Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation
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Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404,862 chrX SNPs to levels of twelve commonly studied cardiometabolic and anthropometric traits in 19,697 Finnish and Swedish individuals with replication data on 5,032 additional Finns. By using a linear mixed model, we estimate that on average 2.6% of the additive genetic variance in these twelve traits is attributable to chrX, this being in proportion to the number of SNPs in the chromosome. In a chrX-wide association analysis, we identify three novel loci: two for height (rs182838724 near FGF16/ATRX/MAGT1, joint P-value = 2.71×10(-9), and rs1751138 near ITM2A, P-value = 3.03×10(-10)) and one for fasting insulin (rs139163435 in Xq23, P-value = 5.18×10(-9)). Further, we find that effect sizes for variants near ITM2A, a gene implicated in cartilage development, show evidence for a lack of dosage compensation. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1557452", "https://ndownloader.figshare.com/files/1557454", "https://ndownloader.figshare.com/files/1557455", "https://ndownloader.figshare.com/files/1557456", "https://ndownloader.figshare.com/files/1557457", "https://ndownloader.figshare.com/files/1557458", "https://ndownloader.figshare.com/files/1557459", "https://ndownloader.figshare.com/files/1557460", "https://ndownloader.figshare.com/files/1557461", "https://ndownloader.figshare.com/files/1557462", "https://ndownloader.figshare.com/files/1557463"], "description"=>"<div><p>The X chromosome (chrX) represents one potential source for the “missing heritability” for complex phenotypes, which thus far has remained underanalyzed in genome-wide association studies (GWAS). Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404,862 chrX SNPs to levels of twelve commonly studied cardiometabolic and anthropometric traits in 19,697 Finnish and Swedish individuals with replication data on 5,032 additional Finns. By using a linear mixed model, we estimate that on average 2.6% of the additive genetic variance in these twelve traits is attributable to chrX, this being in proportion to the number of SNPs in the chromosome. In a chrX-wide association analysis, we identify three novel loci: two for height (rs182838724 near <i>FGF16/ATRX/MAGT1</i>, joint P-value = 2.71×10<sup>−9</sup>, and rs1751138 near <i>ITM2A</i>, P-value = 3.03×10<sup>−10</sup>) and one for fasting insulin (rs139163435 in Xq23, P-value = 5.18×10<sup>−9</sup>). Further, we find that effect sizes for variants near <i>ITM2A</i>, a gene implicated in cartilage development, show evidence for a lack of dosage compensation. This observation is further supported by a sex-difference in <i>ITM2A</i> expression in whole blood (P-value = 0.00251), and is also in agreement with a previous report showing <i>ITM2A</i> escapes from X chromosome inactivation (XCI) in the majority of women. Hence, our results show one of the first links between phenotypic variation in a population sample and an XCI-escaping locus and pinpoint <i>ITM2A</i> as a potential contributor to the sexual dimorphism in height. In conclusion, our study provides a clear motivation for including chrX in large-scale genetic studies of complex diseases and traits.</p></div>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "x-wide", "identifies", "loci", "fasting", "insulin", "incomplete", "dosage"], "article_id"=>1077037, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004127.s001", "https://dx.doi.org/10.1371/journal.pgen.1004127.s002", "https://dx.doi.org/10.1371/journal.pgen.1004127.s003", "https://dx.doi.org/10.1371/journal.pgen.1004127.s004", "https://dx.doi.org/10.1371/journal.pgen.1004127.s005", "https://dx.doi.org/10.1371/journal.pgen.1004127.s006", "https://dx.doi.org/10.1371/journal.pgen.1004127.s007", "https://dx.doi.org/10.1371/journal.pgen.1004127.s008", "https://dx.doi.org/10.1371/journal.pgen.1004127.s009", "https://dx.doi.org/10.1371/journal.pgen.1004127.s010", "https://dx.doi.org/10.1371/journal.pgen.1004127.s011"], "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosome_X_Wide_Association_Study_Identifies_Loci_for_Fasting_Insulin_and_Height_and_Evidence_for_Incomplete_Dosage_Compensation_/1077037", "title"=>"Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-06 10:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1557433"], "description"=>"<p>The estimates are based on an analysis of the individuals from six Finnish cohorts using the program GCTA and 217,112 common and low-frequency chrX SNPs (MAF>1%) directly genotyped or imputed with high-quality (info >0.8) and 319,445 directly genotyped autosomal SNPs (MAF>1%).</p><p>h<sub>X</sub>: estimate for the proportion of explained variance accountable by the SNPs in chromosome X in per cent; se<sub>X</sub>: standard error in per cent for the X chromosome variance estimate; P-value: P-value for the test of h<sub>X</sub> = 0; h<sub>aut</sub>: estimate for the proportion of explained variance accountable by the SNPs in autosomes in per cent; se<sub>aut</sub>: standard error in per cent for the autosomal variance estimate; SBP: systolic blood pressure; HDL-C: high-density lipoprotein cholesterol; TG: total triglycerides; CRP: C-reactive protein; WHR: waist-hip-ratio; BMI: body-mass-index; DBP: diastolic blood pressure; LDL-C: low-density lipoprotein cholesterol; TC: total cholesterol.</p>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "explained", "variances", "quantitative", "phenotypes", "attributable", "chromosome", "snps", "autosomal", "separately", "variance"], "article_id"=>1077019, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004127.t002", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_the_explained_variances_in_the_twelve_quantitative_phenotypes_attributable_to_chromosome_X_SNPs_and_autosomal_SNPs_separately_using_equal_variance_EV_model_/1077019", "title"=>"Estimates of the explained variances in the twelve quantitative phenotypes attributable to chromosome X SNPs and autosomal SNPs separately using equal variance (EV) model.