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Genetic susceptibility to visceral leishmaniasis (VL) is indicated by differences in incidence and clinical phenotypes between ethnic groups in Sudan. In mice, innate susceptibility to Leishmania donovani, the etiological agent of VL, is controlled by Slc11a1 (formerly Nramp1). We therefore examined polymorphisms at SLC11A1 in 59 multicase families of VL from the high-incidence Masalit tribe in Sudan. Multipoint nonparametric analysis in ALLEGRO shows a significant linkage across SLC11A1 (Z lr scores 2.38–2.55; 0.008⩽ P⩽ 0.012; information content 0.88). The extended transmission disequilibrium test shows biased transmission of alleles at 5′ polymorphisms in the promoter (P= 0.0145), exon 3 (P= 0.0037) and intron 4 (P= 0.0049), and haplotypes formed by them (P= 0.0089), but not for 3′ polymorphisms at exon 15 or the 3′ UTR. Stepwise logistic regression analysis using a case/pseudo-control data …