A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk
Identifieur interne : 001135 ( Ncbi/Merge ); précédent : 001134; suivant : 001136A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk
Auteurs : Samuel G. Younkin [États-Unis] ; Robert B. Scharpf [États-Unis] ; Holger Schwender [Allemagne] ; Margaret M. Parker [États-Unis] ; Alan F. Scott [États-Unis] ; Mary L. Marazita [États-Unis] ; Terri H. Beaty [États-Unis] ; Ingo Ruczinski [États-Unis]Source :
- BMC Genetics [ 1471-2156 ] ; 2014.
Abstract
Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate
We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where
This study presents a region where
Url:
DOI: 10.1186/1471-2156-15-24
PubMed: 24528994
PubMed Central: 3929298
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PMC:3929298Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A genome-wide study of <italic>de novo</italic>
deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk</title>
<author><name sortKey="Younkin, Samuel G" sort="Younkin, Samuel G" uniqKey="Younkin S" first="Samuel G" last="Younkin">Samuel G. Younkin</name>
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<author><name sortKey="Parker, Margaret M" sort="Parker, Margaret M" uniqKey="Parker M" first="Margaret M" last="Parker">Margaret M. Parker</name>
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<author><name sortKey="Scott, Alan F" sort="Scott, Alan F" uniqKey="Scott A" first="Alan F" last="Scott">Alan F. Scott</name>
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<author><name sortKey="Ruczinski, Ingo" sort="Ruczinski, Ingo" uniqKey="Ruczinski I" first="Ingo" last="Ruczinski">Ingo Ruczinski</name>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate <italic>de novo</italic>
deletions defined as DNA segments missing in an oral cleft proband but present in both unaffected parents. We compare <italic>de novo</italic>
deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios.</p>
</sec>
<sec><title>Results</title>
<p>We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where <italic>de novo</italic>
deletions occur more frequently among oral cleft cases than controls. We also observed wider <italic>de novo</italic>
deletions among cleft lip and palate (CLP) cases than seen among cleft palate (CP) and cleft lip (CL) cases.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study presents a region where <italic>de novo</italic>
deletions appear to be involved in the etiology of oral clefts, although the underlying biological mechanisms are still unknown. Larger <italic>de novo</italic>
deletions are more likely to interfere with normal craniofacial development and may result in more severe clefts. Study protocol and sample DNA source can severely affect estimates of <italic>de novo</italic>
deletion frequencies. Follow-up studies are needed to further validate these findings and to potentially identify additional structural variants underlying oral clefts.</p>
</sec>
</div>
</front>
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<author><name sortKey="Leisch, F" uniqKey="Leisch F">F Leisch</name>
</author>
<author><name sortKey="Li, C" uniqKey="Li C">C Li</name>
</author>
<author><name sortKey="Maechler, M" uniqKey="Maechler M">M Maechler</name>
</author>
<author><name sortKey="Rossini, Aj" uniqKey="Rossini A">AJ Rossini</name>
</author>
<author><name sortKey="Sawitzki, G" uniqKey="Sawitzki G">G Sawitzki</name>
</author>
<author><name sortKey="Smith, C" uniqKey="Smith C">C Smith</name>
</author>
<author><name sortKey="Smyth, G" uniqKey="Smyth G">G Smyth</name>
</author>
<author><name sortKey="Tierney, L" uniqKey="Tierney L">L Tierney</name>
</author>
<author><name sortKey="Yang, Jyh" uniqKey="Yang J">JYH Yang</name>
</author>
<author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Olshen, Ab" uniqKey="Olshen A">AB Olshen</name>
</author>
<author><name sortKey="Venkatraman, Es" uniqKey="Venkatraman E">ES Venkatraman</name>
</author>
<author><name sortKey="Lucito, R" uniqKey="Lucito R">R Lucito</name>
</author>
<author><name sortKey="Wigler, M" uniqKey="Wigler M">M Wigler</name>
</author>
</analytic>
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</listBibl>
</div1>
</back>
</TEI>
<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">BMC Genet</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Genet</journal-id>
<journal-title-group><journal-title>BMC Genetics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2156</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24528994</article-id>
<article-id pub-id-type="pmc">3929298</article-id>
<article-id pub-id-type="publisher-id">1471-2156-15-24</article-id>
<article-id pub-id-type="doi">10.1186/1471-2156-15-24</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>A genome-wide study of <italic>de novo</italic>
deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Younkin</surname>
<given-names>Samuel G</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>syounkin@jhsph.edu</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Scharpf</surname>
<given-names>Robert B</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>rscharpf@jhsph.edu</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Schwender</surname>
