The genetic dissection of fetal haemoglobin persistence in sickle cell disease in Nigeria

Background : The clinical severity of sickle cell disease (SCD) is strongly influenced by the level of fetal haemoglobin (HbF) persistent in each patient. Three major HbF loci ( BCL11A , HBS1L-MYB , and Xmn1-HBG2 ) have been reported, but a considerable hidden heritability remains. Aim : Building on the power of a large and genetically diverse patient pool present in Nigeria, we conducted a genome-wide association study for HbF levels in patients from three regions of the country with a diverse ethnic make-up. Methods : We analysed genome-wide trait association in 1006 Nigerian patients with SCD (HbSS/HbS β), followed by a replication and meta-analysis exercise in four independent SCD cohorts (3,582 patients). To dissect association signals at the major loci, we performed stepwise conditional analysis, haplotype association analysis and included public functional annotation data (fGCTA). Results : Association signals were detected for BCL11A (lead SNP rs6706648, β =-0.39, P = 4.96 x 10-34) and HBS1L-MYB (lead SNP rs61028892, β = 0.73, P = 1.18 x 10-9), whereas the variant allele for Xmn1-HBG2 was found to be very rare. Genetically dissecting the two major loci, we defined trait-boosting haplotypes containing suspected or so-far unidentified causal variants. At BCL11A , one such haplotype (trait increase P < 0.0001) contains the putative functional variant rs1427407- T and a second haplotype ( P < 0.0001) is tagged by the rs7565301- A allele, with no obvious candidate causal variant. At HBS1L-MYB , one haplotype (trait increase P < 0.0001) contains the likely functional rs66650371 (Δ3-bp), and a second ( P < 0.0001) is tagged by the C allele of rs6102889. Together, variants at BCL11A and HBS1L-MYB SNPs explained 24.1% of the trait variance. We detected three novel association signals: SLC28A3 on chromosome 9 (rs115555854: β = -0.73, P = 2.52 x 10-8), TICRR on chromosome 15 (rs140496989: β =-0.43, P = 3.34 x 10-8), and PIEZO2 on chromosome 18 (rs58817161: β = -0.63, P = 8.04 x 10-8). These appeared to be restricted to the Nigerian patient cohort and were not confirmed in the replication cohorts. Conclusions : Studying a diverse cohort of Nigerian patients with sickle cell disease, we genetically dissected the known fetal-haemoglobin loci BCL11A and HBS1L-MYB and detected three putative new trait-associated regions. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded in principle by MRC grant MR/T013389/1 (to SM and JS), with additional funding from EPSRC (Newton/GCRF) grant EP/X527920/1, from LIBRA and from the Kings College Hospital Charity. Twins UK is supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z with additional support from the NIHR Oxford BRC. AG and CG were supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z with additional support from the NIHR Oxford BRC. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was approved by the Health Research Ethics Committee of Lagos University Teaching Hospital (ADM/DCST/HREC/1686), University of Abuja Teaching Hospital (FCT/UATH/HREC/PR/144), and Ahmadu Bello University ethics committee (ABUCUHSR/2021/031). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.