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Background  Little is known about the parasite/host factors that lead to Post Kala-azar Dermal Leishmaniasis (PKDL) in some visceral leishmaniasis (VL) patients after drug-cure. Studies in Sudan provide evidence for association between polymorphisms in the gene ( IFNGR1 ) encoding the alpha chain of interferon-γ receptor type I and risk of PKDL. This study aimed to identify putative functional polymorphisms in the  IFNGR1  gene, and to determine whether differences in expression of interferon-γ (IFNG) and IFNGR1 at the RNA level are associated with pathogenesis of VL and/or PKDL in Sudan.    Methods  Sanger sequencing was used to re-sequence 841 bp of upstream, exon1 and intron1 of the  IFNGR1  gene in DNA from 30 PKDL patients. LAGAN and SYNPLOT bioinformatics tools were used to compare human, chimpanzee and dog sequences to identify conserved noncoding sequences carrying putative regulatory elements. The relative expression of IFNG and IFNGR1 in paired pre- and post-treatment RNA samples from the lymph nodes of 24 VL patients, and in RNA samples from skin biopsies of 19 PKDL patients, was measured using real time PCR. Pre- versus post-treatment expression was evaluated statistically using the nonparametric Wilcoxon matched pairs signed-rank test.    Results  Ten variants were identified in the 841 bp of sequence, four of which are novel polymorphisms at -77A/G, +10 C/T, +18C/T and +91G/T relative to the  IFNGR1  initiation site. A cluster of conserved non-coding sequences with putative regulatory variants was identified in the distal promoter of  IFNGR1 . Variable expression of IFNG was detected in lymph node aspirates of VL patients before treatment, with a marked reduction ( P  = 0.006) in expression following treatment. IFNGR1 expression was also variable in lymph node aspirates from VL patients, with no significant reduction in expression with treatment. IFNG expression was undetectable in the skin biopsies of PKDL cases, while IFNGR1 expression was also uniformly low.    Conclusions  Uniformly low expression of IFN and IFNGR1 in PKDL skin biopsies could explain parasite persistence and is consistent with prior demonstration of genetic association with  IFNGR1  polymorphisms. Identification of novel potentially functional rare variants at  IFNGR1  makes an important general contribution to knowledge of rare variants of potential relevance in this Sudanese population.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-014-0662-5) contains supplementary material, which is available to authorized users.

Insights into the possible role of IFNG and IFNGR1 in Kala-azar and Post Kala-azar Dermal Leishmaniasis in Sudanese patients