Rare Copy Number Variants Are a Common Cause of Short Stature
Publication Date
March 14, 2013
Journal
PLOS Genetics
Authors
Diana Zahnleiter, Steffen Uebe, Arif B. Ekici, Juliane Hoyer, et al
Volume
9
Issue
3
Pages
e1003365
DOI
https://dx.plos.org/10.1371/journal.pgen.1003365
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1003365
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23516380
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597495
Europe PMC
http://europepmc.org/abstract/MED/23516380
Web of Science
000316866700041
Scopus
84875975345
Mendeley
http://www.mendeley.com/research/rare-copy-number-variants-common-cause-short-stature-4
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Mendeley | Further Information

{"title"=>"Rare Copy Number Variants Are a Common Cause of Short Stature", "type"=>"journal", "authors"=>[{"first_name"=>"Diana", "last_name"=>"Zahnleiter", "scopus_author_id"=>"36723033800"}, {"first_name"=>"Steffen", "last_name"=>"Uebe", "scopus_author_id"=>"6507425429"}, {"first_name"=>"Arif B.", "last_name"=>"Ekici", "scopus_author_id"=>"6603821550"}, {"first_name"=>"Juliane", "last_name"=>"Hoyer", "scopus_author_id"=>"16245104300"}, {"first_name"=>"Antje", "last_name"=>"Wiesener", "scopus_author_id"=>"6506296028"}, {"first_name"=>"Dagmar", "last_name"=>"Wieczorek", "scopus_author_id"=>"55748804700"}, {"first_name"=>"Erdmute", "last_name"=>"Kunstmann", "scopus_author_id"=>"6701808602"}, {"first_name"=>"André", "last_name"=>"Reis", "scopus_author_id"=>"7202573897"}, {"first_name"=>"Helmuth Guenther", "last_name"=>"Doerr", "scopus_author_id"=>"36824863400"}, {"first_name"=>"Anita", "last_name"=>"Rauch", "scopus_author_id"=>"7005730702"}, {"first_name"=>"Christian T.", "last_name"=>"Thiel", "scopus_author_id"=>"7006568845"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84875975345", "doi"=>"10.1371/journal.pgen.1003365", "sgr"=>"84875975345", "isbn"=>"1553-7404 (Electronic) 1553-7390 (Linking)", "pmid"=>"23516380", "issn"=>"15537390", "pui"=>"368694414"}, "id"=>"e53d2463-e5e3-3a7d-bff2-dbf0672f34a2", "abstract"=>"Human growth has an estimated heritability of about 80%-90%. Nevertheless, the underlying cause of shortness of stature remains unknown in the majority of individuals. Genome-wide association studies (GWAS) showed that both common single nucleotide polymorphisms and copy number variants (CNVs) contribute to height variation under a polygenic model, although explaining only a small fraction of overall genetic variability in the general population. Under the hypothesis that severe forms of growth retardation might also be caused by major gene effects, we searched for rare CNVs in 200 families, 92 sporadic and 108 familial, with idiopathic short stature compared to 820 control individuals. Although similar in number, patients had overall significantly larger CNVs (p-value<1x10(-7)). In a gene-based analysis of all non-polymorphic CNVs>50 kb for gene function, tissue expression, and murine knock-out phenotypes, we identified 10 duplications and 10 deletions ranging in size from 109 kb to 14 Mb, of which 7 were de novo (p<0.03) and 13 inherited from the likewise affected parent but absent in controls. Patients with these likely disease causing 20 CNVs were smaller than the remaining group (p<0.01). Eleven (55%) of these CNVs either overlapped with known microaberration syndromes associated with short stature or contained GWAS loci for height. Haploinsufficiency (HI) score and further expression profiling suggested dosage sensitivity of major growth-related genes at these loci. Overall 10% of patients carried a disease-causing CNV indicating that, like in neurodevelopmental disorders, rare CNVs are a frequent cause of severe growth retardation.", "link"=>"http://www.mendeley.com/research/rare-copy-number-variants-common-cause-short-stature-4", "reader_count"=>22, "reader_count_by_academic_status"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Bachelor"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Bachelor"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Medicine and Dentistry"=>7, "Agricultural and Biological Sciences"=>10, "Veterinary Science and Veterinary Medicine"=>1, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "Italy"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/988446"], "description"=>"<p>(A) Example representation of the copy number analysis of patient 1 using the Affymetrix Genotyping Console 3.0.2 software. The red bar shows the 2.2 Mb deletion region (CNSegments). (B) Graphical presentation of the deletion region including 33 candidate genes (modified from UCSC genome browser). (C) MLPA confirmation with a probe in the <i>NFASC</i> gene region. A relative quantity value (RQ) below 0.75 was considered as confirmation of a deletion, above 1.25 as confirmation of a duplication. Detailed data for the remaining patients is presented in the supporting information.