Number of genetic variants identified.

<p>Number of genetic variants identified.</p

<i>TLR1</i> Variant H305L Associated with Protection from Pulmonary Tuberculosis

<div><p>Toll like receptors (TLR) are key elements of the innate immune response and involved in the recognition of pathogens. To test common and rare <i>TLR</i> variants involved in susceptibility or resistance to infection with <i>Mycobacterium tuberculosis</i> we screened the exons of the genes encoding TLR 1, 2, 4, and the adaptor molecule TIRAP in more than 4500 tuberculosis (TB) cases and controls from Ghana. The analysis yielded 109 variants with possible functional impact, including 101 non-synonymous variants, three stop-variants, and five indels. Association analyses yielded a significant result for the <i>TLR1</i> variant rs3923647, conferring strong protection against TB (Odds ratio [OR] 0.21, CI confidence interval [CI] 0.05–0.6, P_{<i>nominal</i>} 1 x 10⁻³) when applying a recessive model of inheritance. Replication analyses with an additional 3370 Ghanaian cases and control samples, and with data from a recent TB study of 533 African-Americans confirmed the protective effect and resulted in a combined OR of 0.19, with a nominal P value of 2.2 x 10⁻⁵, and a corrected P value of 4.1 x 10⁻⁴. The SNP is located near the binding pocket of TLR1 and causes an amino acid exchange from histidine to leucine at position 305. The observed effect may, therefore, be attributable to structural changes in the recognition site of the TLR1 molecule, allowing to bind those mycobacterial ligands which preferentially may induce a protective immune response. This is supported by the analysis of BCG-stimulated peripheral blood mononuclear cells, showing increased induction of the proinflammatory cytokine IFN-γ in carriers of the mutant TLR1 rs3923647 TT genotype, compared to the IFN-γ levels of individuals with the AT and AA genotypes.</p></div

Gene-set associations tests.

<p>Gene-set associations tests.</p

IFN-y expression in <i>M</i>. <i>bovis</i> BCG stimulated cultured PBMCs.

<p>Comparison of IFN-y mRNA expression in <i>M</i>. <i>bovis</i> BCG stimulated cultured PBMCs of Ghanaian individuals carrying either the TT genotype or the AT/AA genotype of TLR1 SNP rs3923647. Comparison of IFN-y levels yields a significant difference between TT and AT/AA carriers (* P = 0.05, T-test).</p

Association results of TLR1 variant rs3923647.

<p>Association results of TLR1 variant rs3923647.</p

PROCR rare variant analyses including SNPs with MAF ≤1%.

<p>CMC, combined and multivariate collapsing; WSS, weighted sum statistic; VT, variable thresholds methods.</p>a<p>Adjusted for age, gender, and ethnic group.</p><p>PROCR rare variant analyses including SNPs with MAF ≤1%.</p

Endothelial Protein C Receptor Gene Variants Not Associated with Severe Malaria in Ghanaian Children

<div><p>Background</p><p>Two recent reports have identified the Endothelial Protein C Receptor (EPCR) as a key molecule implicated in severe malaria pathology. First, it was shown that EPCR in the human microvasculature mediates sequestration of <i>Plasmodium falciparum</i>-infected erythrocytes. Second, microvascular thrombosis, one of the major processes causing cerebral malaria, was linked to a reduction in EPCR expression in cerebral endothelial layers. It was speculated that genetic variation affecting EPCR functionality could influence susceptibility to severe malaria phenotypes, rendering <i>PROCR</i>, the gene encoding EPCR, a promising candidate for an association study.</p><p>Methods</p><p>Here, we performed an association study including high-resolution variant discovery of rare and frequent genetic variants in the <i>PROCR</i> gene. The study group, which previously has proven to be a valuable tool for studying the genetics of malaria, comprised 1,905 severe malaria cases aged 1–156 months and 1,866 apparently healthy children aged 2–161 months from the Ashanti Region in Ghana, West Africa, where malaria is highly endemic. Association of genetic variation with severe malaria phenotypes was examined on the basis of single variants, reconstructed haplotypes, and rare variant analyses.</p><p>Results</p><p>A total of 41 genetic variants were detected in regulatory and coding regions of <i>PROCR</i>, 17 of which were previously unknown genetic variants. In association tests, none of the single variants, haplotypes or rare variants showed evidence for an association with severe malaria, cerebral malaria, or severe malaria anemia.</p><p>Conclusion</p><p>Here we present the first analysis of genetic variation in the <i>PROCR</i> gene in the context of severe malaria in African subjects and show that genetic variation in the <i>PROCR</i> gene in our study population does not influence susceptibility to major severe malaria phenotypes.</p></div

Association tests of <i>PROCR</i> haplotypes with severe malaria, cerebral malaria, and severe malaria anemia.

<p>Aff, affected individuals; unaff, unaffected individuals.</p>a<p>Refers to SNP number as designated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115770#pone-0115770-t002" target="_blank">Table 2</a>.</p>b<p>Results of haplotypic-specific score tests adjusted for gender, age, and ethnicity assuming an additive mode of inheritance.</p>c<p>Simulation p-values are computed based on a permuted re-ordering of the trait and covariates in Haplo Stats <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115770#pone.0115770-Schaid1" target="_blank">[29]</a>.</p><p>Association tests of <i>PROCR</i> haplotypes with severe malaria, cerebral malaria, and severe malaria anemia.</p