NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies
Identifieur interne : 000877 ( Main/Exploration ); précédent : 000876; suivant : 000878NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies
Auteurs : Martin Sauk [Estonie] ; Olga Žilina [Estonie] ; Ants Kurg [Estonie] ; Eva-Liina Ustav [Estonie] ; Maire Peters [Estonie] ; Priit Paluoja [Estonie] ; Anne Mari Roost [Estonie] ; Hindrek Teder [Estonie] ; Priit Palta [Estonie] ; Nathalie Brison [Belgique] ; Joris R. Vermeesch [Belgique] ; Kaarel Krjutškov [Estonie, Suède, Finlande] ; Andres Salumets [Estonie, Finlande] ; Lauris Kaplinski [Estonie]Source :
- Scientific Reports [ 2045-2322 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- Adult, Aneuploidy, Cell-Free Nucleic Acids (chemistry), Cell-Free Nucleic Acids (isolation & purification), Female, Fetus (metabolism), Genetic Testing (methods), Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Pregnancy, Prenatal Care, Sequence Analysis, DNA, User-Computer Interface.
- MESH :
- chemical , chemistry : Cell-Free Nucleic Acids.
- chemical , isolation & purification : Cell-Free Nucleic Acids.
- metabolism : Fetus.
- methods : Genetic Testing.
- Adult, Aneuploidy, Female, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Pregnancy, Prenatal Care, Sequence Analysis, DNA, User-Computer Interface.
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
Url:
DOI: 10.1038/s41598-018-23589-8
PubMed: 29618827
PubMed Central: 5884839
Affiliations:
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Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Palta, Priit" sort="Palta, Priit" uniqKey="Palta P" first="Priit" last="Palta">Priit Palta</name><affiliation wicri:level="1"><nlm:aff id="Aff6"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Estonian Genome Center, University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Brison, Nathalie" sort="Brison, Nathalie" uniqKey="Brison N" first="Nathalie" last="Brison">Nathalie Brison</name><affiliation wicri:level="1"><nlm:aff id="Aff7"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0668 7884</institution-id><institution-id institution-id-type="GRID">grid.5596.f</institution-id><institution>Center for Human Genetics, KU Leuven,</institution></institution-wrap>Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Leuven</wicri:regionArea></affiliation></author><author><name sortKey="Vermeesch, Joris R" sort="Vermeesch, Joris R" uniqKey="Vermeesch J" first="Joris R." last="Vermeesch">Joris R. Vermeesch</name><affiliation wicri:level="1"><nlm:aff id="Aff7"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0668 7884</institution-id><institution-id institution-id-type="GRID">grid.5596.f</institution-id><institution>Center for Human Genetics, KU Leuven,</institution></institution-wrap>Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Leuven</wicri:regionArea></affiliation></author><author><name sortKey="Krjutskov, Kaarel" sort="Krjutskov, Kaarel" uniqKey="Krjutskov K" first="Kaarel" last="Krjutškov">Kaarel Krjutškov</name><affiliation wicri:level="1"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="GRID">grid.487355.8</institution-id><institution>Competence Centre on Health Technologies,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff8"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1937 0626</institution-id><institution-id institution-id-type="GRID">grid.4714.6</institution-id><institution>Department of Biosciences and Nutrition,</institution><institution>Karolinska Institutet,</institution></institution-wrap>Huddinge, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Huddinge</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff9"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0410 2071</institution-id><institution-id institution-id-type="GRID">grid.7737.4</institution-id><institution>Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics,</institution></institution-wrap>Helsinki, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Helsinki</wicri:regionArea></affiliation></author><author><name sortKey="Salumets, Andres" sort="Salumets, Andres" uniqKey="Salumets A" first="Andres" last="Salumets">Andres Salumets</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Department of Obstetrics and Gynaecology,</institution><institution>Institute