Genome-Wide Association Study Reveals Multiple Loci Associated with Primary Tooth Development during Infancy
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{"title"=>"Genome-wide association study reveals multiple loci associated with primary tooth development during infancy", "type"=>"journal", "authors"=>[{"first_name"=>"Demetris", "last_name"=>"Pillas", "scopus_author_id"=>"26323223600"}, {"first_name"=>"Clive J.", "last_name"=>"Hoggart", "scopus_author_id"=>"6602233276"}, {"first_name"=>"David M.", "last_name"=>"Evans", "scopus_author_id"=>"7601570762"}, {"first_name"=>"Paul F.", "last_name"=>"O'Reilly", "scopus_author_id"=>"24504286800"}, {"first_name"=>"Kirsi", "last_name"=>"Sipilä", "scopus_author_id"=>"7006827396"}, {"first_name"=>"Raija", "last_name"=>"Lähdesmäki", "scopus_author_id"=>"8882516100"}, {"first_name"=>"Iona Y.", "last_name"=>"Millwood", "scopus_author_id"=>"6506393527"}, {"first_name"=>"Marika", "last_name"=>"Kaakinen", "scopus_author_id"=>"57194504574"}, {"first_name"=>"Gopalakrishnan", "last_name"=>"Netuveli", "scopus_author_id"=>"9233259300"}, {"first_name"=>"David", "last_name"=>"Blane", "scopus_author_id"=>"7006315470"}, {"first_name"=>"Pimphen", "last_name"=>"Charoen", "scopus_author_id"=>"35589452800"}, {"first_name"=>"Ulla", "last_name"=>"Sovio", "scopus_author_id"=>"6602392590"}, {"first_name"=>"Anneli", "last_name"=>"Pouta", "scopus_author_id"=>"56830266200"}, {"first_name"=>"Nelson", "last_name"=>"Freimer", "scopus_author_id"=>"7006012650"}, {"first_name"=>"Anna Liisa", "last_name"=>"Hartikainen", "scopus_author_id"=>"7004678671"}, {"first_name"=>"Jaana", "last_name"=>"Laitinen", "scopus_author_id"=>"7103329949"}, {"first_name"=>"Sarianna", "last_name"=>"Vaara", "scopus_author_id"=>"35789513100"}, {"first_name"=>"Beate", "last_name"=>"Glaser", "scopus_author_id"=>"8942122500"}, {"first_name"=>"Peter", "last_name"=>"Crawford", "scopus_author_id"=>"56272892000"}, {"first_name"=>"Nicholas J.", "last_name"=>"Timpson", "scopus_author_id"=>"35355373400"}, {"first_name"=>"Susan M.", "last_name"=>"Ring", "scopus_author_id"=>"7005469522"}, {"first_name"=>"Guohong", "last_name"=>"Deng", "scopus_author_id"=>"8451420800"}, {"first_name"=>"Weihua", "last_name"=>"Zhang", "scopus_author_id"=>"55706414700"}, {"first_name"=>"Mark I.", "last_name"=>"McCarthy", "scopus_author_id"=>"7402061249"}, {"first_name"=>"Panos", "last_name"=>"Deloukas", "scopus_author_id"=>"7003287098"}, {"first_name"=>"Leena", "last_name"=>"Peltonen", "scopus_author_id"=>"36051313500"}, {"first_name"=>"Paul", "last_name"=>"Elliott", "scopus_author_id"=>"26643338400"}, {"first_name"=>"Lachlan J.M.", "last_name"=>"Coin", "scopus_author_id"=>"55889865800"}, {"first_name"=>"George Davey", "last_name"=>"Smith", "scopus_author_id"=>"35354080500"}, {"first_name"=>"Marjo Riitta", "last_name"=>"Jarvelin", "scopus_author_id"=>"18535933700"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.1000856", "scopus"=>"2-s2.0-77649210349", "pui"=>"358387552", "issn"=>"15537390", "pmid"=>"20195514", "sgr"=>"77649210349", "isbn"=>"2007201550"}, "id"=>"7d570ff0-287f-320c-8baa-be7c0dadea21", "abstract"=>"Tooth development is a highly heritable process which relates to other growth and developmental processes, and which interacts with the development of the entire craniofacial complex. Abnormalities of tooth development are common, with tooth agenesis being the most common developmental anomaly in humans. We performed a genome-wide association study of time to first tooth eruption and number of teeth at one year in 4,564 individuals from the 1966 Northern Finland Birth Cohort (NFBC1966) and 1,518 individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 5 loci at P<5x10(-8), and 5 with suggestive association (P<5x10(-6)). The