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-06 10:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1557432"], "description"=>"<p>EA: effect allele; OA: other allele; Data set: the data sets included in the meta-analysis: discovery cohorts (discovery), the replication cohort (replication), both discovery and replication cohorts (joint); Sex: the sex in which the analysis was conducted; EAF: effect allele frequency; Beta: effect size for the effect allele; SE: standard error for Beta; P-value: P-value for the association from fixed-effects meta-analysis; N: sample size in the analysis; P-value (sex): P-value for the association from sex-differentiated meta-analysis; P-value (het): P-value from the sex heterogeneity test; Variance explained: the proportion of phenotype variance the lead SNP explains in per cent, calculated from meta-analysis summary statistics (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004127#s4\" target=\"_blank\">Materials and Methods</a>).</p>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "associations", "loci", "chromosome", "x-wide"], "article_id"=>1077018, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004127.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_lead_associations_in_the_three_significantly_associated_loci_in_the_chromosome_X_wide_association_analysis_/1077018", "title"=>"The lead associations in the three significantly associated loci in the chromosome X-wide association analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-06 10:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1557426"], "description"=>"<p>A. Separately estimated effect sizes of the three lead SNPs (dots labeled with rs-numbers) in females (x-axis) and males (y-axis) when female genotypes are coded {0,1,2} and male genotypes {0,2}. Ellipses show the 95% confidence regions for the estimates. The lines show the regions of the expected values of the effects under either full dosage compensation (FDC) or no dosage compensation (NDC) models. The associated traits are fasting insulin (INS) and height (HGT). B. Posterior probability of no dosage compensation (NDC) model at the three lead SNPs when the other candidate is full dosage compensation model and the two models are equally probable <i>a priori</i>. Labels under bars give the rs-number of the SNP, the associated trait (INS = fasting insulin or HGT = height) and the height of the bar.</p>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "dosage", "loci", "applying", "bayesian"], "article_id"=>1077012, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004127.g002", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_dosage_compensation_models_in_the_three_associated_loci_applying_Bayesian_framework_/1077012", "title"=>"Comparison of the dosage compensation models in the three associated loci applying Bayesian framework.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1557409"], "description"=>"<p>A. A Manhattan plot showing the associations of the X chromosome SNPs to the twelve phenotypes in the discovery analysis. The associated loci (P-value<5.0×10<sup>−8</sup>) are highlighted with red dots and solid lines. B. A plot of the height associations in the Xq21.1 region showing two separate association signals. C–E. The association plots for height near <i>ITM2A</i> (C) and height near <i>ATRX</i> (D) and for fasting insulin in Xq23 (E), showing the association P-values in the discovery analysis. Yellow diamonds indicate the SNPs, which showed the strongest evidence of association in each of the loci, and purple diamonds and the P-values given in the plots indicate the associations of these lead SNPs in the joint analysis of discovery and replication data sets. Each circle in the plots indicates a SNP with the color of the circle (in C–E) showing the linkage disequilibrium between the SNP and the highlighted lead SNP: dark blue (r<sup>2</sup><0.2), light blue (r<sup>2</sup>>0.2), green (r<sup>2</sup>>0.4), orange (r<sup>2</sup>>0.6) and red (r<sup>2</sup>>0.8), The r<sup>2</sup> values were calculated using the genotype data from the COROGENE cohort, and the recombination rate, indicated by the blue lines in the background and the right hand y-axis, was estimated from the CEU HapMap data. The bottom panels show the genes (RefSeq Genes) and their positions in each locus. In all plots the dashed red line marks the threshold for genome-wide significance (P-value = 5.0×10<sup>−8</sup>).</p>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "manhattan", "phenotypes"], "article_id"=>1077008, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004127.g001", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Manhattan_plot_across_all_the_twelve_phenotypes_and_regional_association_plots_for_the_three_associated_loci_/1077008", "title"=>"A Manhattan plot across all the twelve phenotypes and regional association plots for the three associated loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-06 10:59:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1557430"], "description"=>"<p>N: maximum number of individuals with phenotype and genotype data available; BMI: Body-mass-index; Age, height and BMI are given as mean ± standard deviation.</p>", "links"=>[], "tags"=>["genetics", "epigenetics", "X chromosome inactivation", "Genome-wide association studies", "replication"], "article_id"=>1077016, "categories"=>["Biological Sciences"], "users"=>["Taru Tukiainen", "Matti Pirinen", "Antti-Pekka Sarin", "Claes Ladenvall", "Johannes Kettunen", "Terho Lehtimäki", "Marja-Liisa Lokki", "Markus Perola", "Juha Sinisalo", "Efthymia Vlachopoulou", "Johan G. Eriksson", "Leif Groop", "Antti Jula", "Marjo-Riitta Jarvelin", "Olli T. Raitakari", "Veikko Salomaa", "Samuli Ripatti"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004127.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_summary_of_the_characteristics_of_the_discovery_and_replication_cohorts_/1077016", "title"=>"A summary of the characteristics of the discovery and replication cohorts.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-06 10:59:21"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Physical sciences", "average_usage"=>[271]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[286]}]}
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