of Clinical Medicine, University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="GRID">grid.487355.8</institution-id><institution>Competence Centre on Health Technologies,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Department of Biomedicine,</institution><institution>Institute of Bio- and Translational Medicine, University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff10"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 0410 2071</institution-id><institution-id institution-id-type="GRID">grid.7737.4</institution-id><institution>Department of Obstetrics and Gynecology,</institution><institution>University of Helsinki and Helsinki University Hospital,</institution></institution-wrap>Helsinki, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Helsinki</wicri:regionArea></affiliation></author><author><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0943 7661</institution-id><institution-id institution-id-type="GRID">grid.10939.32</institution-id><institution>Institute of Molecular and Cell Biology, University of Tartu,</institution></institution-wrap>Tartu, Estonia</nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea>Tartu</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adult</term><term>Aneuploidy</term><term>Cell-Free Nucleic Acids (chemistry)</term><term>Cell-Free Nucleic Acids (isolation & purification)</term><term>Female</term><term>Fetus (metabolism)</term><term>Genetic Testing (methods)</term><term>Genetic Variation</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Pregnancy</term><term>Prenatal Care</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adulte</term><term>Analyse de séquence d'ADN</term><term>Aneuploïdie</term><term>Dépistage génétique ()</term><term>Femelle</term><term>Foetus (métabolisme)</term><term>Grossesse</term><term>Humains</term><term>Interface utilisateur</term><term>Prise en charge prénatale</term><term>Séquençage nucléotidique à haut débit</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cell-Free Nucleic Acids</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>Cell-Free Nucleic Acids</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Fetus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genetic Testing</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Foetus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adult</term><term>Aneuploidy</term><term>Female</term><term>Genetic Variation</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Pregnancy</term><term>Prenatal Care</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adulte</term><term>Analyse de séquence d'ADN</term><term>Aneuploïdie</term><term>Dépistage génétique</term><term>Femelle</term><term>Grossesse</term><term>Humains</term><term>Interface utilisateur</term><term>Prise en charge prénatale</term><term>Séquençage nucléotidique à haut débit</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="Par1">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 <ext-link ext-link-type="uri" xlink:href="http://bioinfo.ut.ee/NIPTMer/">http://bioinfo.ut.ee/NIPTMer/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lo, Ym" uniqKey="Lo Y">YM Lo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lun, Fm" uniqKey="Lun F">FM Lun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bayindir, B" uniqKey="Bayindir B">B Bayindir</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jiang, F" uniqKey="Jiang F">F Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Azam, S" uniqKey="Azam S">S Azam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Ez" uniqKey="Chen E">EZ Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gullapalli, Rr" uniqKey="Gullapalli R">RR Gullapalli</name></author><author><name sortKey="Desai, Kv" uniqKey="Desai K">KV Desai</name></author><author><name sortKey="Santana Santos, L" uniqKey="Santana Santos L">L Santana-Santos</name></author><author><name sortKey="Kant, Ja" uniqKey="Kant J">JA Kant</name></author><author><name sortKey="Becich, Mj" uniqKey="Becich M">MJ Becich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Precone, V" uniqKey="Precone V">V Precone</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pajuste, Fd" uniqKey="Pajuste F">FD Pajuste</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Canick, Ja" uniqKey="Canick J">JA