Haplotype Transmission Disequilibrium Test (TDT) of association with severe malaria in Gambian, Kenyan and Malawian child-parental trios.

<p>The table shows the common haplotypes (frequency higher than 5%) within each LD block identified in the gene, their frequency and the results of family-based test of association with severe malaria in the three populations of affected child-parental trios. Freq: frequency of the haplotype in trio parents. These are not unbiased estimates of the population frequencies. OR: Odds Ratio comparing the risk of the untransmitted versus the transmitted haplotype. All other abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004206#pone-0004206-t002" target="_blank">Table 2</a>.</p

Minor allele frequency of <i>HBB</i> and <i>IRF1</i> Single Nucleotide Polymorphisms (SNPs) in trio parents from The Gambia, Kenya and Malawi.

<p>The table shows the SNPs that have been genotyped in the affected child parental trio studies and their frequency in trio parents from The Gambia, Kenya and Malawi. These are not unbiased estimates of the population frequencies. Chr coord is the SNP chromosome coordinate (chromosome: base pair) based on Ensemble release 40. Location: location of the SNP with respect to the <i>HBB</i> or <i>IRF1</i> locus. Alleles: minor and major alleles (major allele is shown in brackets). MAF: Minor Allele Frequency in pedigree parents (The Gambia, N = 1100; Kenya, N = 408; Malawi, N = 404). StE: Standard Error of the MAF. MAF comparison: P-values of Yates corrected χ² Test for comparison of MAF between populations; a P-value<0.05 is considered statistically significant. G: The Gambia. K: Kenya. M: Malawi.</p

The <i>IRF1</i> locus and Single Nucleotide Polymorphisms (SNPs) tested for association with severe malaria in child-parental trios.

<p>From top to bottom, the figure shows: human chromosome 5 with its G-banding patterns (black, grey and black bands) where the location of the 5q31.1 band is indicated; genes contained within a 642 kb segment of the 5q31.1 band known as the “Th2 cytokine cluster”; <i>IRF1</i> gene region, where the arrow indicates the direction of transcription, horizontal lines indicate intergenic regions, white boxes indicate 5′ and 3′ un-transcribed regions (UTR), black boxes indicate exons and diagonal lines indicate introns; SNPs that were tested for severe malaria in our study populations and their location with respect to the <i>IRF1</i> gene region. Coordinates quoted (Mb) are based on Ensembl release 40.</p

Single marker Transmission Disequilibrium Test (TDT) of association with severe malaria in Gambian, Kenyan and Malawian child-parental trios.

<p>The table shows the SNPs tested in association analysis with severe malaria and results of the TDT in the three populations of affected child-parental trios. Inform is the number of informative trios. OR: Odds Ratio comparing the risk of the minor vs major allele. LCL and UCL: Lower and Upper Confidence Limits of a 95% Confidence Interval respectively. TDT P: P-value for the family-based test of association. P-values<0.05 are shown in bold.</p

Linkage Disequilibrium (LD ) architecture of the <i>IRF1</i> locus in The Gambia, Kenya and Malawi.

<p>Typed single nucleotide polymorphisms (SNPs) are represented on the vertical axis and ordered by chromosome position as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004206#pone-0004206-t001" target="_blank">Table 1</a>. Diagonal lines in two directions link each SNP to each of the other 17 SNPs. The LD (Δ²) between each pair of markers is represented by diamonds of different colours (see legend). Δ² is a simple measure of correlation between markers and is calculated as follows: (f_AB f_ab−f_Ab f_aB)²/(f_A f_a f_B f_b), where f stands for frequency, A and a denote the alleles at the first marker, B and b denote the alleles at the second marker, Ab is the haplotype carrying the major allele for the first marker and the minor allele for the second marker and so on. Blocks 1 and 2 are set of markers in high LD identified within the gene using the HAPLOVIEW application <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004206#pone.0004206-Barrett1" target="_blank">[16]</a>.</p