Genome wide linkage study, using a 250K SNP map, of Plasmodium falciparum infection and mild malaria attack in a Senegalese population

Abstract

Multiple factors are involved in the variability of host's response to P. falciparum infection, like the intensity and seasonality of malaria transmission, the virulence of parasite and host characteristics like age or genetic make-up. Although admitted nowadays, the involvement of host genetic factors remains unclear. Discordant results exist, even concerning the best-known malaria resistance genes that determine the structure or function of red blood cells. Here we report on a genome-wide linkage and association study for P. falciparum infection intensity and mild malaria attack among a Senegalese population of children and young adults from 2 to 18 years old. A high density single nucleotide polymorphisms (SNP) genome scan (Affimetrix GeneChip Human Mapping 250K-nsp) was performed for 626 individuals: i.e. 249 parents and 377 children out of the 504 ones included in the follow-up. The population belongs to a unique ethnic group and was closely followed-up during 3 years. Genome-wide linkage analyses were performed on four clinical and parasitological phenotypes and association analyses using the family based association tests (FBAT) method were carried out in regions previously linked to malaria phenotypes in literature and in the regions for which we identified a linkage peak. Analyses revealed three strongly suggestive evidences for linkage: between mild malaria attack and both the 6p25.1 and the 12q22 regions (empirical p-value=5x10(-5) and 9x10(-5) respectively), and between the 20p11q11 region and the prevalence of parasite density in asymptomatic children (empirical p-value=1.5x10(-4)). Family based association analysis pointed out one significant association between the intensity of plasmodial infection and a polymorphism located in ARHGAP26 gene in the 5q31-q33 region (p-value=3.7x10(-5)). This study identified three candidate regions, two of them containing genes that could point out new pathways implicated in the response to malaria infection. Furthermore, we detected one gene associated with malaria infection in the 5q31-q33 region.

Figure 1. Distribution of raw data and phenotypes of analysis sample (372 children).

(Ai to Di) Raw data. (Ai) Mean of the whole parasite density values per children. (Bi) Mean of parasite density values per children considering only positive thick blood smears. (Ci) Rate of positive thick blood smears per child during the follow-up. (Di) Total number of mild clinical malaria attacks experienced per children during the active clinical survey. (Aii to Dii) Phenotypes. (Aii) Mean level of P.falciparum density. (Bii) Intensity of P.falciparum infection. (Cii) Prevalence of P.falciparum infection. (Dii) Mild Malaria Attack.

Figure 2. Results of quantitative multipoint linkage analysis obtained from the regress-based method implemented in MERLIN program for chromosomes 1–12.

Genetic position (cM) is plotted along the x axis. The dotted line indicates the LOD score associated with the threshold p-value of 10⁻³ and the dashed-dotted line the LOD score associated the threshold p-value of 10⁻⁴.

Figure 3. Results of quantitative multipoint linkage analysis obtained from the regress-based method implemented in MERLIN program for chromosomes 13–22 and pseudo-autosomal region of chromosome X.

Genetic position (cM) is plotted along the x axis. The dotted line indicates the LOD score associated with the threshold p-value of 10⁻³ and the dashed-dotted line the LOD score associated the threshold p-value of 10⁻⁴.