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

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

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

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

Meta-analysis results for SNPs associated with normal pressure glaucoma (NPG) (IOP <22 mmHg) located in the CDKN2BAS region on chromosome 9p21.

<p>The most significant SNP (rs2157719, p = 1.17×10⁻¹²) is indicated with a solid diamond.</p

Glaucoma association results for SNPs in gene regions associated with quantitative optic nerve parameters optic nerve area and cup-to-disc ratio (CDR).

*<p>The SNP in the gene region with the best evidence of association, either in the overall meta-analysis or in the HPG or NPG subgroups was selected for inclusion in this table. The effect allele is listed after the SNP number. Complete results are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002654#pgen.1002654.s015" target="_blank">Table S4</a>. Abbreviations: POAG (primary open angle glaucoma); HPG (high-pressure glaucoma); NPG (normal-pressure glaucoma); OR (odds ratio).</p

Genome-wide association results with normal pressure glaucoma (NPG) (IOP <22 mm Hg) in the GLAUGEN-NEIGHBOR meta-analysis (720 cases and 3487 controls).

<p>The red line identifies a p-value of 5×10⁻⁸. Covariates include: (NEIGHBOR) age, gender, study site and eigenvectors 1 and 2; (GLAUGEN) age, gender, study site, DNA extraction method, DNA specimen type and eigenvectors 1, 2 and 6.</p

Association results for genome-wide significant SNPs for the Normal Pressure Glaucoma (NPG) analyses.

<p><b>Chr = </b>chromosome; <b>MAF = </b>minor allele frequency; <b>OR = </b>odds ratio; <b>CI = </b>confidence interval.</p