Summary of Metabochip SNPs by SNP category.

<p> <i>Numbers in parenthesis represents the proportion of the SNPs in the previous column. A SNP may fall into multiple categories.</i></p

Coverage of 257 Metabochip fine-mapping regions.

<p>Fraction of 1000 Genomes Project SNPs in strong linkage disequilibrium (r²≥.8) with HapMap 3 (green squares) or Metabochip (blue dots) SNPs as a function of minor allele frequencies: (A) 1000 Genomes Pilot 1 SNPs, (B) 1000 Genomes Phase 1 SNPs (May 2011 release).</p

Summary of Metabochip SNPs by trait: Fine-mapping and replication.

<p> <i>SNP counts are numbers of SNPs successfully manufactured on the Metabochip array.</i></p>*<p> <i>Waist-to-hip ratio and waist circumference were adjusted for body mass index.</i></p

Example of signal fine mapping (SFM) and locus fine mapping (LFM) regions.

<p>A SFM region seeks to map the initial association signal. SFM regions were designed using linkage disequilibrium (LD) r² estimates from the 1000 Genomes Project and HapMap CEU data. Initial boundaries were determined by identifying all SNPs satisfying r²≥.5 with the index SNP, and then expanded to the nearest flanking recombination hotspot, but stopped if there was no hotspot nearby. LFM regions (blue) were similarly designed but expanded to capture functional units of interest such as nearby coding genes. The figure plots LD r² for SNPs (red dots) within the region and recombination rate (blue lines) as a function of position on the chromosome. Gene positions and structures are displayed in the lower panel. MI = myocardial Infarction; CAD = cardiovascular disease; HDL = high-density lipoprotein; LDL = low-density lipoprotein; T2D = type 2 diabetes.</p

Regional association plots for LDL cholesterol association in the SardiNIA study.

<p>Association plots for a study of 2,432 Sardinian individuals for five Metabochip fine-mapping regions using 1000 Genomes data as reference set and Affymetrix genotypes (left panels : A,C,E,G,H) or Metabochip genotypes (right panels : B,D,F,H,J) as target sets. The figures plot −log₁₀ of the association p-value within the region and recombination rate (blue lines) as a function of position on the chromosome. Blue, green, and red dots and triangles indicate genotyped and imputed SNPs with minor allele frequencies less than 0.02, greater than or equal 0.02 and less than 0.05, and greater than or equal 0.05, respectively. Gene positions and structures are displayed in the lower panel.</p

Seven SNPs show sex difference.

a<p>Trait and sex for which the SNP was selected;</p>b<p>Gene labels state the nearest gene or the gene as published previously; details on all genes near the association signal can be found in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003500#pgen.1003500.s002" target="_blank">Figure S2</a>;</p>c<p>One-sided P-Values.</p>d<p>larger sample size due to one additional study that did not have hip circumference, and therefore could not contribute to WHRadjBMI.</p>e<p>smaller sample size as this SNP was not on Metabochip.</p><p>Shown are the seven SNPs with significant (at 5% false discovery rate) sex difference in the follow-up data. These seven SNPs exhibit genome-wide significant association in women (joint discovery and follow-up <i>P_women</i><5×10−8) and only two of these show nominally significant association in men (joint <i>P_men</i><0.05). The three loci MAP3K1, HSD17B4, and PPARG are shown here for the first time for their anthropometric trait association as well as for sex-difference.</p

Consistently higher effect sizes for women for all seven loci.

<p>Shown are beta-estimates and 95% confidence intervals for the seven identified SNPs (also stating the phenotype for which the SNP was selected for).</p

Genome-wide scan for sex-specific genome-wide association highlights numerous loci.

<p>(a) Manhattan plot showing the men-specific (upward, up to 60,586 men) and women-specific (downward, up to 73,137 women) association P-values from the discovery with the 619 selected loci colored by the phenotype for which the locus was selected; (b) QQ-plot showing the sex-specific association P-values as observed against those expected under the null overall phenotypes (black) and for each phenotypes separately (colored).</p

Overview of design and findings.

<p>Among the 7 identified loci, we defined those close to (<1 cM) published hits <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003500#pgen.1003500-LangoAllen1" target="_blank">[25]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003500#pgen.1003500-Speliotes1" target="_blank">[29]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003500#pgen.1003500-Heid1" target="_blank">[31]</a> as <i>near published hit</i>s and <i>novel</i> otherwise. Novel loci with sex-combined discovery P-value<5.8×10⁻⁵, which is the P-value cut-off corresponding to 5% FDR, were declared as loci that <i>could have been discovered also with sex-combined analysis</i>, and otherwise that these <i>would have been missed without the sex-stratified analyses</i>. FDR = false discovery rate.</p

Seven identified SNPs compared to previously published loci.

a<p>The Effect allele refers to a positive effect direction in the discovery stage for the trait and gender, the SNP was selected for;</p>b<p>Gene near this SNP which was published previously from sex-combined analyses.</p><p>The seven SNPs with sex difference are considered to depict a known locus, if the index SNP is close to a published top SNP (<1 cM). These include four of the previously reported sexually dimorphic WHR loci (Heid et al., Nat Genet 2010).</p