Summary of subjects, methods and analyses.

<p>a. Number of SNP pairs for which interaction testing was performed - may not equal the number of possible pair-wise tests [n*(n−1)/2] because some pairs were captured in previous Analyses (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041730#pone.0041730.s001" target="_blank">File S1</a> Supporting <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041730#pone-0041730-g002" target="_blank">Figure 2</a>), and some tests were not feasible due to low allele frequencies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041730#pone.0041730.s001" target="_blank">File S1</a> Section 3.3). b. Significance threshold computed using permutations under the null hypothesis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041730#pone.0041730.s001" target="_blank">File S1</a> Section 3.4) c. SNP pairs with p-value for interaction within 3 orders of magnitude of the significance threshold for each Analysis were brought forward for validation in the WTCCC sample; the numbers of SNP pairs for which data were available in the WTCCC study are shown. <i>LDL</i>, concentration of LDL cholesterol; <i>HDL</i>, concentration of HDL cholesterol; <i>TG</i>, triglyceride concentration; <i>BP</i>, blood pressure; <i>CH</i>, carbohydrate metabolism (loci associated with risk of Type II diabetes and related phenotypes, such as fasting glucose concentration); <i>SMK</i>, smoking; <i>OB</i>, obesity; <i>small LDL</i>, concentration of small atherogenic LDL particles; <i>Lp(a)</i>, plasma levels of lipoprotein(a); <i>CHD</i>, risk of coronary heart disease; <i>MI</i>, risk of myocardial infarction.</p

Results of gene-gene interaction search among CVRF SNPs (Analysis 1).

<p><i>Panel A</i>. Plot of the top result (arrow) from Analysis 1 against the distribution of the top results from 10,000 permutations under the null hypothesis (dotted line). The permuted top results are expected to follow a beta-distribution (solid line, parameters obtained from permuted top results), the 95^th percentile of which was taken as the significance level required to obtain a Type II error of 0.05 (arrow). <i>Inset</i>: While the significance level computed in Analysis 1 (dashed black line) was estimated using 10,000 null permutations, this estimate was found to stabilize rapidly with increasing number of permutations (black points) and to change little after 100–200 permutations. Consequently, we progressively reduced the number of permutations used to estimate the significance level in subsequent Analyses. <i>Panel B</i>. Quantile-quantile plot showing rank-ordered observed results (black points) from 29,161 tests in Analysis 1 (<i>y-axis</i>) against expected results (<i>x-axis</i>) estimated from 10,000 permutations under the null hypothesis (randomized phenotype). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041730#pone.0041730.s001" target="_blank">File S1</a> Section 3.5 for computation methods. The shaded area corresponds to the 95%CI of the permuted expected results. The 95%CI of a normal distribution is indicated by the dotted lines. <i>Panel C</i>. Estimation of the interaction effect sizes this analysis has 80% power to detect across a range of MAF under an additive × additive interaction model. The heights of the vertical bars correspond to the effect size (OR) detectable for a typical pair of SNPs whose MAFs are as indicated on the horizontal axes.</p