Identifying Darwinian selection acting on different human APOL1 variants among diverse African populations

Abstract

Disease susceptibility can arise as a consequence of adaptation to infectious disease. Recent findings have suggested that higher rates of chronic kidney disease (CKD) in individuals with recent African ancestry might be attributed to two risk alleles (G1 and G2) at the serum-resistance-associated (SRA)-interacting-domain-encoding region of APOL1. These two alleles appear to have arisen adaptively, possibly as a result of their protective effects against human African trypanosomiasis (HAT), or African sleeping sickness. In order to explore the distribution of potential functional variation at APOL1, we studied nucleotide variation in 187 individuals across ten geographically and genetically diverse African ethnic groups with exposure to two Trypanosoma brucei subspecies that cause HAT. We observed unusually high levels of nonsynonymous polymorphism in the regions encoding the functional domains that are required for lysing parasites. Whereas allele frequencies of G2 were similar across all populations (3%-8%), the G1 allele was only common in the Yoruba (39%). Additionally, we identified a haplotype (termed G3) that contains a nonsynonymous change at the membrane-addressing-domain-encoding region of APOL1 and is present in all populations except for the Yoruba. Analyses of long-range patterns of linkage disequilibrium indicate evidence of recent selection acting on the G3 haplotype in Fulani from Cameroon. Our results indicate that the G1 and G2 variants in APOL1 are geographically restricted and that there might be other functional variants that could play a role in HAT resistance and CKD risk in African populations.

Figure 1

Geographic Distribution of the Endemicity of HAT and Sampled Populations in Sub-Saharan Africa The map of the endemicity of HAT was adapted from the World Health Organization Report on Global Surveillance of Epidemic-Prone Infectious Diseases. The endemicity distribution is marked by a black line separating HAT into the West African form, which is caused by Trypanosoma brucei gambiense, and the East African form, which is caused by T. b. rhodesiense.

Figure 2

Spatial Distribution of Genetic Variants at the Functional-Domain-Encoding Region of APOL1 The APOL1 genetic region, which codes for the pore-forming (blue), membrane-addressing (green), and SRA-interacting (orange) domains, and the adjacent intron are marked by genetic variants identified in this study. Each synonymous and intronic SNP is labeled by a gray line. Each nonsynonymous SNP is labeled by a black line with its genomic position (based on NCBI Genome browser build 36.1) and reference SNP ID if it is described in dbSNP. For those nonsynonymous SNPs that are not present in dbSNP (build 137), the changes of nucleotide state are given according to RefSeq NG_023228.1. The indel variant (i.e., G2 allele) is labeled by an inverted triangle. The nucleotide site of each variant at our sequence alignment is labeled at the bottom of the gene. The nucleotide sites that define the G3 haplotype are labeled with asterisks.

Figure 3

Heatmap of Pairwise LD and Haplotype Network for the APOL1 Variants in African Populations (A) Pairwise estimates of r² between the APOL1 variants. Each pixel represents a pairwise LD measurement using the squared correlation coefficient (r²). r² was measured for all possible pairs of polymorphic sites. Levels of LD ranging from 0 to 1 are illustrated according to a white-to-red color gradient. The sequence position of each variant is marked by a black line segment on a diagonal line, and the positions for the G3 SNPs marked by asterisks are labeled in blue. The sequence positions (i.e., sites 1,228 and 1,356) of G1 SNPs are labeled in black. (B) Network analysis of the APOL1 haplotypes. Each node represents a haplotype, and the nodes representing the G1, G2, and G3 haplotypes are labeled. The size for a given node is proportional to its haplotype frequency. The sequence positions of the eight SNPs that define the G3 haplotype (G3) are labeled.

Figure 4

Plots of iHS Values for SNPs of APOL1 and the Adjacent Chromosomal Regions in African Populations The absolute values of standardized iHS (|iHS|) are plotted against the genomic positions (NCBI Genome browser build 36.1) of SNPs at APOL1 and the neighboring genetic regions on chromosome 22 for a subset of our samples in each population. The number of chromosomes (n) is given for each population. The estimates of |iHS| are colored in red for the G1 SNPs and in orange for the G3 SNPs. The 95% cutoff value (1.96) of the empirical distribution of standardized iHS is given in each plot (dashed line).

Figure 5

Decay of EHH for APOL1 Variants in Three African Populations The decay of EHH for the eight SNPs of the G3 haplotype in the Fulani in Cameroon (A), for the G1 allele in the Yoruba in Nigeria (B), and for the two intron SNPs identified as outliers in the iHS analysis in the Borana in Kenya (C). The ancestral (anc) and derived (drv) alleles that show unusual long-range haplotype homozygosity are labeled by their positions in our sequenced region (see Figure 2). The sex-averaged standardized recombination rates (labeled as “recomb rate” on the right y axis) in 10 kb bins are plotted (in dashed line) against the chromosomal positions according to Kong et al.

Figure 6

Decay of LD for the APOL1 Variants in African Populations Plots of r² estimates between polymorphic sites against the physical distance across a 30 kb region flanking the last exon of APOL1 in the six African populations. The r² estimates are colored in orange for all pairwise estimates within the G3-associated SNPs. In each plot, the fitted nonlinear regression line (solid line) and its 95% prediction interval (dashed line) were plotted on the basis of all r² estimates except for the orange dots.