African populations pose a special challenge for imputation because they are among the most genetically diverse in the world (Rosenberg et al. 2010). Genetic relationships among African populations have been shaped by complex demographic histories, deep ancestries, and strong selective pressures, which can cause patterns of haplotype sharing in Africa to look much different than patterns in other parts of the world (Bryc et al. 2010; Campbell and Tishkoff 2008, 2010; Reed and Tishkoff 2006; Tishkoff et al. 2007, 2009). African populations also carry substantial burdens of common disease, yet few large-scale GWAS have been conducted in this setting. Efforts like the 1000 Genomes Project and MalariaGEN are changing this landscape, so it will be important to define effective reference panels for GWAS in a variety of African populations.