loci included several genes with links to tooth and other organ development (KCNJ2, EDA, HOXB2, RAD51L1, IGF2BP1, HMGA2, MSRB3). Genes at four of the identified loci are implicated in the development of cancer. A variant within the HOXB gene cluster associated with occlusion defects requiring orthodontic treatment by age 31 years.", "link"=>"http://www.mendeley.com/research/genomewide-association-study-reveals-multiple-loci-associated-primary-tooth-development-during-infan-1", "reader_count"=>50, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>3, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>3, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Medicine and Dentistry"=>19, "Agricultural and Biological Sciences"=>20, "Arts and Humanities"=>1, "Neuroscience"=>1, "Chemistry"=>1, "Social Sciences"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>19}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Latvia"=>1, "United States"=>2, "United Kingdom"=>1, "Germany"=>1}, "group_count"=>4}

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  • {"files"=>["https://ndownloader.figshare.com/files/861447"], "description"=>"<p>Estimates and 95% confidence intervals for regression coefficients are given for the effect of delayed teething allele in Gaussian regression on time to first tooth and an ordinal regression on number of teeth.</p>", "links"=>[], "tags"=>["genotype", "snps", "attaining", "genome-wide"], "article_id"=>531872, "categories"=>["Developmental Biology", "Neuroscience", "Genetics"], "users"=>["Demetris Pillas", "Clive J. Hoggart", "David M. Evans", "Paul F. O'Reilly", "Kirsi Sipilä", "Raija Lähdesmäki", "Iona Y. Millwood", "Marika Kaakinen", "Gopalakrishnan Netuveli", "David Blane", "Pimphen Charoen", "Ulla Sovio", "Anneli Pouta", "Nelson Freimer", "Anna-Liisa Hartikainen", "Jaana Laitinen", "Sarianna Vaara", "Beate Glaser", "Peter Crawford", "Nicholas J. Timpson", "Susan M. Ring", "Guohong Deng", "Weihua Zhang", "Mark I. McCarthy", "Panos Deloukas", "Leena Peltonen", "Paul Elliott", "Lachlan J. M. Coin", "George Davey Smith", "Marjo-Riitta Jarvelin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000856.g002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Meta_analysis_for_primary_tooth_development_by_genotype_for_the_five_SNPs_attaining_genome_wide_significance_/531872", "title"=>"Meta-analysis for primary tooth development by genotype for the five SNPs attaining genome-wide significance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-02-26 00:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/427657", "https://ndownloader.figshare.com/files/427716", "https://ndownloader.figshare.com/files/427805", "https://ndownloader.figshare.com/files/427831", "https://ndownloader.figshare.com/files/427863"], "description"=>"<div><p>Tooth development is a highly heritable process which relates to other growth and developmental processes, and which interacts with the development of the entire craniofacial complex. Abnormalities of tooth development are common, with tooth agenesis being the most common developmental anomaly in humans. We performed a genome-wide association study of time to first tooth eruption and number of teeth at one year in 4,564 individuals from the 1966 Northern Finland Birth Cohort (NFBC1966) and 1,518 individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 5 loci at <em>P</em><5×10<sup>−8</sup>, and 5 with suggestive association (<em>P</em><5×10<sup>−6</sup>). The loci included several genes with links to tooth and other organ development (<em>KCNJ2</em>, <em>EDA</em>, <em>HOXB2</em>, <em>RAD51L1</em>, <em>IGF2BP1</em>, <em>HMGA2</em>, <em>MSRB3</em>). Genes at four of the identified loci are implicated in the development of cancer. A variant within the <em>HOXB</em> gene cluster associated with occlusion defects requiring orthodontic treatment by age 31 years.