Participants by institution and genotyping center in combined gold/silver standard association study.

<p>Abbreviations: MF, Marshfield Clinic Personalized Medicine Research Project; VU, Vanderbilt University BioVU; GH, Group Health/University of Washington Adult Changes in Thought and Alzheimer's Disease Patient Registry; MAYO, Mayo Clinic biobank; CIDR, Center for Inherited Disease Research.</p

Error in asymptotic model.

<p>Percentage error in asymptotic model plotted against non-centrality, λ(ω), for various ω in Ω. Grey bands give approximate 90% bounds on percentage error, such that 90% of realizations in any λ-interval lie inside the region enclosed by the error bands.</p

Empirical power and asymptotic power.

<p>Comparison of empirical power (E) to asymptotic (A) for various <i>γ_ca</i> and <i>R</i> = 1 (solid line), <i>R</i> = 2 (dashed), <i>R</i> = 4 (dotted) at two loci that nominally replicate in the gold standard subset. Power is shown as 20^th percentile of X² statistics over 1000 bootstrapped replicates for empirical graphs or as 20^th percentile of the chi squared distribution for asymptotic graphs, with non-centrality determined from genotypic disease model given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063481#pone-0063481-t002" target="_blank">table 2</a>.</p

Concordance between power in logistic regression and slope of power curve given by equation 6.

<p>Proportion of scenarios in which observed change in power agreed with predicted slope of chi-square power. The observed change in power is calculated as the sign of the difference of the median likelihood ratio statistic at γca  = 0 and at γca  = 1. 160 parameter values were considered, a subset of the parameter space described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063481#pone-0063481-t001" target="_blank">table 1</a>. 500 realizations at γca  = 0 and at γca  = 1 of each combination were undertaken to find the median likelihood ratio statistics.</p

The parameter space Ω considered in simulation of power.

†<p>denotes null model with no genetic risk.</p

A subset with increasing power.

<p>Values of φ (y axis, between. 4 and 1) and <i>R</i> (x axis, values between 1 and 4) for which power is decreasing (dark) and increasing (light). Each panel shows a combination of prevalence, <i>k</i> by row (.05, .3) and homozygous relative risk RR_AA by column, range 2–7. Prevalences <.05 are not shown here because of similarity to the panels for <i>k</i>  = .05.</p

Regional association plot for the chromosome 18:6,420,000–6,520,000 region and the hippocampal sclerosis (any vs. none) analysis.

<p>The purple dot indicates the most associated SNP in the region. The x-axis is basepair position and y-axis is the −log(p-value), base 10.</p

Clinico-pathologic analysis of IGAP loci.

<p>*Lambert et al., 2013 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004606#pgen.1004606-Lambert1" target="_blank">[11]</a>.</p><p>IGAP: International Genomics of Alzheimer's Project.</p><p>Bolded OR indicates an OR more extreme than that reported by the IGAP paper <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004606#pgen.1004606-Lambert1" target="_blank">[11]</a>.</p><p>Bolded p-value indicates a p-value significant at the alpha = 0.05 level, uncorrected.</p><p>Clinico-pathologic analysis of IGAP loci.</p

Regional association plot for <i>GALNT7</i> and the neuritic plaque (any vs. none) analysis.

<p>The purple dot indicates the most associated SNP in the region. The x-axis is basepair position, and y-axis is the −log(p-value), base 10.</p