Discovering genes and functional pathways associated with American cutaneous leishmaniasis (ACL) caused by Leishmania brasiliensis. Leishmaniasis is caused by protozoan parasites. There are 12 million cases world-wide, with an annual incidence is 0.9 to 1.6 million cases and a disease burden calculated by WHO as 1.98 million disability adjusted life years. American cutaneous leishmaniasis (ACL) caused by Leishmania braziliensis is among the worst forms of cuteneous leishmaniasis (CL) disease, and is associated with a clinical spectrum that ranges from one or more ulcers with raised borders to debilitating diffuse or mucosal forms of disease. Frontline drugs are those used half a century ago which are toxic and prone to development of drug resistance. There are no vaccines against leishmaniasis, making novel approaches to developing and understanding the molecular basis of how vaccines work a crucial area for continuing research.  Familial clustering of disease, racial differences in asymptomatic:disease ratios, high relative-risk ratios for siblings, and studies in mice all point to a genetic component for disease susceptibility. Previous model-based segregation analysis that allowed joint estimation of genetic and environmental effects and took gene x covariate interactions into account supports a major single gene controlling the onset of the primary cutaneous lesion caused by L.  braziliensis. Many candidate gene studies have been reported to try to identify the genetic risk factors for ACL, but all have been underpowered. The only definitive way to identify genetic risk factors is to undertake well-powered genome-wide studies using large sample sizes.  Using such an approach for the visceral form of leishmaniasis we provided clear and unambiguous evidence that polymorphisms in the Class II region of the Human Leukocyte Antigen (HLA) complex are the single major genetic determinant of VL (Pcombined=2.76E-17; odds ratio=1.41; 95% confidence interval=1.30-1.52 over three cohorts from India and Brazil). This robust demonstration that the most important genetic risk factor for VL lies at the heart of eliciting host CD4+ T-cell mediated immunity against Leishmania parasites has major implications for vaccine design.  Our aim here is to emulate this major advance in understanding the visceral form of disease by undertaking a costeffective, large-scale GWAS of ACL disease. In particular, to determine whether there is the same clear cut evidence for a major role of the HLA Class II region in determining ACL disease outcome, and/or whether other important genetic risk factors play a role. To achieve this, we will (i) undertake a stage 1 discovery GWAS by genotyping 547,644 single nucleotide polymorphisms (SNPs) in 1123 ACL cases and 1122 healthy controls using the Illumina HumanCoreExome beadchip, imputing against the 1000 genomes reference panel, and using mixed models to take account of relatedness and population structure in undertaking an association analysis; (ii) undertake a stage 2 discovery GWAS by genotyping 547,644 SNPs on a second set of DNAs for 1000 ACL cases and 1000 healthy controls using the Illumina HumanCoreExome beadchip, imputing against the 1000G reference panel, and using mixed models to take account of relatedness and population structure in an association analysis; (iii) carry out detailed immunological profiling and sample banking during prospective collection of a subset of stage 2 samples; (iv) combine data for the two cohorts in a metaanalysis to provide formal evidence for replication; (v) carry out pathway analyses and functional validation of genotype against phenotype.  Overall, this proposal provides the first adequately powered study of genetic risk factors for American cutaneous leishmaniasis. Genes and pathways identified as risk factors for ACL may provide novel insights in pathogenesis of disease, seeding further research into the identification of novel therapeutic and with the potential to inform development of vaccines against this debilitating parasitic infection. The Newton Fund builds research and innovation partnerships with developing countries across the world to promote the economic development and social welfare of the partner countries.