</p>", "links"=>[], "tags"=>["karyotyping", "mlpa", "confirmation"], "article_id"=>652928, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.g002", "stats"=>{"downloads"=>0, "page_views"=>45, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_karyotyping_and_MLPA_confirmation_of_identified_loci_/652928", "title"=>"Molecular karyotyping and MLPA confirmation of identified loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:36:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/988449"], "description"=>"<p>(A) Presentation of the Odds Ratio (light blue) and –log10(p-value) (dark blue) for determination of the size threshold of the number of CNVs in patients vs. controls. The Odds Ratio and the –log10(p-value) confirms a CNV size cut-off at 99.2 kb (OR 1.26 and p-value 4.98×10<sup>−8</sup>). (B) Fraction of copy numbers segments in cases (grey) vs. control (white) quintiles (* p<0.005). Quintile borders were Q1: 68.3 kb, Q2: 99.3 kb, Q3 149.6 kb, Q4 298.1 kb, and Q5: 72,571.3 kb. The y axis presents the fraction of CNVs inside the corresponding quintile bin. Significance levels are calculated using Fisher's exact test. The figure shows a shift towards segments above 100 kb in patients (** p-value 1.188×10<sup>−7</sup>).</p>", "links"=>[], "tags"=>["incidence", "cnvs", "100", "kb", "affected"], "article_id"=>652929, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Higher_incidence_of_CNVs_with_a_length_of_above_100_kb_in_affected_individuals_/652929", "title"=>"Higher incidence of CNVs with a length of above 100 kb in affected individuals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:38:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/988451"], "description"=>"<p>Height distribution (SDS) of all 200 patients (blue) compared to the 20 patients with identified CNVs (green). The mean SD score for height was −3.34. Patients with identified CNVs showed a significant difference in the SDS distribution (p-value 0.03).</p>", "links"=>[], "tags"=>["genetics and genomics", "developmental biology", "pediatrics and child health"], "article_id"=>652930, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.g004", "stats"=>{"downloads"=>1, "page_views"=>49, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Height_distribution_of_the_study_group_/652930", "title"=>"Height distribution of the study group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:39:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/988453"], "description"=>"<p>The values of r<sup>2</sup> are based on the CEU 1000genomes Nov 2010 samples. The blue line and right-hand y axis represent recombination rates. The SNPs with the min p values are highlighted as purple diamond. The figures were created using LocusZoom (<a href=\"http://csg.sph.umich.edu/locuszoom/\" target=\"_blank\">http://csg.sph.umich.edu/locuszoom/</a>).</p>", "links"=>[], "tags"=>["GWAS", "loci"], "article_id"=>652931, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.g005", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_significant_association_of_GWAS_loci_for_height_distribution_in_the_3_CNVs_/652931", "title"=>"Genome-wide significant association of GWAS loci for height distribution in the 3 CNVs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:40:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/988465", "https://ndownloader.figshare.com/files/988466", "https://ndownloader.figshare.com/files/988468", "https://ndownloader.figshare.com/files/988482", "https://ndownloader.figshare.com/files/988484", "https://ndownloader.figshare.com/files/988485", "https://ndownloader.figshare.com/files/988486", "https://ndownloader.figshare.com/files/988487", "https://ndownloader.figshare.com/files/988489", "https://ndownloader.figshare.com/files/988490", "https://ndownloader.figshare.com/files/988491"], "description"=>"<div><p>Human growth has an estimated heritability of about 80%–90%. Nevertheless, the underlying cause of shortness of stature remains unknown in the majority of individuals. Genome-wide association studies (GWAS) showed that both common single nucleotide polymorphisms and copy number variants (CNVs) contribute to height variation under a polygenic model, although explaining only a small fraction of overall genetic variability in the general population. Under the hypothesis that severe forms of growth retardation might also be caused by major gene effects, we searched for rare CNVs in 200 families, 92 sporadic and 108 familial, with idiopathic short stature compared to 820 control individuals. Although similar in number, patients had overall significantly larger CNVs (p-value<1×10<sup>−7</sup>). In a gene-based analysis of all non-polymorphic CNVs>50 kb for gene function, tissue expression, and murine knock-out phenotypes, we identified 10 duplications and 10 deletions ranging in size from 109 kb to 14 Mb, of which 7 were <i>de novo</i> (p<0.03) and 13 inherited from the likewise affected parent but absent in controls. Patients with these likely disease causing 20 CNVs were smaller than the remaining group (p<0.01). Eleven (55%) of these CNVs either overlapped with known microaberration syndromes associated with short stature or contained GWAS loci for height. Haploinsufficiency (HI) score and further expression profiling suggested dosage sensitivity of major growth-related genes at these loci. Overall 10% of patients carried a disease-causing CNV indicating that, like in neurodevelopmental disorders, rare CNVs are a frequent cause of severe growth retardation.