Founder analysis results on JT lineages.

<p>Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using <i>f1</i> (blue line) and <i>f2</i> criteria (red line), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (A) whole-mtDNA genomes or (C) HVS-I for haplogroups J and T; and probabilistic proportion of founder clusters considering different migration events, using <i>f1</i> (blue bar) and <i>f2</i> criteria (red bar), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (B) whole-mtDNA genomes or (D) HVS-I for haplogroups J and T.</p

Founder analysis results.

<p>Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using <i>f1</i> (blue line) and <i>f2</i> criteria (red line), when considering putative migrations: (A) from the Near East, Iran and Pakistan to Arabia; (C) from Africa into Arabia plus the Near East and Iran; (E) Arabia plus the Near East and Iran into eastern Africa; (G) Arabia plus the Near East and Iran into North Africa; and probabilistic proportion of founder clusters considering different migration events, using <i>f1</i> (blue bar) and <i>f2</i> criteria (red bar), when considering putative migrations: (B) from the Near East, Iran and Pakistan to Arabia; (D) from African into Arabia plus the Near East and Iran; (F) Arabia plus the Near East and Iran into eastern Africa; (H) Arabia plus the Near East and Iran into North Africa.</p

Matrices of <i>F</i>_<i>ST</i> distances.

<p>Matrices of <i>F</i>_<i>ST</i> values between ADMIXTURE components (A) and Arabian and Near Eastern populations (B).</p

ADMIXTURE results.

<p>Population structure inferred by ADMIXTURE analysis. Each individual is represented by a vertical (100%) stacked column of genetic components proportions shown in colour for K = 6.</p

Estimates of admixture proportions (%) and date of admixture (in generations) calculated in ROLLOFF when using western (Yoruba) and eastern (Maasai) African and Italians + Spanish as ancestral populations.

<p>N/A—not assigned.</p><p>* By eliminating one individual with a high level of African ancestry.</p><p>Estimates of admixture proportions (%) and date of admixture (in generations) calculated in ROLLOFF when using western (Yoruba) and eastern (Maasai) African and Italians + Spanish as ancestral populations.</p

PCA results.

<p>Scatter plot of individuals, showing the first two principal components. Each symbol corresponds to one individual and the colour indicates the region of origin.</p

The relevant region on chromosome 3 containing the <i>OSBPL10</i> gene

<p><b>(A)</b> Manhattan plot for the association analysis in the 54 fine-matched population structure corrected Cuban pairs of asymptomatic/control versus DHF subjects. <b>(B)</b> The region on chromosome 3, with the haplotype defined by the six significantly associated SNPs indicated by the red box. Genes on the forward sense are indicated in blue; genes on the reverse sense are indicated in light brown. <b>(C)</b> Worldwide frequency of the African (blue), European (red) and other (grey) <i>OSBPL10</i> haplotypes for populations of the 1000 Genomes project, and also for asymptomatic/control and DHF in Cuba. <b>(D)</b> mRNA expression for homozygous genotypes for African and European <i>OSBPL10</i> haplotypes in the 1000 Genomes project transcriptome information.</p

Gene expression for <i>RXRA</i> and <i>OSBPL10</i> in Cuban dengue patients along the course of disease

<p>Data is shown for all Cuban patients, Cuban patients with warning signs, and the Thai transcriptome dataset for whole blood. [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006220#ppat.1006220.ref022" target="_blank">22</a>]</p

Odds ratios of the African <i>OSBPL10</i> haplotype and <i>RXRA</i> alleles in DHF when compared with asymptomatic/control and tests (identified by Y) where statistical significant evidence was detected for each gene.

<p>Odds ratios of the African <i>OSBPL10</i> haplotype and <i>RXRA</i> alleles in DHF when compared with asymptomatic/control and tests (identified by Y) where statistical significant evidence was detected for each gene.</p

Functional assay of <i>OSBPL10</i> knockdown and its effect on DENV-replication

<p><b>(A)</b> Box plots for the <i>OSBPL10</i> mRNA expression in the various THP1 cells (non-transfected and transfected with mock, sh1 and sh2 plasmids). The boxes represent the interquartile range, the little square the mean, the line the median and the whiskers are the 5% and 95% quartiles. The *** symbol indicates that the two-tailed t-test p-values for comparisons between THP1sh1/OSBPL10 and THP1/non-transfected or THP1/mock, as well as for THP1sh2/OSBPL10 and THP1/non-transfected or THP1/mock are significant. <b>(B)</b> Viral load (log10 of PFU/mL), measured intracellularly and extracellularly, in the various THP1 cells (non-transfected and transfected with mock, sh1 and sh2 plasmids) when infected by DENV2. The *** symbol indicates that the two-tailed t-test p-values for pairwise comparisons (THP1sh1/OSBPL10 vs. THP1/non-transfected or THP1/mock, THP1sh2/OSBPL10 vs. THP1/non-transfected or THP1/mock) are significant.</p