Additional file 1: Figure S1. of Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

Long distance LD pr. Mb separated by the chromosome for each population LD for each SNP pair with a distance between 10 kb and 1 Mb taken into account. Figure S2. Accuracy and yield of imputation between each location of SNPs. Figure S3. Comparing minor allele frequencies of SNPs between imputed and actual genotypes before quality control of imputed results separately plot by each SNP location. Figure S4. Comparing allele frequencies of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted by each SNP location. Figure S5. Proportion of SNPs with lower AF after imputation vs initial AF. Figure S6. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes before quality control of imputed results separately plotted by each SNP location. Figure S7. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted according to each SNP location. Figure S8. Average linkage disequilibrium as r-squared for each region. SNPs were assigned to gene locations. Figure S9. LD, measured as r2, plotted against physical distance. (PDF 1286 kb

Additional file 2: Table S1. of Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

Summary of SNPs used in study of SNP annotation to imputation outcome. (XLS 26 kb

Worldwide (from the 1000 Genomes database) and Thai dengue cohorts (control, DF and DSS) frequencies for significantly associated haplotypes in the various genes.

<p>A- <i>PLCB4</i>; B- <i>PLCE1</i>; C- <i>MICB</i>; D- <i>CHST10</i>; E- <i>AHRR</i>; F- <i>GRIP1</i>; G- <i>PPP2R5E</i>. The protective and causative haplotypes are highlighted.</p

Global ancestry inferred through RFMix when using three parental ancestries (South, Northeast and Southeast Asian) for the global dataset.

<p>Each vertical line represents an individual, and the three colours represent the proportion of the three parental populations in each genome (light orange for South Asian, dark orange for Southeast Asian and blue for Northeast Asian).</p

Confocal imaging of PPP2R5E and NS5 from DENV1 and DENV2.

<p>A. The main link motifs in NS5 proteins from DENV1 and DENV2. B. Subcellular localization of PPP2R5E in Huh7 control cells. C. Subcellular localization of PPP2R5E in Huh7 control and after 24h, 48h and 72h of transfection with DENV2-NS5 protein. D. Subcellular localization of mutated PPP2R5E in Huh7 control and after 24h, 48h and 72h of transfection with DENV2-NS5 protein. E. Subcellular localization of PPP2R5E in Huh7 control and after 24h, 48h and 72h of transfection with DENV1-NS5 protein. Green immunofluorescence indicates PPP2R5E, red indicates NS5, blue flags nucleus. Yellow signals indicate co-localization of NS5 and PPP2R5E, and was obtained by overlapping the two panels. Original magnification, ×630.</p