Contingency table for American subpopulations, rows correspond to detected communities, columns to actual subpopulations.

<p>PUR—Puerto Rican, CLM—Colombian, MXL–Mexican</p><p>Contingency table for American subpopulations, rows correspond to detected communities, columns to actual subpopulations.</p

Average proportions of significant SNPs in the simulation study.

<p>The values in the table represent the proportions of SNPs (averaged over 10 replications) found to be significant. The significance level was set to 0.0001. The results are present for 4 scenarios, which are described in the section: "Evaluation via simulated association studies ".</p><p>* For these methods in the scenario with 3 underlying discrete subpopulations we took 2 principal components and 2 ancestry estimates, as recommended by the authors.</p><p>Average proportions of significant SNPs in the simulation study.</p

3 American subpopulations.

<p>The polygons around the nodes represent the detected communities. The node colors represent the actual labels.</p

3 African subpopulations.

<p>The polygons around the nodes represent the detected communities. The node colors represent the actual labels.</p

5 European subpopulations.

<p>The polygons around the nodes represent the detected communities. The node colors represent the actual labels.</p

Description of datasets, used in the analysis.

<p>Description of datasets, used in the analysis.</p

A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data

Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical power Results: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content. Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.</p

Power curves for RITSS1, RITSS2, GESAT, and GAMsv over increasing signal density <i>p</i>_<i>XE</i>.

Significance level α = 0.005, μXE = 0.05, and results based on 1,000 replicates. Power was simulated for pXE = 0.05, 0.1, 0.2, 0.3, 0.4, 0.5.</p

Power curves for RITSS1, RITSS2, GESAT, and GAMsv over increasing signal density <i>p</i>_<i>XE</i>.

Significance level α = 0.005, μXE = 0.1, and results based on 1,000 replicates. Power was simulated for pXE = 0.05, 0.1, 0.2, 0.3, 0.4, 0.5.</p

Analysis configurations and number of genetic variants incorporated.

Analysis configurations and number of genetic variants incorporated.</p