |
| dc.contributor.author | Roost, AM. | |
| dc.contributor.author | Teder, H. | |
| dc.contributor.author | Palta, P. | |
| dc.contributor.author | Brison, N. | |
| dc.contributor.author | Vermeesch, JR. | |
| dc.contributor.author | Krjutškov, K. | |
| dc.contributor.author | Salumets, A. | |
| dc.contributor.author | Kaplinski, L. | |
| dc.date.accessioned | 2019-02-26T14:41:47Z | |
| dc.date.available | 2019-02-26T14:41:47Z | |
| dc.date.issued | 2018 | |
| dc.description.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/. | et |
| dc.identifier.uri | https://doi.org/10.1038/s41598-018-23589-8 | |
| dc.identifier.uri | http://hdl.handle.net/10062/63421 | |
| dc.language.iso | eng | et |
| dc.relation | info:eu-repo/grantAgreement/EC/H2020/692065///WIDENLIFE | et |
| dc.relation.ispartofseries | Sci Rep. 2018;Apr 4;8(1):5616. | |
| dc.rights | info:eu-repo/semantics/openAccess | et |
| dc.subject | Next-generation sequencing | et |
| dc.subject | Computational biology and bioinformatics | et |
| dc.title | NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies | et |
| dc.type | info:eu-repo/semantics/article | et |
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