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

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

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

Association of the <i>PLB1</i> locus in RA GWAS meta-analysis.

<p>(A) Coding regions of <i>PLB1</i> and p.G755R mutation identified in the consanguineous RA pedigree. <i>PLB1</i> consists of 58 exons (NM_153021), and p.G755R (c.2263G>C) mutation was located at exon 33 (the black triangle). (B) Regional association of <i>PLB1</i> in RA GWAS meta-analysis including 8,875 RA cases and 29,367 controls from the European populations. Upper panel showed the results of nominal association, and the lower panel showed the results of conditional analysis with rs116018341, the top SNP in the nominal associations. The red diamond-shaped dots represent P-values of the SNPs in the GWAS meta-analysis, and the intensity of the red color in the dots represents the <i>r²</i> value with the most significantly associated SNP. Stepwise logistic regression analysis demonstrated multiple independent signals driven by non-coding variants. (C) H3K4me3 peak of T_reg primary cells in the <i>PLB1</i> locus. Non-coding RA risk SNP of rs116018341 overlapped with one of the H3K4me3 peaks as the SNP located in the most vicinity of the peak summit (a vertical dashed red line).</p

Results of rare variant tests for <i>PLB1</i> coding variants in the European RA case-control cohort.

a<p>Low-frequency rare coding variant (MAF≤0.01) obtained from deep sequencing of 1,088 RA cases and 1,088 controls were selected.</p><p>RA; rheumatoid arthritis, ACPA; anti-citrullinated protein antibodies.</p><p>BURDEN; burden test, VT; variable threshold test, FRQWGT; frequency-weighted test, CALPHA; C-alpha test, SKAT; sequence kernel association test.</p