NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.
Identifieur interne : 000947 ( PubMed/Curation ); précédent : 000946; suivant : 000948NIPTmer: 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] ; Andres Salumets [Estonie] ; 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 http://bioinfo.ut.ee/NIPTMer/ .
DOI: 10.1038/s41598-018-23589-8
PubMed: 29618827
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andres.salumets@ccht.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu</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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. lauris.kaplinski@ut.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29618827</idno><idno type="pmid">29618827</idno><idno type="doi">10.1038/s41598-018-23589-8</idno><idno type="wicri:Area/PubMed/Corpus">000947</idno><idno 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wicri:level="1"><nlm:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Kurg, Ants" sort="Kurg, Ants" uniqKey="Kurg A" first="Ants" last="Kurg">Ants Kurg</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Ustav, Eva Liina" sort="Ustav, Eva Liina" uniqKey="Ustav E" first="Eva-Liina" last="Ustav">Eva-Liina Ustav</name><affiliation wicri:level="1"><nlm:affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Peters, Maire" sort="Peters, Maire" uniqKey="Peters M" first="Maire" last="Peters">Maire Peters</name><affiliation wicri:level="1"><nlm:affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Paluoja, Priit" sort="Paluoja, Priit" uniqKey="Paluoja P" first="Priit" last="Paluoja">Priit Paluoja</name><affiliation wicri:level="1"><nlm:affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Competence Centre on Health Technologies, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Roost, Anne Mari" sort="Roost, Anne Mari" uniqKey="Roost A" first="Anne Mari" last="Roost">Anne Mari Roost</name><affiliation wicri:level="1"><nlm:affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Competence Centre on Health Technologies, Tartu</wicri:regionArea></affiliation></author><author><name sortKey="Teder, Hindrek" sort="Teder, Hindrek" uniqKey="Teder H" first="Hindrek" last="Teder">Hindrek Teder</name><affiliation wicri:level="1"><nlm:affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Competence Centre on Health Technologies, 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:affiliation>Estonian Genome Center, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Estonian Genome Center, University of Tartu, 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:affiliation>Center for Human Genetics, KU Leuven, Leuven, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Human Genetics, KU Leuven, 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:affiliation>Center for Human Genetics, KU Leuven, Leuven, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Human Genetics, KU Leuven, 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:affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Competence Centre on Health Technologies, Tartu</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:affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia. andres.salumets@ccht.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu</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:affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. lauris.kaplinski@ut.ee.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Institute of Molecular and Cell Biology, University of Tartu, Tartu</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2018" type="published">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">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/ .</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29618827</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>27</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>27</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>04</Month><Day>04</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.</ArticleTitle><Pagination><MedlinePgn>5616</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-018-23589-8</ELocationID><Abstract><AbstractText>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/ .</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sauk</LastName><ForeName>Martin</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Žilina</LastName><ForeName>Olga</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kurg</LastName><ForeName>Ants</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ustav</LastName><ForeName>Eva-Liina</ForeName><Initials>EL</Initials><AffiliationInfo><Affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Women's Clinic, Tartu University Hospital, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peters</LastName><ForeName>Maire</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paluoja</LastName><ForeName>Priit</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0002-2016-661X</Identifier><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Roost</LastName><ForeName>Anne Mari</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Teder</LastName><ForeName>Hindrek</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0001-6608-7979</Identifier><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biomedicine, Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Palta</LastName><ForeName>Priit</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Estonian Genome Center, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brison</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Center for Human Genetics, KU Leuven, Leuven, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vermeesch</LastName><ForeName>Joris R</ForeName><Initials>JR</Initials><AffiliationInfo><Affiliation>Center for Human Genetics, KU Leuven, Leuven, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krjutškov</LastName><ForeName>Kaarel</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salumets</LastName><ForeName>Andres</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia. andres.salumets@ccht.ee.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Competence Centre on Health Technologies, Tartu, Estonia. andres.salumets@ccht.ee.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biomedicine, Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia. andres.salumets@ccht.ee.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. andres.salumets@ccht.ee.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaplinski</LastName><ForeName>Lauris</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institute of Molecular and Cell 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