GSV analysis of candidate obesity loci.

<p>SNP genotyping data from 3 separate cohorts were analysed using the cnvHap algorithm, and GSVs were identified that corresponded to the GSVs under investigation. For GSVs identified in at least one individual, association with obesity status (excluding overweight individuals from the analysis) was tested according to Fisher’s exact test. For GSVs identified in at least 3 members of the NFBC1966 cohort, association with log₁₀BMI as a quantitative trait was tested by 2-way ANOVA with gender as the second covariate. Italics denote a direction of effect opposite to that in the original report.</p>a<p>refers to the Illumina Human CNV370 array.</p>b<p>re-calculated after excluding individuals with deletions of the neighbouring 16p11.2 obesity-associated region (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058048#pone.0058048.s006" target="_blank">Text S1</a>).</p

Procedure for identification of GSVs.

<p>Following data export and QC, GSV calling was carried out using the cnvHap algorithm. Illustrative data for 3 GSV loci (shaded) show all positive GSV calls (black) together with examples of calls not meeting the necessary criteria (grey); probes at which copy number changes were identified are also indicated (circles).</p

Reduced BMI in carriers of deletions in the <i>FOXP2</i> region.

<p>Deletions within <i>FOXP2</i> are shown relative to selected tracks from the UCSC browser (<a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>) for the corresponding region of chromosome 7: <i>FOXP2</i> coding transcripts (UCSC Genes); histone modifications H3K4Me1, H3K4Me3, H3K27Ac (ENCODE Regulation); and binding by transcription factor NF-κB (ENCODE TFBS). Multiple additional transcription factors bind at the apparent NF-κB binding site. The minimum extent of each predicted deletion, the probes at which copy number changes were identified and the BMI for carriers of each deletion are as shown. Grey shading indicates the region previously associated with BMI <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058048#pone.0058048-Glessner1" target="_blank">[16]</a>.</p