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Genetic variants at three quantitative trait loci (QTL) for fetal haemoglobin (HbF),  BCL11A ,  HBS1L-MYB  and the β-globin gene cluster, have attracted interest as potential targets of therapeutic strategies for HbF reactivation in sickle cell anaemia (SCA). We carried out the first systematic evaluation of critical single nucleotide polymorphisms at these disease modifier loci in Nigerian patients with SCA. Common variants for  BCL11A  and  HBS1L-MYB  were strongly associated with HbF levels. At both loci, secondary association signals were detected, illustrating the mapping resolution attainable in this population. For  BCL11A , the two independent sites of association were represented by  rs1427407  (primary site, p = 7.0 x 10 −10 ) and  rs6545816  (secondary site, conditioned on  rs1427407 : p = 0.02) and for  HBS1L-MYB  by  rs9402686  ( HMIP-2B , p = 1.23 x 10 −4 ) and  rs66650371  ( HMIP-2A , p = 0.002). Haplotype analysis revealed similarities in the genetic architecture of  BCL11A  and  HBS1L-MYB  in Nigerian patients. Variants at both loci also alleviated anaemia. The variant allele for the γ globin gene promoter polymorphism  XmnI-HBG2  was too infrequent in our patients to be evaluated in this relatively small study. Studying the large and diverse SCA patient populations in African countries such as Nigeria will be key for a clearer understanding of how these loci work and for the discovery of new disease modifier genes.

A survey of genetic fetal-haemoglobin modifiers in Nigerian patients with sickle cell anaemia