EXCAVATOR: detecting copy number variants from whole-exome sequencing data
Identifieur interne : 000345 ( Pmc/Curation ); précédent : 000344; suivant : 000346EXCAVATOR: detecting copy number variants from whole-exome sequencing data
Auteurs : Alberto Magi [Italie] ; Lorenzo Tattini [Italie] ; Ingrid Cifola [Italie] ; Romina D Urizio [Italie] ; Matteo Benelli [Italie] ; Eleonora Mangano [Italie] ; Cristina Battaglia [Italie] ; Elena Bonora [Italie] ; Ants Kurg [Estonie] ; Marco Seri [Italie] ; Pamela Magini [Italie] ; Betti Giusti [Italie] ; Giovanni Romeo [Italie] ; Tommaso Pippucci [Italie] ; Gianluca De Bellis [Italie] ; Rosanna Abbate [Italie] ; Gian Franco Gensini [Italie]Source :
- Genome Biology [ 1465-6906 ] ; 2013.
Abstract
We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at
Url:
DOI: 10.1186/gb-2013-14-10-r120
PubMed: 24172663
PubMed Central: 4053953
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<front><div type="abstract" xml:lang="en"><sec><title></title>
<p>We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at <ext-link ext-link-type="uri" xlink:href="http://sourceforge.net/projects/excavatortool/">http://sourceforge.net/projects/excavatortool/</ext-link>
.</p>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id>
<journal-title-group><journal-title>Genome Biology</journal-title>
</journal-title-group>
<issn pub-type="ppub">1465-6906</issn>
<issn pub-type="epub">1465-6914</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24172663</article-id>
<article-id pub-id-type="pmc">4053953</article-id>
<article-id pub-id-type="publisher-id">gb-2013-14-10-r120</article-id>
<article-id pub-id-type="doi">10.1186/gb-2013-14-10-r120</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Method</subject>
</subj-group>
</article-categories>
<title-group><article-title>EXCAVATOR: detecting copy number variants from whole-exome sequencing data</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes" id="A1"><name><surname>Magi</surname>
<given-names>Alberto</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>albertomagi@gmail.com</email>
</contrib>
<contrib contrib-type="author" corresp="yes" equal-contrib="yes" id="A2"><name><surname>Tattini</surname>
<given-names>Lorenzo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>lorenzotattini@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Cifola</surname>
<given-names>Ingrid</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>ingrid.cifola@itb.cnr.it</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>D’Aurizio</surname>
<given-names>Romina</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>romina.daurizio@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Benelli</surname>
<given-names>Matteo</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<email>matteo.benelli@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Mangano</surname>
<given-names>Eleonora</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>eleonora.mangano@itb.cnr.it</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Battaglia</surname>
<given-names>Cristina</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<xref ref-type="aff" rid="I6">6</xref>
<email>cristina.battaglia@unimi.it</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Bonora</surname>
<given-names>Elena</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>elena.bonora6@unibo.it</email>
</contrib>
<contrib contrib-type="author" id="A9"><name><surname>Kurg</surname>
<given-names>Ants</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>akurg@ebc.ee</email>
</contrib>
<contrib contrib-type="author" id="A10"><name><surname>Seri</surname>
<given-names>Marco</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>marco.seri@unibo.it</email>
</contrib>
<contrib contrib-type="author" id="A11"><name><surname>Magini</surname>
<given-names>Pamela</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>pamela.magini@unibo.it</email>
</contrib>
<contrib contrib-type="author" id="A12"><name><surname>Giusti</surname>
<given-names>Betti</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>betti.giusti@unifi.it</email>
</contrib>
<contrib contrib-type="author" id="A13"><name><surname>Romeo</surname>
<given-names>Giovanni</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>egf.giovanni.romeo@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A14"><name><surname>Pippucci</surname>
<given-names>Tommaso</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>tommaso.pippucci@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A15"><name><surname>Bellis</surname>
<given-names>Gianluca De</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>gianluca.debellis@itb.cnr.it</email>
</contrib>
<contrib contrib-type="author" id="A16"><name><surname>Abbate</surname>
<given-names>Rosanna</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>rosanna.abbate@unifi.it</email>
</contrib>
<contrib contrib-type="author" id="A17"><name><surname>Gensini</surname>
<given-names>Gian Franco</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>gfgensini@gmail.com</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy</aff>
<aff id="I2"><label>2</label>
Laboratory of Molecular Genetics, G. Gaslini Institute, Genoa, Italy</aff>
<aff id="I3"><label>3</label>
Institute for Biomedical Technologies, National Research Council, Segrate, Milano, Italy</aff>
<aff id="I4"><label>4</label>
Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council, Pisa, Italy</aff>
<aff id="I5"><label>5</label>
Diagnostic Genetic Unit, Careggi Hospital, Florence, Italy</aff>
<aff id="I6"><label>6</label>
Dipartimento di Biotecnologie Mediche e Medicina Traslazionale (BIOMETRA), University of Milan, Milan, Italy</aff>
<aff id="I7"><label>7</label>
Medical Genetics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy</aff>
<aff id="I8"><label>8</label>
Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia</aff>
<pub-date pub-type="ppub"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>30</day>
<month>10</month>
<year>2013</year>
</pub-date>
<volume>14</volume>
<issue>10</issue>
<fpage>R120</fpage>
<lpage>R120</lpage>
<history><date date-type="received"><day>15</day>
<month>6</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>30</day>
<month>10</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013 Magi et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Magi et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://genomebiology.com/2013/14/10/R120"></self-uri>
<abstract><sec><title></title>
<p>We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at <ext-link ext-link-type="uri" xlink:href="http://sourceforge.net/projects/excavatortool/">http://sourceforge.net/projects/excavatortool/</ext-link>
.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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