</p></div>", "links"=>[], "tags"=>["genome-wide", "reveals", "loci", "infancy"], "article_id"=>144422, "categories"=>["Developmental Biology", "Neuroscience", "Genetics"], "users"=>["Demetris Pillas", "Clive J. Hoggart", "David M. Evans", "Paul F. O'Reilly", "Kirsi Sipilä", "Raija Lähdesmäki", "Iona Y. Millwood", "Marika Kaakinen", "Gopalakrishnan Netuveli", "David Blane", "Pimphen Charoen", "Ulla Sovio", "Anneli Pouta", "Nelson Freimer", "Anna-Liisa Hartikainen", "Jaana Laitinen", "Sarianna Vaara", "Beate Glaser", "Peter Crawford", "Nicholas J. Timpson", "Susan M. Ring", "Guohong Deng", "Weihua Zhang", "Mark I. McCarthy", "Panos Deloukas", "Leena Peltonen", "Paul Elliott", "Lachlan J. M. Coin", "George Davey Smith", "Marjo-Riitta Jarvelin"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000856.s001", "https://dx.doi.org/10.1371/journal.pgen.1000856.s002", "https://dx.doi.org/10.1371/journal.pgen.1000856.s003", "https://dx.doi.org/10.1371/journal.pgen.1000856.s004", "https://dx.doi.org/10.1371/journal.pgen.1000856.s005"], "stats"=>{"downloads"=>16, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Association_Study_Reveals_Multiple_Loci_Associated_with_Primary_Tooth_Development_during_Infancy/144422", "title"=>"Genome-Wide Association Study Reveals Multiple Loci Associated with Primary Tooth Development during Infancy", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-02-26 01:13:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/861298"], "description"=>"<p>(A) <i>KCNJ2</i> gene region for time to first tooth eruption. (B) <i>EDA</i> gene region for time to first tooth. (C) <i>MSRB3</i> gene region for time to first tooth. (D) <i>IGF2BP1</i> gene region for number of teeth at 12 months (SNP with high <i>P</i> at 44000 kb is that near <i>HOXB2</i>, rs6504340). Note: This is a gene-rich region, so most genes are omitted to simplify the plot. (E) <i>RAD51L1</i> gene region for number of teeth at 12 months. -log<sub>10</sub> p-value is plotted against genomic position (NCBI build 36). Most significant SNP in each region is plotted in blue, r<sup>2</sup> with top SNP is colour coded red (0.8 – 1.0), orange (0.5 – 0.8), yellow (0.2 – 0.5), and white <0.2. Gene annotations are based on Genome Browser (RefSeq Genes) and arrows represent direction of transcription. Recombination rate is estimated by LDhat using HapMap CEU sample. All r<sup>2</sup> values are calculated in NFBC1966.</p>", "links"=>[], "tags"=>["disequilibrium", "loci", "genome-wide", "meta-analysis", "nfbc1966"], "article_id"=>531708, "categories"=>["Developmental Biology", "Neuroscience", "Genetics"], "users"=>["Demetris Pillas", "Clive J. Hoggart", "David M. Evans", "Paul F. O'Reilly", "Kirsi Sipilä", "Raija Lähdesmäki", "Iona Y. Millwood", "Marika Kaakinen", "Gopalakrishnan Netuveli", "David Blane", "Pimphen Charoen", "Ulla Sovio", "Anneli Pouta", "Nelson Freimer", "Anna-Liisa Hartikainen", "Jaana Laitinen", "Sarianna Vaara", "Beate Glaser", "Peter Crawford", "Nicholas J. Timpson", "Susan M. Ring", "Guohong Deng", "Weihua Zhang", "Mark I. McCarthy", "Panos Deloukas", "Leena Peltonen", "Paul Elliott", "Lachlan J. M. Coin", "George Davey Smith", "Marjo-Riitta Jarvelin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000856.g001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linkage_disequilibrium_and_association_at_loci_reaching_genome_wide_significance_for_primary_tooth_development_in_meta_analysis_of_NFBC1966_and_ALSPAC_/531708", "title"=>"Linkage disequilibrium and association at loci reaching genome-wide significance for primary tooth development in meta-analysis of NFBC1966 and