Additional file 1: of Analysis of circulating angiopoietin-like protein 3 and genetic variants in lipid metabolism and liver health: the DiOGenes study

Figure S1. QQ plot of the relationship between expected and observed distribution at baseline. Quantile-quantile plot of baseline data. The relationship between observed (y-axis) and expected (x-axis) distribution. The statistical significance is measured by the negative log of the corresponding p-value for each SNP. (JPEG 92 kb

Additional file 3: of Analysis of circulating angiopoietin-like protein 3 and genetic variants in lipid metabolism and liver health: the DiOGenes study

Table S1. Effect of rs4360730 on BMI, Lipid Profile and Liver Markers. Table S2 Effect of rs9994520 on BMI, Lipid Profile and Liver Markers. (DOCX 21 kb

Additional file 2: of Analysis of circulating angiopoietin-like protein 3 and genetic variants in lipid metabolism and liver health: the DiOGenes study

Figure S2. QQ plot of the relationship between expected and observed distribution during weight loss period. Quantile-quantile plot for the analysis of the weight loss period. The relationship between observed (y-axis) and expected (x-axis) distribution. The statistical significance is measured by the negative log of the corresponding p-value for each SNP. (JPEG 94 kb

PCA after SNPClust application.

<p>First principal components of the PCA on the 261 SNPs and 331 haplotypes from 5,433 patients, with 95% confidence ellipses. The principal components did not discriminate SLE patients from controls.</p

Performances of feature selection methods.

<p>Associations of the input dataset without or with population stratification correction by genomic control and Eigenstrat (with 5 and 10 principal components considered) compared with SNPClust.</p

Selection of strong SNP contributors.

<p><b>(a)</b> The 2,000 most contributing SNPs to each of the first 8 principal components are displayed by chromosomal position and colored by chromosomes. Principal components were driven by large localized SNP groups and the chromosome 6 locus <i>HLA</i> was the strongest and largest contributor in all of the first 8 principal components, except principal component 5. <b>(b)</b> Selection of SNPs by the Gaussian mixtures based method. Selected SNPs are colored in red. SNPs are displayed on the x-axis by rank of chromosomic position, <i>i.e.</i> SNPs are regularly spaced and ordered by chromosome and position.</p

Haplotype summarization of the <i>8p23</i> locus.

<p>The haplotypes estimated from the 875 selected SNPs from chromosome 8 were best fitted by two groups. The resulting three groups, plotted with 95% confidence ellipses, accurately represented the three clusters in principal component 3 and showed that haplotypes preserved information carried by SNPs.</p

Initial grouping of genetic data.

<p>Two first principal components of the PCA on 379,190 SNPs from 5,433 European SLE patients and controls with 95% confidence ellipses. Northern and Southern Europeans were discriminated in the first principal component. Eastern and Western Europeans were discriminated in the second. 2,733 individuals (50%) did not have geographic information and were colored in gray.</p