Additional file 6: Figure S3. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Plot of the number of alleles (distinct NAT2 sequence haplotypes) observed in samples as a function of sample size. The dashed line shows the linear regression of number of haplotypes on sample size, and Pearson’s product–moment correlation coefficient is shown in the bottom-right caption. (PDF 2 kb

Additional file 11: Figure S8. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

MDS plot of pairwise Reynolds genetic distances between the 29 populations of the FP dataset. The Stress value is 0.045. The same plot is reproduced 4 times, with populations color-coded according to: (a) geographical region, (b) linguistic affiliation, (c) subsistence mode, and (d) biome (see text). (PDF 11 kb

Results of the inter-regional <i>F_ST</i>, intra-regional <i>F_ST</i>, XP-EHH and iHS tests in the seven geographic regions.

a<p>Derived allele frequency estimated at the global level.</p>b<p><i>F_ST</i> estimated at the inter-regional level, <i>i.e.</i> between a given geographic region and the remaining ones.</p>c<p><i>P</i>-values are derived from the genome-wide empirical distribution of <i>F_ST</i> values.</p>d<p><i>F_ST</i> estimated at the intra-regional level, <i>i.e.</i> among populations within a region.</p>e<p><i>P</i>-values are derived from the empirical distribution of the iHS and XP-EHH scores along the chromosome 16.</p>*<p><i>p</i><0.05; ** <i>p</i><0.01; *** <i>p</i><0.005.</p><p>NA: Not Applicable (for iHS: when a gap>200 kb between successive SNPs is found in the region in the region delimited by the SNPs where the EHH value drops below 0.05 around the core SNP).</p

Detailed analysis of a 1.1 Mb genomic region surrounding the <i>VKORC1</i> gene locus in East Asia.

<p>The boundaries of the region displayed (chr16:30,271,572-31,391,123; UCSC human genome build hg18) were chosen so as to include the three clusters of significant scores detected in East Asia by the selection tests in the 2 Mb region centered on <i>VKORC1</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053049#pone-0053049-g003" target="_blank">Figure 3</a>). (<b>A</b>) <b>Name and location of genes.</b> Exons are displayed as blue boxes and the transcribed strand is indicated with an arrow. Genes located in the block of strong LD encompassing <i>VKORC1</i> and including the SNPs in the red box shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053049#pone-0053049-g004" target="_blank">Figure 4C</a>, are highlighted in the grey area. (<b>B</b>) <b>XP-EHH results in East Asia.</b> The significance of the XP-EHH scores (−log₁₀ empirical <i>p</i>-value) are shown for individual SNPs with a MAF ≥0.01 in East Asia. Horizontal dashed lines indicate 0.05 and 0.01 chromosome-wide significance levels. Recombination hotspots detected in HapMap Phase II data are indicated by red vertical dotted lines. The data and methods used to derive these hotspots are available from the HapMap website (<a href="http://www.hapmap.org/" target="_blank">http://www.hapmap.org/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053049#pone.0053049-McVean1" target="_blank">[83]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053049#pone.0053049-Winckler1" target="_blank">[84]</a>. (<b>C</b>) <b>LD plot.</b> Pairwise LD values, depicted as <i>D</i>’, are shown for SNPs with a MAF ≥0.01 in East Asia. <i>D</i>’ values are displayed in different colors from yellow to red for <i>D</i>’ = 0 to <i>D</i>’ = 1, respectively. The red box highlights SNPs included in the LD block encompassing <i>VKORC1.</i> The plot was produced using the snp.plotter R package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053049#pone.0053049-Luna1" target="_blank">[74]</a>.</p

Atypical patterns of genetic differentiation observed for <i>VKORC1</i> SNPs.

<p>Genome-wide empirical distributions of <i>F_ST</i> values were constructed from 644,143 SNPs having a MAF ≥0.001 at the global level. Individual values of <i>F_ST</i> calculated for each of the seven <i>VKORC1</i> SNPs are plotted against their global MAF. The functional rs9923231 SNP is shown in red. The 50^th, 95^th and 99^th percentiles are indicated as dotted, dashed and full red lines, respectively.</p

Additional file 4: Table S1. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

NAT2 coding-exon SNPs and haplotypes observed in all sequenced African population samples. (XLSX 32 kb

Distribution of –log₁₀ (<i>p-</i>values) for four selection tests across a 2 Mb region centered on <i>VKORC1</i>.

<p>A black vertical line indicates the physical position of <i>VKORC1</i> on chromosome 16. Horizontal red dotted and dashed lines show 0.05 and 0.01 chromosome-wide significance levels, respectively. The selection tests (inter-regional <i>F_ST</i>, XP-CLR, XP-EHH and iHS, respectively) were separately applied in each of the seven geographic regions.</p

Additional file 3: Figure S2. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Schematic diagram of the NAT2 870 bp-long single protein-coding Exon (Exon 2) on 8p22. The first (+1) and last positions (+873) of the ORF are indicated on top of it. The positions of the 30 polymorphic sites (SNPs) observed among the 1192 individuals from the 39 African samples analyzed in this study are shown as heavy-black (non-synonymous mutations) or light-gray (synonymous mutations) vertical bars below the diagram. Segments link the SNPs positions to the list of 61 haplotypes inferred from the combination of the 30 SNPs. Haplotypes’ associated acetylation activity (taken from the official NAT2 gene nomenclature, http://nat.mbg.duth.gr/ ) and average frequency among the 39 population samples are shown on the left and right sides of the list, respectively. (PDF 21 kb

Additional file 1: Figure S1. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Map showing the location of African populations screened for sequence variation in NAT2, including the six Sahelian populations of this study. The ASW sample of African Americans from the 1000 Genomes Project is not located on this map. Map created with the QGis open source software [98]. (PDF 2240 kb

Identification of a Major Dimorphic Region in the Functionally Critical N-Terminal ID1 Domain of VAR2CSA

<div><p>The VAR2CSA protein of <i>Plasmodium falciparum</i> is transported to and expressed on the infected erythrocyte surface where it plays a key role in placental malaria (PM). It is the current leading candidate for a vaccine to prevent PM. However, the antigenic polymorphism integral to VAR2CSA poses a challenge for vaccine development. Based on detailed analysis of polymorphisms in the sequence of its ligand-binding N-terminal region, currently the main focus for vaccine development, we assessed <i>var2csa</i> from parasite isolates infecting pregnant women. The results reveal for the first time the presence of a major dimorphic region in the functionally critical N-terminal ID1 domain. Parasite isolates expressing VAR2CSA with particular motifs present within this domain are associated with gravidity- and parasite density-related effects. These observations are of particular interest in guiding efforts with respect to optimization of the VAR2CSA-based vaccines currently under development.</p></div