Loadings, p values, indirect and overall effects of 12 SNPs, PRS on body shape with adjustment for sex and age.

<p>Loadings, p values, indirect and overall effects of 12 SNPs, PRS on body shape with adjustment for sex and age.</p

Fitted model for the 12 SNPs from the 12 gene regions with adjustment for sex and age for multiple traits (a) as with distribution of its PRS and cumulative effects of these variants (b).

<p>Fitted model for the 12 SNPs from the 12 gene regions with adjustment for sex and age for multiple traits (a) as with distribution of its PRS and cumulative effects of these variants (b).</p

Distribution of body shape types and characteristics of body shape score (BSS) by sex in the EPIC-Norfolk study.

<p>Distribution of body shape types and characteristics of body shape score (BSS) by sex in the EPIC-Norfolk study.</p

PLSPM-based models.

<p>(a) Scan statistic model, where <i>ξ₁</i> represents genomic region containing <i>P</i> SNPs and <i>β₂₁</i> the regional effect on the body shape score <i>ξ₁</i>; (<b>b</b>) Polygenic effect model, where <i>ξ'₁</i> represents polygenic risk score and <i>β'₂₁</i> the polygenic effect. In both models, <i>λ</i>'s are the loadings while <i>β</i>'s are the path coefficients.</p

Power Calculations

<p>Power of the current Cambridgeshire Case-Control Study to detect associations with risk allele of varying frequencies and with a Type 1 error rate of 5%. Abbreviations: p0, frequency of the predisposing allele; chr, number of chromosomes. Graphs were plotted with the PS power and sample-size program (available at <a href="http://www.mc.vanderbilt.edu/prevmed/ps" target="_blank">http://www.mc.vanderbilt.edu/prevmed/ps</a>; <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0000020#pbio-0000020-DuPont1" target="_blank">DuPont and Plummer 1997</a>).</p

Spearman correlations between <i>P</i>_<i>int</i> in <i>SNP × Physical Activity</i> and <i>SNP × Smoking</i> on BMI analyses and marginal effects <i>P</i>_m or heterogeneity of variance from Levene's test <i>P</i>_<i>v</i>.

<p>Spearman correlations between <i>P</i>_<i>int</i> in <i>SNP × Physical Activity</i> and <i>SNP × Smoking</i> on BMI analyses and marginal effects <i>P</i>_m or heterogeneity of variance from Levene's test <i>P</i>_<i>v</i>.</p

Data flow-chart.

<p>Three sources of genome-wide results were used: i) meta-analysis of Levene’s test results for between-genotype heterogeneity of phenotypic variances; ii) published results for marginal effects genome-wide association studies undertaken by the GIANT and GLGC consortia; iii) published results for SNP <b>×</b> physical activity and SNP <b>×</b> smoking in BMI (from the GIANT consortium).</p

Comparison of Levene's test <i>P</i>_v ranks from different centiles of the <i>P</i>_m rank-ordered distribution for the index traits.

<p>Comparison of Levene's test <i>P</i>_v ranks from different centiles of the <i>P</i>_m rank-ordered distribution for the index traits.</p

Enrichment of SNPs with nominally significant <i>P</i>_int for test of <i>SNP × Smoking</i> and <i>SNP × Physical Activity</i> interaction for BMI (<i>P</i>_int<0.05) by SNPs with nominally significant Levene's test (<i>P</i>_<i>v</i><0.05).

<p>Enrichment of SNPs with nominally significant <i>P</i>_int for test of <i>SNP × Smoking</i> and <i>SNP × Physical Activity</i> interaction for BMI (<i>P</i>_int<0.05) by SNPs with nominally significant Levene's test (<i>P</i>_<i>v</i><0.05).</p