Genome Scan, Fine-Mapping, and Candidate Gene Analysis of Non-Syndromic Cleft Lip with or without Cleft Palate Reveals Phenotype-Specific Differences in Linkage and Association Results
Identifieur interne : 006269 ( Main/Exploration ); précédent : 006268; suivant : 006270Genome Scan, Fine-Mapping, and Candidate Gene Analysis of Non-Syndromic Cleft Lip with or without Cleft Palate Reveals Phenotype-Specific Differences in Linkage and Association Results
Auteurs : Mary L. Marazita [États-Unis] ; Andrew C. Lidral [États-Unis] ; Jeffrey C. Murray [États-Unis] ; L. Leigh Field [Canada] ; Brion S. Maher [États-Unis] ; Toby Goldstein Mchenry [États-Unis] ; Margaret E. Cooper [États-Unis] ; Manika Govil [États-Unis] ; Sandra Daack-Hirsch [États-Unis] ; Bridget Riley [États-Unis] ; Astanand Jugessur [Australie] ; Temis Felix [Brésil] ; Lina Morene [États-Unis] ; M. Adela Mansilla [États-Unis] ; Alexandre R. Vieira [États-Unis] ; Kim Doheny [États-Unis] ; Elizabeth Pugh [États-Unis] ; Consuelo Valencia-Ramirez [États-Unis] ; Mauricio Arcos-Burgos [États-Unis]Source :
- Human Heredity [ 0001-5652 ] ; 2009.
Abstract
Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P).
We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results.
Significant (multipoint HLOD ≥3.2) or genome-wide-significant (HLOD ≥4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in
These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.
Url:
DOI: 10.1159/000224636
PubMed: 19521098
PubMed Central: 2709160
Affiliations:
- Australie, Brésil, Canada, États-Unis
- Iowa, Pennsylvanie, Rio Grande do Sul
- Iowa City, Pittsburgh, Porto Alegre
- Université de Pittsburgh, Université de l'Iowa, Université fédérale du Rio Grande do Sul
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Le document en format XML
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<author><name sortKey="Morene, Lina" sort="Morene, Lina" uniqKey="Morene L" first="Lina" last="Morene">Lina Morene</name>
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<author><name sortKey="Valencia Ramirez, Consuelo" sort="Valencia Ramirez, Consuelo" uniqKey="Valencia Ramirez C" first="Consuelo" last="Valencia-Ramirez">Consuelo Valencia-Ramirez</name>
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<author><name sortKey="Arcos Burgos, Mauricio" sort="Arcos Burgos, Mauricio" uniqKey="Arcos Burgos M" first="Mauricio" last="Arcos-Burgos">Mauricio Arcos-Burgos</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome Scan, Fine-Mapping, and Candidate Gene Analysis of Non-Syndromic Cleft Lip with or without Cleft Palate Reveals Phenotype-Specific Differences in Linkage and Association Results</title>
<author><name sortKey="Marazita, Mary L" sort="Marazita, Mary L" uniqKey="Marazita M" first="Mary L." last="Marazita">Mary L. Marazita</name>
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<author><name sortKey="Field, L Leigh" sort="Field, L Leigh" uniqKey="Field L" first="L. Leigh" last="Field">L. Leigh Field</name>
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<wicri:regionArea>Department of Medical Genetics, University of British Columbia, and B.C. Research Institute for Children's and Women's Health, Vancouver, BC</wicri:regionArea>
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<author><name sortKey="Maher, Brion S" sort="Maher, Brion S" uniqKey="Maher B" first="Brion S." last="Maher">Brion S. Maher</name>
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<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Goldstein Mchenry, Toby" sort="Goldstein Mchenry, Toby" uniqKey="Goldstein Mchenry T" first="Toby" last="Goldstein Mchenry">Toby Goldstein Mchenry</name>
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<author><name sortKey="Cooper, Margaret E" sort="Cooper, Margaret E" uniqKey="Cooper M" first="Margaret E." last="Cooper">Margaret E. Cooper</name>