</p> </div>", "links"=>[], "tags"=>["variants", "stature"], "article_id"=>652937, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003365.s001", "https://dx.doi.org/10.1371/journal.pgen.1003365.s002", "https://dx.doi.org/10.1371/journal.pgen.1003365.s003", "https://dx.doi.org/10.1371/journal.pgen.1003365.s004", "https://dx.doi.org/10.1371/journal.pgen.1003365.s005", "https://dx.doi.org/10.1371/journal.pgen.1003365.s006", "https://dx.doi.org/10.1371/journal.pgen.1003365.s007", "https://dx.doi.org/10.1371/journal.pgen.1003365.s008", "https://dx.doi.org/10.1371/journal.pgen.1003365.s009", "https://dx.doi.org/10.1371/journal.pgen.1003365.s010", "https://dx.doi.org/10.1371/journal.pgen.1003365.s011"], "stats"=>{"downloads"=>110, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rare_Copy_Number_Variants_Are_a_Common_Cause_of_Short_Stature__/652937", "title"=>"Rare Copy Number Variants Are a Common Cause of Short Stature", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-15 14:46:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007323"], "description"=>"<p>Overview of the phenotypic characteristics of the patient group.</p>", "links"=>[], "tags"=>["phenotypic"], "article_id"=>667946, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_phenotypic_characteristics_of_the_patient_group_/667946", "title"=>"Overview of the phenotypic characteristics of the patient group.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-14 02:12:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007305"], "description"=>"<p>Summary phenotype of patients with identified CNVs.</p>", "links"=>[], "tags"=>["phenotype", "patients"], "article_id"=>667923, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.t003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_phenotype_of_patients_with_identified_CNVs_/667923", "title"=>"Summary phenotype of patients with identified CNVs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-14 02:12:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007280"], "description"=>"1<p>Known short stature causing genes.</p>2<p>MD = Microdeletion/Microduplication syndromes;</p>3<p>Details in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003365#pgen.1003365.s007\" target=\"_blank\">Table S3</a>;</p>4<p># of genes expressed in relevant growth tissues (bone, cartilage) according to GEPIS-tissue;</p>5<p>Patients in Decipher with overlapping CNVs and short stature;</p>6<p># of genes with short stature in the mouse model,</p>7<p>min p-value in GIANT association study;</p>8<p># of genes with Haploinsufficiency score<10%.</p>", "links"=>[], "tags"=>["genetics and genomics", "developmental biology", "pediatrics and child health"], "article_id"=>667898, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lines_of_Evidence_/667898", "title"=>"Lines of Evidence.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-14 02:11:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/988445"], "description"=>"<p>Molecular karyotyping was performed for 200 patients with short stature after thorough clinical evaluation and for 820 healthy control samples. Exclusion of common variants using the control samples and scoring CNVs above 50 kb resulted in an approx. reduction of 80% of the CNVs identified in the patient samples. 60.5% of these CNVs affect reference sequence gene regions. Functional characterization includes segregation analysis using parental arrays and/or MLPA as well as gene and CNV based evaluation.</p>", "links"=>[], "tags"=>["genetics and genomics", "developmental biology", "pediatrics and child health"], "article_id"=>652927, "categories"=>["Developmental Biology", "Genetics", "Medicine"], "users"=>["Diana Zahnleiter", "Steffen Uebe", "Arif B. Ekici", "Juliane Hoyer", "Antje Wiesener", "Dagmar Wieczorek", "Erdmute Kunstmann", "André Reis", "Helmuth-Guenther Doerr", "Anita Rauch", "Christian T. Thiel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003365.g001", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CNV_discovery_and_characterization_/652927", "title"=>"CNV discovery and characterization.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:35:39"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Medicine and health sciences/Pediatrics", "average_usage"=>[248, 430, 563, 680, 778, 859, 949, 1017, 1115, 1199, 1281, 1364, 1431]}]}
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