Phylogenetic analysis of the E gene haplotype and consensus sequences of DENV-1.

<p>Consensus sequences for each strain have been highlighted. Bootstrap values (100 replications) for key nodes are shown. A distance bar is shown below the tree. Lineage A became extinct in 1998 about the same time lineages B and C appeared. No examples of lineage B have been recovered since 2002, but lineage C still circulated in 2008. Lineage D, first detected in 2006, also still circulated in 2008. For the purposes of analysis, lineages A and B are considered to have become extinct in 1998 and 2002, respectively. Lineages C and D were deemed to be still circulating in 2008.</p

Detecting variants, stop codons and deletions using two different sequence analysis platforms.

<p>^a The number of bases that are different from the reference genome.</p><p>^<i>b</i> Genetic diversity of recombinant DENV-1 strain showing in italic.</p><p>Detecting variants, stop codons and deletions using two different sequence analysis platforms.</p

Phylogenetic analyses of nt 1–1087 and nt 1088–1485 of the consensus sequences of the E genes of DENV-1 from lineages B and C and of the sequences of the same regions of the E genes of M47317 haplotypes.

<p>Bootstrap values (100 replicates) for key nodes are shown.</p

Discordance (%) between imputed genotypes and actually observed minor allele genotypes¹ at rare and low-frequency SNPs on the exome chip but not in the Omni2.5.

1<p>A minor allele genotype is defined as a genotype that carries at least one copy of the minor allele, and discordance here is measured against the total number of observed minor allele genotypes at rare and low-frequency SNPs.</p>2<p>Phase 1 of the 1KGP, consisting of 1,092 subjects.</p>3<p>Singapore Sequencing Malay Project, consisting of 96 Southeast Asian Malays that have been whole-genome sequenced at 30X.</p>4<p>Singapore Sequencing Indian Project, consisting of 36 South Asian Indians that have been whole-genome sequenced at 30X.</p><p>Discordance (%) between imputed genotypes and actually observed minor allele genotypes^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#nt104" target="_blank">1</a>} at rare and low-frequency SNPs on the exome chip but not in the Omni2.5.</p

Strains of DENV-1 used.

<p>I.C: Infectious clone</p><p>^a: The European Nucleotide Archive</p><p>Strains of DENV-1 used.</p

The percentage of polymorphic exome chip SNPs in each of the three populations that can be reliably imputed against three different reference panels using the SNPs on the Illumina HumanOmni2.5 as input.

<p>Each of these SNPs is categorized according to the minor allele frequency (MAF) as rare (0%< MAF ≤1%), low-frequency (1%< MAF ≤5%) and common (MAF >5%). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#pone.0106681.s001" target="_blank">Figures S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#pone.0106681.s002" target="_blank">S2</a> in the Supplementary Material for the equivalent figures when SNPs on the HumanHap550 and Human1M are used as input respectively. The total number of imputed exome SNPs when using Illumina HumanOmni2.5/HumanHap550/Human1M as the study panel is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#pone.0106681.s006" target="_blank">Table S4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#pone.0106681.s007" target="_blank">S5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106681#pone.0106681.s008" target="_blank">S6</a>.</p

Evaluating the Coverage and Potential of Imputing the Exome Microarray with Next-Generation Imputation Using the 1000 Genomes Project - Figure 1

<p>(A) The proportion of monomorphic and polymorphic exonic variants in the Illumina exome chip when assessed in each of the three Singapore populations. The exonic variants on the exome chip are further categorized according to whether they are present in any of the reference panels from the 1000 Genomes Project or the Singapore Sequencing Study for the Malays and Indians (“Covered”) and can in theory be imputed, or not present in any of the existing reference panels and thus cannot be recovered through imputation (“Not covered”). (B) Distribution of SNPs on the exome chip according to the minor allele frequencies (MAFs) into monomorphic (MAF  = 0%), rare (0%< MAF ≤1%), low-frequency (1%< MAF ≤5%) and common (MAF >5%) in each of the three populations. (C) MAF categorization of the polymorphic exome chip SNPs in each of the three populations according to whether these SNPs are present (non-purple bars) or not (purple bars) in the respective reference panels. Numbers in brackets indicate the number of SNPs in the respective categories.</p

Discordance (%) between imputed genotypes and actually observed genotypes at SNPs on Omni2.5 but not in the exome chip.

1<p>Phase 1 of the 1KGP, consisting of 1,092 subjects.</p>2<p>Singapore Sequencing Malay Project, consisting of 96 Southeast Asian Malays that have been whole-genome sequenced at 30X.</p>3<p>Singapore Sequencing Indian Project, consisting of 36 South Asian Indians that have been whole-genome sequenced at 30X.</p><p>Discordance (%) between imputed genotypes and actually observed genotypes at SNPs on Omni2.5 but not in the exome chip.</p

Genotypes of drug resistant <i>M</i>. <i>tuberculosis</i> based on spoligotpying and 24 loci MIRU-VNTR.

<p>Genotypes of drug resistant <i>M</i>. <i>tuberculosis</i> based on spoligotpying and 24 loci MIRU-VNTR.</p

Venn diagram comparing the number of SNPs shared by serially isolated <i>M</i>. <i>tuberculosis</i> isolates.

<p>Venn diagram comparing the number of SNPs shared by serially isolated <i>M</i>. <i>tuberculosis</i> isolates.</p