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<country xml:lang="fr">États-Unis</country>
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</author>
<author><name sortKey="Govil, Manika" sort="Govil, Manika" uniqKey="Govil M" first="Manika" last="Govil">Manika Govil</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa.</wicri:regionArea>
<orgName type="university">Université de Pittsburgh</orgName>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Daack Hirsch, Sandra" sort="Daack Hirsch, Sandra" uniqKey="Daack Hirsch S" first="Sandra" last="Daack-Hirsch">Sandra Daack-Hirsch</name>
<affiliation wicri:level="4"><nlm:aff id="aff7">College of Nursing, University of Iowa, Iowa City, Iowa, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>College of Nursing, University of Iowa, Iowa City, Iowa</wicri:regionArea>
<placeName><region type="state">Iowa</region>
<settlement type="city">Iowa City</settlement>
</placeName>
<orgName type="university">Université de l'Iowa</orgName>
</affiliation>
</author>
<author><name sortKey="Riley, Bridget" sort="Riley, Bridget" uniqKey="Riley B" first="Bridget" last="Riley">Bridget Riley</name>
<affiliation wicri:level="1"><nlm:aff id="aff10">New York University School of Medicine, New York, N.Y., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>New York University School of Medicine, New York, N.Y.</wicri:regionArea>
<wicri:noRegion>N.Y.</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jugessur, Astanand" sort="Jugessur, Astanand" uniqKey="Jugessur A" first="Astanand" last="Jugessur">Astanand Jugessur</name>
<affiliation wicri:level="1"><nlm:aff id="aff11">Craniofacial Development, Musculoskeletal Disorders, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Craniofacial Development, Musculoskeletal Disorders, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne</wicri:regionArea>
<wicri:noRegion>Melbourne</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Felix, Temis" sort="Felix, Temis" uniqKey="Felix T" first="Temis" last="Felix">Temis Felix</name>
<affiliation wicri:level="4"><nlm:aff id="aff12">Hospital de Clinicas Porto Allegre-RS, Universidade Federal do Rio Grande do Sul, Brazil</nlm:aff>
<country xml:lang="fr">Brésil</country>
<wicri:regionArea>Hospital de Clinicas Porto Allegre-RS, Universidade Federal do Rio Grande do Sul</wicri:regionArea>
<placeName><settlement type="city">Porto Alegre</settlement>
<region type="state">Rio Grande do Sul</region>
</placeName>
<orgName type="university">Université fédérale du Rio Grande do Sul</orgName>
</affiliation>
</author>
<author><name sortKey="Morene, Lina" sort="Morene, Lina" uniqKey="Morene L" first="Lina" last="Morene">Lina Morene</name>
<affiliation wicri:level="4"><nlm:aff id="aff5">Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, Iowa, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, Iowa</wicri:regionArea>
<placeName><region type="state">Iowa</region>
<settlement type="city">Iowa City</settlement>
</placeName>
<orgName type="university">Université de l'Iowa</orgName>
</affiliation>
</author>
<author><name sortKey="Mansilla, M Adela" sort="Mansilla, M Adela" uniqKey="Mansilla M" first="M. Adela" last="Mansilla">M. Adela Mansilla</name>
<affiliation wicri:level="4"><nlm:aff id="aff6">Department of Pediatrics College of Medicine, University of Iowa, Iowa City, Iowa, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Pediatrics College of Medicine, University of Iowa, Iowa City, Iowa</wicri:regionArea>
<placeName><region type="state">Iowa</region>
<settlement type="city">Iowa City</settlement>
</placeName>
<orgName type="university">Université de l'Iowa</orgName>
</affiliation>
</author>