ALSPAC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-02-26 00:28:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/861663"], "description"=>"<p>SNPs at genome wide significance <i>P</i><5<b>×</b>10<sup>−8</sup> and SNPS with suggestive evidence at 5<b>×</b>10<sup>−6</sup>><i>P</i>>5<b>×</b>10<sup>−8</sup>. The <i>P</i> value of each cohort is corrected for sex, gestational age and population structure using principal components and genomic control. The combined <i>P</i> value is calculated using a fixed effects inverse variance meta-analysis. When no gene is within 50 kb of the SNP the chromosome band is given. Positions of SNPs are reported in NCBI build 36 coordinates. The alleles all refer to the forward strand. The effect allele is defined as the allele associated with later tooth eruption and a smaller number of teeth. % var is the percentage of variance explained by each SNP. <i>P</i> values attaining overall GWA significance are in bold.</p>", "links"=>[], "tags"=>["gwa", "signals", "locus", "meta-analysis", "nfbc1966"], "article_id"=>532074, "categories"=>["Developmental Biology", "Neuroscience", "Genetics"], "users"=>["Demetris Pillas", "Clive J. Hoggart", "David M. Evans", "Paul F. O'Reilly", "Kirsi Sipilä", "Raija Lähdesmäki", "Iona Y. Millwood", "Marika Kaakinen", "Gopalakrishnan Netuveli", "David Blane", "Pimphen Charoen", "Ulla Sovio", "Anneli Pouta", "Nelson Freimer", "Anna-Liisa Hartikainen", "Jaana Laitinen", "Sarianna Vaara", "Beate Glaser", "Peter Crawford", "Nicholas J. Timpson", "Susan M. Ring", "Guohong Deng", "Weihua Zhang", "Mark I. McCarthy", "Panos Deloukas", "Leena Peltonen", "Paul Elliott", "Lachlan J. M. Coin", "George Davey Smith", "Marjo-Riitta Jarvelin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000856.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_top_GWA_signals_at_each_locus_from_a_meta_analysis_of_NFBC1966_and_ALSPAC_/532074", "title"=>"The top GWA signals at each locus from a meta-analysis of NFBC1966 and ALSPAC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-02-26 00:34:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/861552"], "description"=>"<p>Subjects are classified by the number of delayed tooth eruption alleles. SNPs are chosen so that they had the strongest signal for number of teeth at each locus. Mean time of first tooth eruption is plotted in red and number of teeth by the age of one year in black. The bars represent the number of individuals for each count of ‘delayed tooth eruption’ alleles. The line through points is a linear regression fit.</p>", "links"=>[], "tags"=>["delayed", "eruption", "alleles", "loci"], "article_id"=>531975, "categories"=>["Developmental Biology", "Neuroscience", "Genetics"], "users"=>["Demetris Pillas", "Clive J. Hoggart", "David M. Evans", "Paul F. O'Reilly", "Kirsi Sipilä", "Raija Lähdesmäki", "Iona Y. Millwood", "Marika Kaakinen", "Gopalakrishnan Netuveli", "David Blane", "Pimphen Charoen", "Ulla Sovio", "Anneli Pouta", "Nelson Freimer", "Anna-Liisa Hartikainen", "Jaana Laitinen", "Sarianna Vaara", "Beate Glaser", "Peter Crawford", "Nicholas J. Timpson", "Susan M. Ring", "Guohong Deng", "Weihua Zhang", "Mark I. McCarthy", "Panos Deloukas", "Leena Peltonen", "Paul Elliott", "Lachlan J. M. Coin", "George Davey Smith", "Marjo-Riitta Jarvelin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000856.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_combined_impact_of_the_delayed_tooth_eruption_alleles_in_5_identified_loci_at_P_8722_8_in_the_NFBC1966_/531975", "title"=>"The combined impact of the delayed tooth eruption alleles in 5 identified loci at <i>P</i><5×10<sup>−8</sup> in the NFBC1966.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-02-26 00:32:55"}

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