Individual ancestry proportion estimation assuming 4 (K = 4) ancestral populations (color-coded).

<p>X-axis shows individuals and y-axis shows ancestry proportions. A) 4 related Hapmap populations: CEU, CHB, ASW, and MEX; B) Chagas cohorts stratified by self-reported races.</p

Genomic positions that associated to traits (unadjusted P-value <10⁻⁶, intergenic positions not shown).

<p>Genomic positions that associated to traits (unadjusted P-value <10⁻⁶, intergenic positions not shown).</p

Population stratification of Brazilian Chagas cohort along with Hapmap populations.

<p>Each point on the plot represents an individual; each population is coded in a different color. The populations are: ASW: African ancestry in Southwest USA; CEU: Utah residents with Northern and Western European ancestry from the CEPH collection; CHB: Han Chinese in Beijing, China; CHD: Chinese in Metropolitan Denver, Colorado; GIH: Gujarati Indians in Houston, Texas; JPT: Japanese in Tokyo, Japan; LWK: Luhya in Webuye, Kenya; MEX: Mexican ancestry in Los Angeles, California; MKK: Maasai in Kinyawa, Kenya; TSI: Toscans in Italy; YRI: Yoruba in Ibadan, Nigeria.A) Dimension 1 vs. Dimension 2; B) Dimension 2 vs Dimension 3.</p

−log <i>P</i> -plots of the improved and novel T2D signals around index SNPs: rs10923931, rs10965250 and rs1111875 found by fine-mapping analysis.

<p>−Log <i>P</i>-value for risk-associated allele from the logistic regression model adjusted for age, sex, dialect and global ancestry (the first 10 principal components). Pairwise correlations (r²) in the 1000 Genomes Asian population are shown in relation to markers identified through fine-mapping in our sample. Squares denote genotyped SNPs; circles, imputed SNPs. Gray squares and circles denote that r² cannot be estimated (not in 1000 Genomes). Red arrows and diamond denote the index SNP. Blue arrows denote the novel signal. The plots were generated using LocusZoom <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087762#pone.0087762-Pruim1" target="_blank">[86]</a>.</p

Characteristics of subjects comparing T2D cases and controls.

*<p>Variables are presented as mean (standard deviation). Two-sample independent t-test is used to test the mean differences between cases and controls.</p>†<p>Variables are not normally distributed and are presented as median (25^th, 75^th percentiles). Wilcoxon rank-sum test is used to compare the median differences between cases and controls.</p>‡<p>Categorical variables are presented as frequencies (%).χ² test is used to test whether the distribution between cases and controls is different.</p>§<p>Variables have 59 cases and 55 controls missing.</p

Summary risk scores in association with T2D.

<p>Summary risk scores in association with T2D.</p

Differential gene expression in blood from TB patients and controls determined by microarrays.

<p>Heat map of 875 transcripts which were statistically different in one condition from the other condition, using ANOVA and were hierarchically clustered. active = patients with active disease, treatment = patients after 8 weeks of treatment, recovered = patients after 28 weeks of treatment and controls = healthy controls. Red represents an increase in gene expression and green represents a decrease in gene expression.</p

Validation by qRT-PCR of 26 genes differentially expressed in all three models based on microarray analyses.

<p>For successful validation, the direction for the fold-change in gene expression using qRT-PCR should be consistent with the microarray findings.</p>a<p>in longitudinal cohort of TB patients.</p

QQ-plot of 55 T2D SNPs reported by GWAS-catalog.

<p>Observed distribution of −log <i>P</i>-values were compared to the expected (null) distribution.</p

Comparison of differential gene expression between patients with active TB and mice infected <i>M.tb in vivo</i> model.

<p>Venn diagram representing the 875 significantly differentially expressed in TB patients and 1674 transcripts significantly differentially expressed in TB actively infected mice. A total of 121 transcripts were found to be in common between these two systems. Red – transcripts for TB patient only; Green – Common between TB patients and mice infected with TB; Blue – transcripts for mice infected with TB only.</p