<author><name sortKey="Vieira, Alexandre R" sort="Vieira, Alexandre R" uniqKey="Vieira A" first="Alexandre R." last="Vieira">Alexandre R. Vieira</name>
<affiliation wicri:level="4"><nlm:aff id="aff1">Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa.</wicri:regionArea>
<orgName type="university">Université de Pittsburgh</orgName>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff2">Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa.</wicri:regionArea>
<orgName type="university">Université de Pittsburgh</orgName>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff4">Department of Pediatric Dentistry, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Pediatric Dentistry, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa.</wicri:regionArea>
<orgName type="university">Université de Pittsburgh</orgName>
<placeName><settlement type="city">Pittsburgh</settlement>
<region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Doheny, Kim" sort="Doheny, Kim" uniqKey="Doheny K" first="Kim" last="Doheny">Kim Doheny</name>
<affiliation wicri:level="1"><nlm:aff id="aff13">Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Md., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Md.</wicri:regionArea>
<wicri:noRegion>Md.</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pugh, Elizabeth" sort="Pugh, Elizabeth" uniqKey="Pugh E" first="Elizabeth" last="Pugh">Elizabeth Pugh</name>
<affiliation wicri:level="1"><nlm:aff id="aff13">Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Md., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Md.</wicri:regionArea>
<wicri:noRegion>Md.</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Valencia Ramirez, Consuelo" sort="Valencia Ramirez, Consuelo" uniqKey="Valencia Ramirez C" first="Consuelo" last="Valencia-Ramirez">Consuelo Valencia-Ramirez</name>
<affiliation wicri:level="1"><nlm:aff id="aff14">College of Dentistry, Universidad de Antioquia, Medellin, Colombia, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>College of Dentistry, Universidad de Antioquia, Medellin, Colombia</wicri:regionArea>
<wicri:noRegion>Colombia</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Arcos Burgos, Mauricio" sort="Arcos Burgos, Mauricio" uniqKey="Arcos Burgos M" first="Mauricio" last="Arcos-Burgos">Mauricio Arcos-Burgos</name>
<affiliation wicri:level="1"><nlm:aff id="aff15">Division of Child Psychiatry, Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Miami, Fla., USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Child Psychiatry, Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Miami, Fla.</wicri:regionArea>
<wicri:noRegion>Fla.</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Human Heredity</title>
<idno type="ISSN">0001-5652</idno>
<idno type="eISSN">1423-0062</idno>
<imprint><date when="2009">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Objectives</title>
<p>Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P).</p>
</sec>
<sec><title>Methods</title>
<p>We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results.</p>
</sec>
<sec><title>Results</title>
<p>Significant (multipoint HLOD ≥3.2) or genome-wide-significant (HLOD ≥4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in <italic>IRF6</italic>
(1q32) and in or near <italic>FOXE1</italic>
(9q21) reached formal genome-wide wFDR-adjusted significance. Further, results were phenotype dependent in that the <italic>IRF6</italic>
region results were most significant for families in which affected individuals have CL alone, and the <italic>FOXE1</italic>
region results were most significant in families in which some or all of the affected individuals have CL with CP.</p>
</sec>
<sec><title>Conclusions</title>
<p>These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.</p>
</sec>
</div>
</front>
</TEI>
<affiliations><list><country><li>Australie</li>
<li>Brésil</li>