Canick</name></author><author><name sortKey="Palomaki, Ge" uniqKey="Palomaki G">GE Palomaki</name></author><author><name sortKey="Kloza, Em" uniqKey="Kloza E">EM Kloza</name></author><author><name sortKey="Lambert Messerlian, Gm" uniqKey="Lambert Messerlian G">GM Lambert-Messerlian</name></author><author><name sortKey="Haddow, Je" uniqKey="Haddow J">JE Haddow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wataganara, T" uniqKey="Wataganara T">T Wataganara</name></author><author><name sortKey="Bui, Th" uniqKey="Bui T">TH Bui</name></author><author><name sortKey="Choy, Kw" uniqKey="Choy K">KW Choy</name></author><author><name sortKey="Leung, Ty" uniqKey="Leung T">TY Leung</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Sk" uniqKey="Kim S">SK Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kaplinski, L" uniqKey="Kaplinski L">L Kaplinski</name></author><author><name sortKey="Lepamets, M" uniqKey="Lepamets M">M Lepamets</name></author><author><name sortKey="Remm, M" uniqKey="Remm M">M Remm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leitsalu, L" uniqKey="Leitsalu L">L Leitsalu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seal, Hl" uniqKey="Seal H">HL Seal</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>Estonie</li><li>Finlande</li><li>Suède</li></country></list><tree><country name="Estonie"><noRegion><name sortKey="Sauk, Martin" sort="Sauk, Martin" uniqKey="Sauk M" first="Martin" last="Sauk">Martin Sauk</name></noRegion><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><name sortKey="Krjutskov, Kaarel" sort="Krjutskov, Kaarel" uniqKey="Krjutskov K" first="Kaarel" last="Krjutškov">Kaarel Krjutškov</name><name sortKey="Kurg, Ants" sort="Kurg, Ants" uniqKey="Kurg A" first="Ants" last="Kurg">Ants Kurg</name><name sortKey="Palta, Priit" sort="Palta, Priit" uniqKey="Palta P" first="Priit" last="Palta">Priit Palta</name><name sortKey="Paluoja, Priit" sort="Paluoja, Priit" uniqKey="Paluoja P" first="Priit" last="Paluoja">Priit Paluoja</name><name sortKey="Peters, Maire" sort="Peters, Maire" uniqKey="Peters M" first="Maire" last="Peters">Maire Peters</name><name sortKey="Peters, Maire" sort="Peters, Maire" uniqKey="Peters M" first="Maire" last="Peters">Maire Peters</name><name sortKey="Roost, Anne Mari" sort="Roost, Anne Mari" uniqKey="Roost A" first="Anne Mari" last="Roost">Anne Mari Roost</name><name sortKey="Salumets, Andres" sort="Salumets, Andres" uniqKey="Salumets A" first="Andres" last="Salumets">Andres Salumets</name><name sortKey="Salumets, Andres" sort="Salumets, Andres" uniqKey="Salumets A" first="Andres" last="Salumets">Andres Salumets</name><name sortKey="Salumets, Andres" sort="Salumets, Andres" uniqKey="Salumets A" first="Andres" last="Salumets">Andres Salumets</name><name sortKey="Teder, Hindrek" sort="Teder, Hindrek" uniqKey="Teder H" first="Hindrek" last="Teder">Hindrek Teder</name><name sortKey="Teder, Hindrek" sort="Teder, Hindrek" uniqKey="Teder H" first="Hindrek" last="Teder">Hindrek Teder</name><name sortKey="Ustav, Eva Liina" sort="Ustav, Eva Liina" uniqKey="Ustav E" first="Eva-Liina" last="Ustav">Eva-Liina Ustav</name><name sortKey="Ustav, Eva Liina" sort="Ustav, Eva Liina" uniqKey="Ustav E" first="Eva-Liina" last="Ustav">Eva-Liina Ustav</name><name sortKey="Zilina, Olga" sort="Zilina, Olga" uniqKey="Zilina O" first="Olga" last="Žilina">Olga Žilina</name></country><country name="Belgique"><noRegion><name sortKey="Brison, Nathalie" sort="Brison, Nathalie" uniqKey="Brison N" first="Nathalie" last="Brison">Nathalie Brison</name></noRegion><name sortKey="Vermeesch, Joris R" sort="Vermeesch, Joris R" uniqKey="Vermeesch J" first="Joris R." last="Vermeesch">Joris R. Vermeesch</name></country><country name="Suède"><noRegion><name sortKey="Krjutskov, Kaarel" sort="Krjutskov, Kaarel" uniqKey="Krjutskov K" first="Kaarel" last="Krjutškov">Kaarel Krjutškov</name></noRegion></country><country name="Finlande"><noRegion><name sortKey="Krjutskov, Kaarel" sort="Krjutskov, Kaarel" uniqKey="Krjutskov K" first="Kaarel" last="Krjutškov">Kaarel Krjutškov</name></noRegion><name sortKey="Salumets, Andres" sort="Salumets, Andres" uniqKey="Salumets A" first="Andres" last="Salumets">Andres Salumets</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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