<given-names>Holger</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>holger.schwender@udo.edu</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Parker</surname>
<given-names>Margaret M</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>mmparker1@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Scott</surname>
<given-names>Alan F</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<email>afscott@jhmi.edu</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Marazita</surname>
<given-names>Mary L</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
<email>marazita@pitt.edu</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Beaty</surname>
<given-names>Terri H</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>tbeaty@jhsph.edu</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Ruczinski</surname>
<given-names>Ingo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>iruczins@jhsph.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA</aff>
<aff id="I2"><label>2</label>
Department of Oncology, Johns Hopkins School of Medicine, Baltimore MD, USA</aff>
<aff id="I3"><label>3</label>
Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany</aff>
<aff id="I4"><label>4</label>
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA</aff>
<aff id="I5"><label>5</label>
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore MD, USA</aff>
<aff id="I6"><label>6</label>
School of Dental Medicine, University of Pittsburgh, Pittsburgh PA, USA</aff>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>14</day>
<month>2</month>
<year>2014</year>
</pub-date>
<volume>15</volume>
<fpage>24</fpage>
<lpage>24</lpage>
<history><date date-type="received"><day>13</day>
<month>5</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>31</day>
<month>1</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Younkin et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>Younkin 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 credited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2156/15/24"></self-uri>
<abstract><sec><title>Background</title>
<p>Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate <italic>de novo</italic>
deletions defined as DNA segments missing in an oral cleft proband but present in both unaffected parents. We compare <italic>de novo</italic>
deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios.</p>
</sec>
<sec><title>Results</title>
<p>We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where <italic>de novo</italic>
deletions occur more frequently among oral cleft cases than controls. We also observed wider <italic>de novo</italic>
deletions among cleft lip and palate (CLP) cases than seen among cleft palate (CP) and cleft lip (CL) cases.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study presents a region where <italic>de novo</italic>
deletions appear to be involved in the etiology of oral clefts, although the underlying biological mechanisms are still unknown. Larger <italic>de novo</italic>
deletions are more likely to interfere with normal craniofacial development and may result in more severe clefts. Study protocol and sample DNA source can severely affect estimates of <italic>de novo</italic>
deletion frequencies. Follow-up studies are needed to further validate these findings and to potentially identify additional structural variants underlying oral clefts.</p>
</sec>
</abstract>
<kwd-group><kwd>Oral clefts</kwd>
<kwd>DNA copy numbers</kwd>
<kwd><italic>de novo</italic>
deletions</kwd>
<kwd>Case-parent trios</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>États-Unis</li>
</country>
<region><li>District de Düsseldorf</li>
<li>Pennsylvanie</li>
<li>Rhénanie-du-Nord-Westphalie</li>
</region>
<settlement><li>Düsseldorf</li>
<li>Pittsburgh</li>
</settlement>
<orgName><li>Université de Pittsburgh</li>
</orgName>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Younkin, Samuel G" sort="Younkin, Samuel G" uniqKey="Younkin S" first="Samuel G" last="Younkin">Samuel G. Younkin</name>
</noRegion>
<name sortKey="Beaty, Terri H" sort="Beaty, Terri H" uniqKey="Beaty T" first="Terri H" last="Beaty">Terri H. Beaty</name>
<name sortKey="Marazita, Mary L" sort="Marazita, Mary L" uniqKey="Marazita M" first="Mary L" last="Marazita">Mary L. Marazita</name>
<name sortKey="Parker, Margaret M" sort="Parker, Margaret M" uniqKey="Parker M" first="Margaret M" last="Parker">Margaret M. Parker</name>
<name sortKey="Ruczinski, Ingo" sort="Ruczinski, Ingo" uniqKey="Ruczinski I" first="Ingo" last="Ruczinski">Ingo Ruczinski</name>
<name sortKey="Scharpf, Robert B" sort="Scharpf, Robert B" uniqKey="Scharpf R" first="Robert B" last="Scharpf">Robert B. Scharpf</name>
<name sortKey="Scott, Alan F" sort="Scott, Alan F" uniqKey="Scott A" first="Alan F" last="Scott">Alan F. Scott</name>
</country>
<country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Schwender, Holger" sort="Schwender, Holger" uniqKey="Schwender H" first="Holger" last="Schwender">Holger Schwender</name>
</region>
</country>
</tree>
</affiliations>
</record>
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