<li>Canada</li>
<li>États-Unis</li>
</country>
<region><li>Iowa</li>
<li>Pennsylvanie</li>
<li>Rio Grande do Sul</li>
</region>
<settlement><li>Iowa City</li>
<li>Pittsburgh</li>
<li>Porto Alegre</li>
</settlement>
<orgName><li>Université de Pittsburgh</li>
<li>Université de l'Iowa</li>
<li>Université fédérale du Rio Grande do Sul</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Marazita, Mary L" sort="Marazita, Mary L" uniqKey="Marazita M" first="Mary L." last="Marazita">Mary L. Marazita</name>
</region>
<name sortKey="Arcos Burgos, Mauricio" sort="Arcos Burgos, Mauricio" uniqKey="Arcos Burgos M" first="Mauricio" last="Arcos-Burgos">Mauricio Arcos-Burgos</name>
<name sortKey="Cooper, Margaret E" sort="Cooper, Margaret E" uniqKey="Cooper M" first="Margaret E." last="Cooper">Margaret E. Cooper</name>
<name sortKey="Daack Hirsch, Sandra" sort="Daack Hirsch, Sandra" uniqKey="Daack Hirsch S" first="Sandra" last="Daack-Hirsch">Sandra Daack-Hirsch</name>
<name sortKey="Doheny, Kim" sort="Doheny, Kim" uniqKey="Doheny K" first="Kim" last="Doheny">Kim Doheny</name>
<name sortKey="Goldstein Mchenry, Toby" sort="Goldstein Mchenry, Toby" uniqKey="Goldstein Mchenry T" first="Toby" last="Goldstein Mchenry">Toby Goldstein Mchenry</name>
<name sortKey="Govil, Manika" sort="Govil, Manika" uniqKey="Govil M" first="Manika" last="Govil">Manika Govil</name>
<name sortKey="Lidral, Andrew C" sort="Lidral, Andrew C" uniqKey="Lidral A" first="Andrew C." last="Lidral">Andrew C. Lidral</name>
<name sortKey="Maher, Brion S" sort="Maher, Brion S" uniqKey="Maher B" first="Brion S." last="Maher">Brion S. Maher</name>
<name sortKey="Mansilla, M Adela" sort="Mansilla, M Adela" uniqKey="Mansilla M" first="M. Adela" last="Mansilla">M. Adela Mansilla</name>
<name sortKey="Marazita, Mary L" sort="Marazita, Mary L" uniqKey="Marazita M" first="Mary L." last="Marazita">Mary L. Marazita</name>
<name sortKey="Marazita, Mary L" sort="Marazita, Mary L" uniqKey="Marazita M" first="Mary L." last="Marazita">Mary L. Marazita</name>
<name sortKey="Morene, Lina" sort="Morene, Lina" uniqKey="Morene L" first="Lina" last="Morene">Lina Morene</name>
<name sortKey="Murray, Jeffrey C" sort="Murray, Jeffrey C" uniqKey="Murray J" first="Jeffrey C." last="Murray">Jeffrey C. Murray</name>
<name sortKey="Pugh, Elizabeth" sort="Pugh, Elizabeth" uniqKey="Pugh E" first="Elizabeth" last="Pugh">Elizabeth Pugh</name>
<name sortKey="Riley, Bridget" sort="Riley, Bridget" uniqKey="Riley B" first="Bridget" last="Riley">Bridget Riley</name>
<name sortKey="Valencia Ramirez, Consuelo" sort="Valencia Ramirez, Consuelo" uniqKey="Valencia Ramirez C" first="Consuelo" last="Valencia-Ramirez">Consuelo Valencia-Ramirez</name>
<name sortKey="Vieira, Alexandre R" sort="Vieira, Alexandre R" uniqKey="Vieira A" first="Alexandre R." last="Vieira">Alexandre R. Vieira</name>
<name sortKey="Vieira, Alexandre R" sort="Vieira, Alexandre R" uniqKey="Vieira A" first="Alexandre R." last="Vieira">Alexandre R. Vieira</name>
<name sortKey="Vieira, Alexandre R" sort="Vieira, Alexandre R" uniqKey="Vieira A" first="Alexandre R." last="Vieira">Alexandre R. Vieira</name>
</country>
<country name="Canada"><noRegion><name sortKey="Field, L Leigh" sort="Field, L Leigh" uniqKey="Field L" first="L. Leigh" last="Field">L. Leigh Field</name>
</noRegion>
</country>
<country name="Australie"><noRegion><name sortKey="Jugessur, Astanand" sort="Jugessur, Astanand" uniqKey="Jugessur A" first="Astanand" last="Jugessur">Astanand Jugessur</name>
</noRegion>
</country>
<country name="Brésil"><region name="Rio Grande do Sul"><name sortKey="Felix, Temis" sort="Felix, Temis" uniqKey="Felix T" first="Temis" last="Felix">Temis Felix</name>
</region>
</country>
</tree>
</affiliations>
</record>
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