Y Chromosome Lineage- and Village-Specific Genes on Chromosomes 1p22 and 6q27 Control Visceral Leishmaniasis in Sudan

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Abstract
Familial clustering and ethnic differences suggest that visceral leishmaniasis caused by Leishmania donovani is under genetic control. A recent genome scan provided evidence for a major susceptibility gene on Chromosome 22q12 in the Aringa ethnic group in Sudan. We now report a genome-wide scan using 69 families with 173 affected relatives from two villages occupied by the related Masalit ethnic group. A primary ten-centimorgan scan followed by refined mapping provided evidence for major loci at 1p22 (LOD score 5.65; nominal p = 1.72 × 10−7; empirical p < 1 × 10−5; λS = 5.1) and 6q27 (LOD score 3.74; nominal p = 1.68 × 10−5; empirical p < 1 × 10−4; λS = 2.3) that were Y chromosome–lineage and village-specific. Neither village supported a visceral leishmaniasis susceptibility gene on 22q12. The results suggest strong lineage-specific genes due to founder effect and consanguinity in these recently immigrant populations. These chance events in ethnically uniform African populations provide a powerful resource in the search for genes and mechanisms that regulate this complex disease. The parasitic disease kala-azar, or visceral leishmaniasis, is associated with liver, spleen, and lymph gland enlargement, as well as fever, weight loss, and anaemia. It is fatal unless treated. Three major foci of disease occur in India, Sudan, and Brazil. Importantly, 80%–90% of infections are asymptomatic. Understanding why two people with the same exposure to infection differ in susceptibility could provide important leads for improved therapies. We studied families with multiple cases of clinical disease from two villages in Sudan. After typing 300–400 genetic markers across the human genome, we determined which chromosomes carry susceptibility genes. We were surprised that our results differed from those published earlier for a village 100 kilometers from our site. All of these villages are occupied by people of the same ethnic group who migrated from western Sudan late last century following a major drought. We stratified our analysis by village, and used male Y chromosome markers to tag extended pedigrees. Our results suggest that recent immigration, in combination with consanguineal marriage in a strongly patriarchal society, has amplified founder effects resulting in different lineages within each village carrying different susceptibility loci. This demonstrates the importance of understanding population genetic substructure in studying genes that regulate complex disease.